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The goal of the Gabriella Miller Kids First Pediatric Research Program (Kids First) is to help researchers uncover new insights into the biology of childhood cancer and congenital anomalies, including the discovery of shared genetic pathways between these disorders.
2025 X01 Projects
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Azeez Butali | HL140516 | University of Iowa | Whole Genome Sequencing of African and Asian Orofacial Clefts Case-Parent Triads | 492 |
| Abstract: DESCRIPTION (provided by applicant): Dr Azeez Butali is a tenure-track Assistant Professor at the Iowa Institute for Oral Health Research, College of Dentistry, and the University of Iowa. His primary research focus is on the genetics and epidemiology of complex traits including orofacial clefts. Dr Terri Beaty is a Professor at the John Hopkins University. Her research focus is on genetic epidemiology studies of several chronic diseases with complex etiologies, where both genetic and environmental risk factors control risk of disease. Co-investigators: Dr Adebowale Adeyemo is Deputy Director at the National Human Genome Research Institute. His focus is on the genetics and genomics of complex traits in African population. Dr Marazita is a Professor at the University of Pittsburgh. She is an expert in statistical genetics application for complex traits and identification of sub-clinical cleft phenotypes. Dr Cao is an Assistant Professor at the University of Iowa. He uses bioinformatics tools to interrogate the human genome and for analyses of gene-regulatory networks. Dr Ruczinski is a Professor at the John Hopkins University. His expertise is in statistical genetics, genomics and proteomics of complex traits. Dr Taub is an Assistant Scientist at the John Hopkins University. Her area of expertise is in genomics and statistical genetics for gene expression data, genotyping data and DNA methylation data Environment: The University of Iowa is a leading institution with a strong reputation for excellence in teaching, research and healthcare. The John Hopkins University is one of the leaders in the research, teaching and healthcare in the US. Both institutions are consistently amongst centers supported by NIH grants Research Study: The focus of this study is to identify novel risk variants for OFC in Africa and Asian OFC case-parent triads through analysis of Whole Genome Sequencing data. PUBLIC HEALTH RELEVANCE: TITLE: Whole Genome Sequencing of African and Asian Orofacial Case-Parent Triads The long-term goal of this study is to identify specific genomic variants through WGS of OFC case-parent triads from African and Asian populations. The knowledge gained from these WGS studies will drive future research on OFC and should eventually lead to more effective interventions to reduce the risk of OFC. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| John R Shaffer | HD114124 | University Of Pittsburgh at Pittsburgh | Epigenomics of Orofacial Clefts | 2543 |
| Abstract: DESCRIPTION (provided by applicant): Orofacial cleft (OFC) birth defects are one of the most common structural birth defects in humans, and the most common craniofacial anomalies, with worldwide incidence of approximately 1 per 700 newborns. OFCs represent a major public health problem due to the associated morbidity, mortality, and significant medical care expenditures. Based on structures affected, OFCs have been categorized as three subtypes: clefts affecting the lip only (cleft lip, CL), clefts affecting both the lip and the palate (cleft lip and palate, CLP), and clefts affecting the palate only (cleft palate, CP). Historically, CL and CLP have been considered variations of the same malformation that differ in severity, whereas the developmental origins of the affected structures, epidemiology, and familial patterns suggest that CP has a separate etiology than CL and CLP. Both genetic and environmental factors play important roles in the development of OFCs, although understanding of these risk factors is incomplete. The proposed project aims to expand the Gabriella Miller Kids First (GMKF) resource by collecting data to investigate the role of DNA methylation – an epigenomic marker of gene activity – on the development of clefts. We propose to collect genome-wide DNA methylation assays in a large cohort of affected children as well as DNA methylation and transcriptomics assays in a subset of children with available discarded surgical tissue. Ultimately, these data will contribute new and complementary types of omics data to the GMKF resource for participants with already-available whole-genome sequencing data. This resource will allow us and others to perform analyses to identify the differentially methylated regions of the genome associated with OFCs and subtypes, and explore the functional roles of previously identified OFC-associated genetic loci. Successful completion of this project will expand and deepen our understanding of the genetic architecture and regulatory landscape of OFCs including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. PUBLIC HEALTH RELEVANCE: This project will expand the Gabriella Miller Kids First resource and deepen our understanding of the genetic architecture and regulatory landscape of non-syndromic orofacial clefts including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. This knowledge may ultimately be useful for applications such as recurrence prediction or personalized therapeutic interventions. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Bruce D Gelb | HL161587 | Icahn School Of Medicine At Mount Sinai | Expanding our understanding of the role of noncoding variation causing congenital heart defects | 1201 |
| Abstract: DESCRIPTION (provided by applicant): The epidemiology of congenital heart defects (CHD) indicates that genetic variation is the overwhelmingly predominant cause of these commonest birth defects, but more than 50% of CHD cases remain unexplained even after trio exome sequencing (ES). The remaining large gap in genetic causality for CHD is what the Pediatric Cardiac Genomics Consortium (PCGC), a component of NHLBI’s Bench-to-Bassinet Program, seeks to address through the Gabriella Miller Kids First (GMKF) Pediatric Research Program. Under the auspices of prior GMKF awards for trio genome sequencing (GS), the PCGC began to elucidate the role of de novo noncoding damaging single nucleotide variants and small insertions and deletions (indels) in CHD causality . The cumulative mean attributed risk from noncoding de novo variants (DNVs) for exome-negative CHD was 17-45%. To further the understanding of the role of genetic variation in causing CHD, the PCGC is requesting GS to perform GS for 500 probands born with tetralogy of Fallot (ToF) or hypoplastic left heart syndrome (HLHS), unsolved after exome sequencing, and their unaffected parents. In addition to increasing cohort size to improve statistical power, we will use a new and larger control trio GS dataset available through TOPMed (n = 1,758) and generate an improved version of our neural network,HeartENN, which predicts functional impact of genetic variation, through incorporation of more-than-double cardiac noncoding regulatory feature data. Of note, the PCGC has the wherewithal to confirm relevant variants with other genomic methods as well as to perform functional cell-based assays to further support claims of pathogenicity. We will also use the GS data to expand our understanding of structural variation underlying CHD. We will use a best-of-class SV calling pipeline, developed by the Talkowski group at the Broad Institute. Analytic focus of SVs will include disruptions of known autosomal dominant CHD genes, 2nd hits in trans to damaging coding variants in known autosomal recessive CHD genes, and burden analysis for apparently damaging SVs combined with existing data about putatively damaging coding variants (SNVs and indels) from > 5000 CHD trios. Finally, in an exploratory portion of this aim, we will attempt calling of SVs such as repeat expansions that are difficult with short-read GS, focusing on a limited number of regions of potential interest based on our analysis of PacBio long-read GS from 200 CHD probands, currently being generated under the auspices of the GMKF pilot program. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Wendy Chung | HD110887 | Boston Children's Hospital | Genomic Analysis of Esophageal Atresia and Tracheoesophageal Fistulas and Associated Congenital Anoma | 360 |
| Abstract: DESCRIPTION (provided by applicant): Project Summary/Abstract Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. There is a 45% incidence of associated congenital malformations, most commonly digestive, cardiovascular, urogenital, and musculoskeletal, often part of a syndrome or complex association, with VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities) being most frequently recognized. Advanced surgical techniques and pre and post-operative care have improved the prognosis and survival of EA/TEF patients over the past decades. However, with improved survival, many of the long-term morbidities of EA/TEF have been exposed. It is likely that the outcome in EA/TEF patients is influenced by multiple genetic and clinical factors; however, determining which factors are critical has been limited by the lack of data, particularly genomic data. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of EA/TEF and define new genes and conditions associated with EA/TEF by performing whole genome sequencing on 100 parent child trios in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions and improve outcomes. PUBLIC HEALTH RELEVANCE: Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. We propose to elucidate the underlying genomic architecture of EA/TEF by performing whole genome sequencing to characterize new clinical syndromes associated with EA/TEF to provide more accurate clinical prognostic information. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Ariadne Letra | DE031445 | University of Pittsburgh | Whole Genome Sequencing Studies Of Multiplex Nonsyndromic Cleft Lip/Palate Families | 923 |
| Abstract: DESCRIPTION (provided by applicant): In this proposal, we request whole genome sequencing (WGS) services of 923 individuals from our cohort of well-characterized, large multigenerational nonsyndromic cleft lip/palate (NSCLP) families of Hispanic and non-Hispanic white ethnicities. NSCLP is a common birth defect accounting for 65% of all birth defects and annually affecting approximately 135,000 newborns worldwide. Despite improvement in treatments, NSCLP imposes significant medical, psychosocial and financial burdens that affect quality of life of affected individuals and their families. NSCLP is complex, caused by genetic and environmental factors, and their interactions. Recent advances in genomic approaches have improved our knowledge of the genetic factors involved in NSCLP; however, most of the variants associated with NSCLP account for ~25% of the genetic liability and reflect common, modest risk-variants often located in noncoding regions of the genome. More recently, it has been suggested that some genetic risk for NSCLP lies in rare variants and this has contributed to the lack of consistent findings and difficulty in unraveling risk alleles. Further, it is likely that the missing heritability of NSCLP result in part due to interactions between common, modest risk variants and rare, high-risk variants. We will analyze WGS data and apply polygenic risk score analysis to identify novel, high-penetrance NSCLP variants and to systematically evaluate the contributions of both common and rare variants to NSCLP, and how they segregate individually and in concert within and between families. The results of this study will provide novel and important insights about the genetic architecture contributing to the complex etiology of NSCLP. Importantly, this proposal will translate into a rich and publicly available resource of NSCLP genotypic and phenotypic data that will be made available to the broader scientific community to foster additional studies on NSCLP, as well as other birth defects and/or associated co-morbidities. Further, this proposal will provide genotype and allele frequency data in Hispanics for which limited data is available on genetic databases. Additional follow-up studies proposed, although beyond the scope of this X01 application, include validating the variants identified in this study in our additional NSCLP trios as well as through joint analysis with data from additional existing Kids First datasets. Successful completion of this study will provide novel and important insights about the genetic architecture contributing to the complex etiology of NSCLP, and will translate into a large, rich resource for genetic and phenotypic information on NSCLP. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Andrew L Hong | HD114129 | Emory University | Basis of Childhood Kidney Cancers and Birth Defects | 932 |
| Abstract: DESCRIPTION (provided by applicant): Wilms Tumor is the most common renal tumor of childhood. Although cure rates approach 90% after initial therapy that includes a combination of surgery, chemotherapy and radiation therapy, our understanding of the biology of how children develop this cancer remains limited due to small patient cohorts. Prior studies have uncovered a number of important genetic alterations associated with Wilms Tumor. However these studies are based on small cohorts. Here, we propose to advance our prior studies with a multi-decade effort to obtain high quality samples from over 200 pediatric institutions through Children’s Oncology Group Renal Tumor studies. With samples from approximately 2,946 patients, we propose to assess the whole genome, methylome and transcriptome of the patient’s germline, normal adjacent kidney and tumor kidney. Given the large sample size, we will be powered for the detection of rare variant alleles and validation of prior studies. Just as importantly, our patient cohort represents the diversity of the United States. The multi-PI team along with senior leadership of the COG Renal Tumor studies have deep expertise in the analyses of epidemiology, genetics, epigenetics and transcriptomics in childhood cancers along with decades experience with the care of children with renal tumors. This proposed study provides a timely opportunity to aid our understanding of cancer risk in children with genitourinary congenital anomalies and more broadly, our understanding of Wilms Tumor, from a diverse population. These data will provide a critical resource for cancer germline risk, congenital anomalies, developmental biology and cancer biology. PUBLIC HEALTH RELEVANCE: Wilms Tumor is the most common kidney cancer in children. Although some predisposition syndromes have been associated with Wilms Tumor (e.g., Beckwith Wiedemann Syndrome, Denys Drash Syndrome, Hemihypertrophy, WAGR Syndrome), recent studies suggest many more children with Wilms Tumor may have an underlying predisposition syndrome. This study will explore how these germline changes relate to the developing kidney or structural birth defects in addition to the development of kidney cancer which may lead to prevention strategies or enhance risk stratification and therapeutic target identification. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Erin Peckham-Gregory and Carl Allen | CA267639 | Texas Children's Hospital | Genomic Analysis Of Histiocytosis | 1008 |
| Abstract: DESCRIPTION (provided by applicant): Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasm characterized by lesions including pathogenic CD207+ dendritic cells among an inflammatory infiltrate. The median age at diagnosis is 30 months, and up-front chemotherapy fails in ~50% of patients resulting in multiple relapse events for 40-50% of cases, and long-term sequelae. Sequencing studies have found recurrent, mutually exclusive somatic activating mutations in MAPK pathway genes in ~85% of LCH lesions, including BRAF V600E in 50-65%. There is a “Misguided Myelomonocytic Precursor Model” in which specific somatic MAPK mutations at critical stages of myeloid differentiation determine extent of disease. However, this model fails to explain the significant differences in LCH risk across ethnicities. Despite advances to elucidate the somatic mutational landscape underlying LCH pathogenesis, germline risk factors remain largely unknown. Therefore, we conducted the first genome-wide association study of LCH and identified a SMAD6 variant associated with increased risk. SMAD6 inhibits bone morphogenetic protein and transforming growth factor-beta/activin signaling, which are determinants of Langerhans cell differentiation. This variant appears to suppress SMAD6 protein expression without a decrease in SMAD6 messenger RNA expression in patients carrying the risk allele. This risk allele is also more common in Hispanics who are at the highest risk of LCH, and absent in blacks who experience the lowest LCH incidence. Our preliminary data also support the emerging observation that LCH somatic activating mutations vary by race/ethnicity. Specifically, sequencing of tumors from black patients indicated that only 25% were BRAF V600E+ (compared to >60% in other populations), whereas 50% had mutations in MAP2K1 (compared to < 10% in other populations). Therefore, the objective of this Kids First X01 application is to more fully elucidate LCH etiology by defining the role of de novo mutations (DNMs) in established LCH genes and novel susceptibility genes, and by comprehensively assessing somatic variation in LCH. Our central hypothesis is that penetrant DNMs and novel germline and somatic variation may contribute to, or in some cases, drive LCH tumorigenesis. 1) We will leverage our ongoing Children's Oncology Group study, Genetic Epidemiology of Childhood Histiocytosis (GECHO), to sequence 300 LCH case-parent trios to evaluate the impact of recurrent DNMs on inherited susceptibility to LCH. 2) We will leverage paired germline-tumor samples from 200 patients enrolled to the Texas Children's Histiocytosis Program protocol or GECHO study to comprehensively assess the somatic landscape of LCH and identify germline variation contributing to somatic mutational profiles. Successful completion of the proposed aims may (1) improve genetic testing and counseling strategies in LCH patients and families; (2) advance surveillance and chemoprevention protocols; and (3) identify novel therapeutic targets. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| David Teachey | HD114203 | Children's Hospital of Pennsylvania | Somatic and Germline Variants in Childhood T-cell acute lymphoblastic leukemia | 730 |
| Abstract: DESCRIPTION (provided by applicant): The outcome for children with relapsed T-cell acute lymphoblastic leukemia (T-ALL) is dismal. Thus, the primary goal in treatment is to prevent relapse, which requires accurate risk stratification. Prior attempts to identify genetic aberrations that are prognostic independent of treatment response have failed. We recently performed comprehensive genomic profiling (whole genome sequencing (WGS), whole exome sequencing (WES), and whole transcriptome profiling (WTS) of tumor; WGS of germline) from >1300 patients with T-ALL treated on the AALL0434 clinical trial through a Gabriella Miller Kids First X01 award (X01HD100702) and made several novel, practice changing observations. We found T-ALL can be classified into 15 distinct groups, many of which are novel. We found that leukemic drivers were in non-coding regions in 60% of cases, highlighting the importance of WGS. We identified multiple subtypes that were predictive of favorable and unfavorable outcome. The successor trial to AALL0434 was AALL1231. On AALL1231, several changes were made to the backbone to eliminate cranial radiation in most patients and these changes had prognostic implications. Before we can prospectively incorporate genetic aberrations into risk stratification, we need to validate our results in an independent cohort treated with current therapy and identify genomic variants that are reproducibly prognostic irrespective of therapeutic backbone. In addition, we found the prognostic impact of some variants differed based on genetic ancestry; some genetic variants that were associated with higher cure rates in children of European ancestry were not associated with higher cure rates in children of African ancestry. We need to increase the number of patients studied from different racial and ethnic groups to ensure equity in future risk stratification. Finally, we were unable to identify the genomic driver in a small percentage of cases (5%) and long-read sequencing may be able to overcome this gap. We hypothesize that comprehensive genomic profiling will identify recurrent genetic alterations that can be used prospectively to risk classify patients with T-ALL. Genomic profiling of a large cohort of patients treated on the AALL1231 trial will serve as a natural extension of our initial X01 award, providing the power to assess the impact of genomic variants on outcome across genetic ancestral groups. We will test our hypothesis with the following specific aims: (1) validate prognostic variants in an independent cohort of patients with T-ALL; (2) identify novel genomic structural variants using long-read sequencing; and (3) determine the association between genetic ancestry, tumor biology and outcomes. The goal of the Kids First Program is to improve understanding of genetic mechanisms of disease, leading to improved diagnostic capabilities and ultimately more targeted therapies. Genomic profiling across two of the largest clinical trials ever performed in children with T-ALL will clearly meet these important goals. This work will not only fundamentally transform the understanding of T-ALL disease biology but also allow us to risk stratify patients accurately and equitably understand differences in tumor biology based on genetic ancestry. PUBLIC HEALTH RELEVANCE: Modern genetic tests have helped find better ways to identify children with T-cell acute lymphoblastic leukemia (T-ALL) who are less likely to be cured. Before we can use these tests in the clinic, we need to show they are helpful regardless of therapy used to treat the leukemia | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Sharon Diskin | CA268005 | Children's Hospital of Pennsylvania | The Genetic Basis Of Treatment Outcomes And Late Effects After High-Risk Neuroblastoma | 407 |
| Abstract: DESCRIPTION (provided by applicant): Children diagnosed with high-risk neuroblastoma receive intensive multi-modal therapy, yet 40-50% die of their primary cancer, and those who survive experience substantial treatment-related morbidities. There is no reliable way to identify those at greatest risk of treatment failure (death) or late effects, and only a nascent understanding of underlying genetic determinants. Our long term goal is to improve neuroblastoma outcomes by first characterizing the events driving tumorigenesis and treatment response so that evidence-based and less toxic therapies can be developed. We hypothesize that comprehensive whole genome sequencing (WGS) of high- risk neuroblastoma subjects treated with modern therapy and annotated with late effect phenotypes will identify genetic determinants of survival and treatment-related morbidities. Through an existing Gabriella Miller Kids First (GMKF) project, we performed WGS of neuroblastoma patient-parent triads/dyads (n=556) together with matched tumor DNA (n=336) and RNA-sequencing (n=207). These data have defined the heritable fraction of rare pathogenic variants in cancer predisposition genes and suggest carriers have worse survival. However, only a subset of cases (n=178) sequenced are high-risk and none include phenotyping of late effects. Here, we will build on existing GMKF profiling to generate germline WGS for 1,100 total children (n=922 new) who received modern high-risk neuroblastoma therapy, along with additional WGS of matched tumor DNA (n=553 new) and RNA-sequencing (n=461 new). All subjects participated in the Children’s Oncology Group (COG) neuroblastoma biology study (ANBL00B1). The entire cohort is annotated with demographic (age, sex, race, ethnicity), clinical (e.g. age at diagnosis, stage, risk group, survival), and tumor biological (e.g. MYCN status) co-variates. A subset (n=367) are 5+ year survivors enrolled in the COG ALTE15N2: Late Effects After High-Risk Neuroblastoma (LEAHRN) study and have undergone extensive clinical assessments, with excellent characterization of late toxicities. We will test our hypothesis through two Specific Aims: 1) Identify germline and somatic variants associated with high-risk neuroblastoma treatment failure. Using a phased approach, we will identify coding and non-coding germline variation, somatic alterations, and transcriptomic profiles predicting refractory disease and survival. 2) Discover genetic risk factors associated with late effects after high-risk neuroblastoma therapy. We will define the spectrum, prevalence, and association of rare pathogenic variants with respect to hearing loss, cardiomyopathy, growth impairment and primary gonadal failure in the LEAHRN subjects. Data from NCI- TARGET (n=1,108), our genome-wide association study (GWAS; n=6,202), and phenotyping in recent high-risk trials will be integrated to validate genetic associations with treatment outcomes. Sequencing of this unique and extensively phenotyped high-risk neuroblastoma cohort will provide an unparalleled opportunity to discover germline and somatic alterations that can be used to identify patients at risk for treatment failure and late effects. This will serve as rationale for the design of future trials aimed at improved survival and reduction in late effects. | ||||
2025 X01 Projects
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Azeez Butali | HL140516 | University of Iowa | Whole Genome Sequencing of African and Asian Orofacial Clefts Case-Parent Triads | 492 |
| Abstract: DESCRIPTION (provided by applicant): Dr Azeez Butali is a tenure-track Assistant Professor at the Iowa Institute for Oral Health Research, College of Dentistry, and the University of Iowa. His primary research focus is on the genetics and epidemiology of complex traits including orofacial clefts. Dr Terri Beaty is a Professor at the John Hopkins University. Her research focus is on genetic epidemiology studies of several chronic diseases with complex etiologies, where both genetic and environmental risk factors control risk of disease. Co-investigators: Dr Adebowale Adeyemo is Deputy Director at the National Human Genome Research Institute. His focus is on the genetics and genomics of complex traits in African population. Dr Marazita is a Professor at the University of Pittsburgh. She is an expert in statistical genetics application for complex traits and identification of sub-clinical cleft phenotypes. Dr Cao is an Assistant Professor at the University of Iowa. He uses bioinformatics tools to interrogate the human genome and for analyses of gene-regulatory networks. Dr Ruczinski is a Professor at the John Hopkins University. His expertise is in statistical genetics, genomics and proteomics of complex traits. Dr Taub is an Assistant Scientist at the John Hopkins University. Her area of expertise is in genomics and statistical genetics for gene expression data, genotyping data and DNA methylation data Environment: The University of Iowa is a leading institution with a strong reputation for excellence in teaching, research and healthcare. The John Hopkins University is one of the leaders in the research, teaching and healthcare in the US. Both institutions are consistently amongst centers supported by NIH grants Research Study: The focus of this study is to identify novel risk variants for OFC in Africa and Asian OFC case-parent triads through analysis of Whole Genome Sequencing data. PUBLIC HEALTH RELEVANCE: TITLE: Whole Genome Sequencing of African and Asian Orofacial Case-Parent Triads The long-term goal of this study is to identify specific genomic variants through WGS of OFC case-parent triads from African and Asian populations. The knowledge gained from these WGS studies will drive future research on OFC and should eventually lead to more effective interventions to reduce the risk of OFC. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| John R Shaffer | HD114124 | University Of Pittsburgh at Pittsburgh | Epigenomics of Orofacial Clefts | 2543 |
| Abstract: DESCRIPTION (provided by applicant): Orofacial cleft (OFC) birth defects are one of the most common structural birth defects in humans, and the most common craniofacial anomalies, with worldwide incidence of approximately 1 per 700 newborns. OFCs represent a major public health problem due to the associated morbidity, mortality, and significant medical care expenditures. Based on structures affected, OFCs have been categorized as three subtypes: clefts affecting the lip only (cleft lip, CL), clefts affecting both the lip and the palate (cleft lip and palate, CLP), and clefts affecting the palate only (cleft palate, CP). Historically, CL and CLP have been considered variations of the same malformation that differ in severity, whereas the developmental origins of the affected structures, epidemiology, and familial patterns suggest that CP has a separate etiology than CL and CLP. Both genetic and environmental factors play important roles in the development of OFCs, although understanding of these risk factors is incomplete. The proposed project aims to expand the Gabriella Miller Kids First (GMKF) resource by collecting data to investigate the role of DNA methylation – an epigenomic marker of gene activity – on the development of clefts. We propose to collect genome-wide DNA methylation assays in a large cohort of affected children as well as DNA methylation and transcriptomics assays in a subset of children with available discarded surgical tissue. Ultimately, these data will contribute new and complementary types of omics data to the GMKF resource for participants with already-available whole-genome sequencing data. This resource will allow us and others to perform analyses to identify the differentially methylated regions of the genome associated with OFCs and subtypes, and explore the functional roles of previously identified OFC-associated genetic loci. Successful completion of this project will expand and deepen our understanding of the genetic architecture and regulatory landscape of OFCs including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. PUBLIC HEALTH RELEVANCE: This project will expand the Gabriella Miller Kids First resource and deepen our understanding of the genetic architecture and regulatory landscape of non-syndromic orofacial clefts including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. This knowledge may ultimately be useful for applications such as recurrence prediction or personalized therapeutic interventions. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Bruce D Gelb | HL161587 | Icahn School Of Medicine At Mount Sinai | Expanding our understanding of the role of noncoding variation causing congenital heart defects | 1201 |
| Abstract: DESCRIPTION (provided by applicant): The epidemiology of congenital heart defects (CHD) indicates that genetic variation is the overwhelmingly predominant cause of these commonest birth defects, but more than 50% of CHD cases remain unexplained even after trio exome sequencing (ES). The remaining large gap in genetic causality for CHD is what the Pediatric Cardiac Genomics Consortium (PCGC), a component of NHLBI’s Bench-to-Bassinet Program, seeks to address through the Gabriella Miller Kids First (GMKF) Pediatric Research Program. Under the auspices of prior GMKF awards for trio genome sequencing (GS), the PCGC began to elucidate the role of de novo noncoding damaging single nucleotide variants and small insertions and deletions (indels) in CHD causality . The cumulative mean attributed risk from noncoding de novo variants (DNVs) for exome-negative CHD was 17-45%. To further the understanding of the role of genetic variation in causing CHD, the PCGC is requesting GS to perform GS for 500 probands born with tetralogy of Fallot (ToF) or hypoplastic left heart syndrome (HLHS), unsolved after exome sequencing, and their unaffected parents. In addition to increasing cohort size to improve statistical power, we will use a new and larger control trio GS dataset available through TOPMed (n = 1,758) and generate an improved version of our neural network,HeartENN, which predicts functional impact of genetic variation, through incorporation of more-than-double cardiac noncoding regulatory feature data. Of note, the PCGC has the wherewithal to confirm relevant variants with other genomic methods as well as to perform functional cell-based assays to further support claims of pathogenicity. We will also use the GS data to expand our understanding of structural variation underlying CHD. We will use a best-of-class SV calling pipeline, developed by the Talkowski group at the Broad Institute. Analytic focus of SVs will include disruptions of known autosomal dominant CHD genes, 2nd hits in trans to damaging coding variants in known autosomal recessive CHD genes, and burden analysis for apparently damaging SVs combined with existing data about putatively damaging coding variants (SNVs and indels) from > 5000 CHD trios. Finally, in an exploratory portion of this aim, we will attempt calling of SVs such as repeat expansions that are difficult with short-read GS, focusing on a limited number of regions of potential interest based on our analysis of PacBio long-read GS from 200 CHD probands, currently being generated under the auspices of the GMKF pilot program. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Wendy Chung | HD110887 | Boston Children's Hospital | Genomic Analysis of Esophageal Atresia and Tracheoesophageal Fistulas and Associated Congenital Anoma | 360 |
| Abstract: DESCRIPTION (provided by applicant): Project Summary/Abstract Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. There is a 45% incidence of associated congenital malformations, most commonly digestive, cardiovascular, urogenital, and musculoskeletal, often part of a syndrome or complex association, with VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities) being most frequently recognized. Advanced surgical techniques and pre and post-operative care have improved the prognosis and survival of EA/TEF patients over the past decades. However, with improved survival, many of the long-term morbidities of EA/TEF have been exposed. It is likely that the outcome in EA/TEF patients is influenced by multiple genetic and clinical factors; however, determining which factors are critical has been limited by the lack of data, particularly genomic data. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of EA/TEF and define new genes and conditions associated with EA/TEF by performing whole genome sequencing on 100 parent child trios in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions and improve outcomes. PUBLIC HEALTH RELEVANCE: Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. We propose to elucidate the underlying genomic architecture of EA/TEF by performing whole genome sequencing to characterize new clinical syndromes associated with EA/TEF to provide more accurate clinical prognostic information. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Ariadne Letra | DE031445 | University of Pittsburgh | Whole Genome Sequencing Studies Of Multiplex Nonsyndromic Cleft Lip/Palate Families | 923 |
| Abstract: DESCRIPTION (provided by applicant): In this proposal, we request whole genome sequencing (WGS) services of 923 individuals from our cohort of well-characterized, large multigenerational nonsyndromic cleft lip/palate (NSCLP) families of Hispanic and non-Hispanic white ethnicities. NSCLP is a common birth defect accounting for 65% of all birth defects and annually affecting approximately 135,000 newborns worldwide. Despite improvement in treatments, NSCLP imposes significant medical, psychosocial and financial burdens that affect quality of life of affected individuals and their families. NSCLP is complex, caused by genetic and environmental factors, and their interactions. Recent advances in genomic approaches have improved our knowledge of the genetic factors involved in NSCLP; however, most of the variants associated with NSCLP account for ~25% of the genetic liability and reflect common, modest risk-variants often located in noncoding regions of the genome. More recently, it has been suggested that some genetic risk for NSCLP lies in rare variants and this has contributed to the lack of consistent findings and difficulty in unraveling risk alleles. Further, it is likely that the missing heritability of NSCLP result in part due to interactions between common, modest risk variants and rare, high-risk variants. We will analyze WGS data and apply polygenic risk score analysis to identify novel, high-penetrance NSCLP variants and to systematically evaluate the contributions of both common and rare variants to NSCLP, and how they segregate individually and in concert within and between families. The results of this study will provide novel and important insights about the genetic architecture contributing to the complex etiology of NSCLP. Importantly, this proposal will translate into a rich and publicly available resource of NSCLP genotypic and phenotypic data that will be made available to the broader scientific community to foster additional studies on NSCLP, as well as other birth defects and/or associated co-morbidities. Further, this proposal will provide genotype and allele frequency data in Hispanics for which limited data is available on genetic databases. Additional follow-up studies proposed, although beyond the scope of this X01 application, include validating the variants identified in this study in our additional NSCLP trios as well as through joint analysis with data from additional existing Kids First datasets. Successful completion of this study will provide novel and important insights about the genetic architecture contributing to the complex etiology of NSCLP, and will translate into a large, rich resource for genetic and phenotypic information on NSCLP. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Andrew L Hong | HD114129 | Emory University | Basis of Childhood Kidney Cancers and Birth Defects | 932 |
| Abstract: DESCRIPTION (provided by applicant): Wilms Tumor is the most common renal tumor of childhood. Although cure rates approach 90% after initial therapy that includes a combination of surgery, chemotherapy and radiation therapy, our understanding of the biology of how children develop this cancer remains limited due to small patient cohorts. Prior studies have uncovered a number of important genetic alterations associated with Wilms Tumor. However these studies are based on small cohorts. Here, we propose to advance our prior studies with a multi-decade effort to obtain high quality samples from over 200 pediatric institutions through Children’s Oncology Group Renal Tumor studies. With samples from approximately 2,946 patients, we propose to assess the whole genome, methylome and transcriptome of the patient’s germline, normal adjacent kidney and tumor kidney. Given the large sample size, we will be powered for the detection of rare variant alleles and validation of prior studies. Just as importantly, our patient cohort represents the diversity of the United States. The multi-PI team along with senior leadership of the COG Renal Tumor studies have deep expertise in the analyses of epidemiology, genetics, epigenetics and transcriptomics in childhood cancers along with decades experience with the care of children with renal tumors. This proposed study provides a timely opportunity to aid our understanding of cancer risk in children with genitourinary congenital anomalies and more broadly, our understanding of Wilms Tumor, from a diverse population. These data will provide a critical resource for cancer germline risk, congenital anomalies, developmental biology and cancer biology. PUBLIC HEALTH RELEVANCE: Wilms Tumor is the most common kidney cancer in children. Although some predisposition syndromes have been associated with Wilms Tumor (e.g., Beckwith Wiedemann Syndrome, Denys Drash Syndrome, Hemihypertrophy, WAGR Syndrome), recent studies suggest many more children with Wilms Tumor may have an underlying predisposition syndrome. This study will explore how these germline changes relate to the developing kidney or structural birth defects in addition to the development of kidney cancer which may lead to prevention strategies or enhance risk stratification and therapeutic target identification. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Erin Peckham-Gregory and Carl Allen | CA267639 | Texas Children's Hospital | Genomic Analysis Of Histiocytosis | 1008 |
| Abstract: DESCRIPTION (provided by applicant): Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasm characterized by lesions including pathogenic CD207+ dendritic cells among an inflammatory infiltrate. The median age at diagnosis is 30 months, and up-front chemotherapy fails in ~50% of patients resulting in multiple relapse events for 40-50% of cases, and long-term sequelae. Sequencing studies have found recurrent, mutually exclusive somatic activating mutations in MAPK pathway genes in ~85% of LCH lesions, including BRAF V600E in 50-65%. There is a “Misguided Myelomonocytic Precursor Model” in which specific somatic MAPK mutations at critical stages of myeloid differentiation determine extent of disease. However, this model fails to explain the significant differences in LCH risk across ethnicities. Despite advances to elucidate the somatic mutational landscape underlying LCH pathogenesis, germline risk factors remain largely unknown. Therefore, we conducted the first genome-wide association study of LCH and identified a SMAD6 variant associated with increased risk. SMAD6 inhibits bone morphogenetic protein and transforming growth factor-beta/activin signaling, which are determinants of Langerhans cell differentiation. This variant appears to suppress SMAD6 protein expression without a decrease in SMAD6 messenger RNA expression in patients carrying the risk allele. This risk allele is also more common in Hispanics who are at the highest risk of LCH, and absent in blacks who experience the lowest LCH incidence. Our preliminary data also support the emerging observation that LCH somatic activating mutations vary by race/ethnicity. Specifically, sequencing of tumors from black patients indicated that only 25% were BRAF V600E+ (compared to >60% in other populations), whereas 50% had mutations in MAP2K1 (compared to < 10% in other populations). Therefore, the objective of this Kids First X01 application is to more fully elucidate LCH etiology by defining the role of de novo mutations (DNMs) in established LCH genes and novel susceptibility genes, and by comprehensively assessing somatic variation in LCH. Our central hypothesis is that penetrant DNMs and novel germline and somatic variation may contribute to, or in some cases, drive LCH tumorigenesis. 1) We will leverage our ongoing Children's Oncology Group study, Genetic Epidemiology of Childhood Histiocytosis (GECHO), to sequence 300 LCH case-parent trios to evaluate the impact of recurrent DNMs on inherited susceptibility to LCH. 2) We will leverage paired germline-tumor samples from 200 patients enrolled to the Texas Children's Histiocytosis Program protocol or GECHO study to comprehensively assess the somatic landscape of LCH and identify germline variation contributing to somatic mutational profiles. Successful completion of the proposed aims may (1) improve genetic testing and counseling strategies in LCH patients and families; (2) advance surveillance and chemoprevention protocols; and (3) identify novel therapeutic targets. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| David Teachey | HD114203 | Children's Hospital of Pennsylvania | Somatic and Germline Variants in Childhood T-cell acute lymphoblastic leukemia | 730 |
| Abstract: DESCRIPTION (provided by applicant): The outcome for children with relapsed T-cell acute lymphoblastic leukemia (T-ALL) is dismal. Thus, the primary goal in treatment is to prevent relapse, which requires accurate risk stratification. Prior attempts to identify genetic aberrations that are prognostic independent of treatment response have failed. We recently performed comprehensive genomic profiling (whole genome sequencing (WGS), whole exome sequencing (WES), and whole transcriptome profiling (WTS) of tumor; WGS of germline) from >1300 patients with T-ALL treated on the AALL0434 clinical trial through a Gabriella Miller Kids First X01 award (X01HD100702) and made several novel, practice changing observations. We found T-ALL can be classified into 15 distinct groups, many of which are novel. We found that leukemic drivers were in non-coding regions in 60% of cases, highlighting the importance of WGS. We identified multiple subtypes that were predictive of favorable and unfavorable outcome. The successor trial to AALL0434 was AALL1231. On AALL1231, several changes were made to the backbone to eliminate cranial radiation in most patients and these changes had prognostic implications. Before we can prospectively incorporate genetic aberrations into risk stratification, we need to validate our results in an independent cohort treated with current therapy and identify genomic variants that are reproducibly prognostic irrespective of therapeutic backbone. In addition, we found the prognostic impact of some variants differed based on genetic ancestry; some genetic variants that were associated with higher cure rates in children of European ancestry were not associated with higher cure rates in children of African ancestry. We need to increase the number of patients studied from different racial and ethnic groups to ensure equity in future risk stratification. Finally, we were unable to identify the genomic driver in a small percentage of cases (5%) and long-read sequencing may be able to overcome this gap. We hypothesize that comprehensive genomic profiling will identify recurrent genetic alterations that can be used prospectively to risk classify patients with T-ALL. Genomic profiling of a large cohort of patients treated on the AALL1231 trial will serve as a natural extension of our initial X01 award, providing the power to assess the impact of genomic variants on outcome across genetic ancestral groups. We will test our hypothesis with the following specific aims: (1) validate prognostic variants in an independent cohort of patients with T-ALL; (2) identify novel genomic structural variants using long-read sequencing; and (3) determine the association between genetic ancestry, tumor biology and outcomes. The goal of the Kids First Program is to improve understanding of genetic mechanisms of disease, leading to improved diagnostic capabilities and ultimately more targeted therapies. Genomic profiling across two of the largest clinical trials ever performed in children with T-ALL will clearly meet these important goals. This work will not only fundamentally transform the understanding of T-ALL disease biology but also allow us to risk stratify patients accurately and equitably understand differences in tumor biology based on genetic ancestry. PUBLIC HEALTH RELEVANCE: Modern genetic tests have helped find better ways to identify children with T-cell acute lymphoblastic leukemia (T-ALL) who are less likely to be cured. Before we can use these tests in the clinic, we need to show they are helpful regardless of therapy used to treat the leukemia | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Sharon Diskin | CA268005 | Children's Hospital of Pennsylvania | The Genetic Basis Of Treatment Outcomes And Late Effects After High-Risk Neuroblastoma | 407 |
| Abstract: DESCRIPTION (provided by applicant): Children diagnosed with high-risk neuroblastoma receive intensive multi-modal therapy, yet 40-50% die of their primary cancer, and those who survive experience substantial treatment-related morbidities. There is no reliable way to identify those at greatest risk of treatment failure (death) or late effects, and only a nascent understanding of underlying genetic determinants. Our long term goal is to improve neuroblastoma outcomes by first characterizing the events driving tumorigenesis and treatment response so that evidence-based and less toxic therapies can be developed. We hypothesize that comprehensive whole genome sequencing (WGS) of high- risk neuroblastoma subjects treated with modern therapy and annotated with late effect phenotypes will identify genetic determinants of survival and treatment-related morbidities. Through an existing Gabriella Miller Kids First (GMKF) project, we performed WGS of neuroblastoma patient-parent triads/dyads (n=556) together with matched tumor DNA (n=336) and RNA-sequencing (n=207). These data have defined the heritable fraction of rare pathogenic variants in cancer predisposition genes and suggest carriers have worse survival. However, only a subset of cases (n=178) sequenced are high-risk and none include phenotyping of late effects. Here, we will build on existing GMKF profiling to generate germline WGS for 1,100 total children (n=922 new) who received modern high-risk neuroblastoma therapy, along with additional WGS of matched tumor DNA (n=553 new) and RNA-sequencing (n=461 new). All subjects participated in the Children’s Oncology Group (COG) neuroblastoma biology study (ANBL00B1). The entire cohort is annotated with demographic (age, sex, race, ethnicity), clinical (e.g. age at diagnosis, stage, risk group, survival), and tumor biological (e.g. MYCN status) co-variates. A subset (n=367) are 5+ year survivors enrolled in the COG ALTE15N2: Late Effects After High-Risk Neuroblastoma (LEAHRN) study and have undergone extensive clinical assessments, with excellent characterization of late toxicities. We will test our hypothesis through two Specific Aims: 1) Identify germline and somatic variants associated with high-risk neuroblastoma treatment failure. Using a phased approach, we will identify coding and non-coding germline variation, somatic alterations, and transcriptomic profiles predicting refractory disease and survival. 2) Discover genetic risk factors associated with late effects after high-risk neuroblastoma therapy. We will define the spectrum, prevalence, and association of rare pathogenic variants with respect to hearing loss, cardiomyopathy, growth impairment and primary gonadal failure in the LEAHRN subjects. Data from NCI- TARGET (n=1,108), our genome-wide association study (GWAS; n=6,202), and phenotyping in recent high-risk trials will be integrated to validate genetic associations with treatment outcomes. Sequencing of this unique and extensively phenotyped high-risk neuroblastoma cohort will provide an unparalleled opportunity to discover germline and somatic alterations that can be used to identify patients at risk for treatment failure and late effects. This will serve as rationale for the design of future trials aimed at improved survival and reduction in late effects. | ||||
2024 X01 Projects
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Austin L Brown | HD117364 | Baylor College of Medicine | Whole genome sequencing to characterize genetic susceptibility and variability in pediatric and AYA classic Hodgkin lymphoma | 1722 |
| Abstract: Hodgkin lymphoma is a lymphoproliferative malignancy and is the most common malignancy diagnosed in individuals between 15 and 20 years of age. Intensive treatment has contributed to five-year survival rates for Hodgkin lymphoma approaching 90%. Unfortunately, curate therapy is associated with profound short- and long- term adverse events. Our long-term goal is to maintain high progression free and overall survival for children and adolescents with Hodgkin lymphoma while reducing their risk of acute and late toxicity. Approaches to avert these adverse events without compromising treatment efficacy rely on a better understanding of the etiology of Hodgkin lymphoma. Two of the strongest risk factors for Hodgkin lymphoma appear to be a family history of disease and disrupted immune function, supporting a role for inherited genetics in the development of Hodgkin lymphoma. However, two questions remain unanswered: 1) what proportion of Hodgkin lymphoma cases may be attributed to inherited genetic variants in established cancer predisposition genes or inborn errors of immunity, and 2) to what extent do these susceptibility variants associated with etiologically distinct disease features. These gaps limit continued progress in the treatment of Hodgkin lymphoma and surveillance of adverse outcomes among affected individuals. This application pursued the central hypothesis that patients with Hodgkin lymphoma frequently harbor likely pathogenic variants in cancer predisposition genes and inborn errors of immunity and the frequency of these variants differ across patient and disease characteristics. Our proposed Kids First study will evaluate this hypothesis in two specific aims: 1) determine the frequency of pathogenic and likely pathogenetic variants in cancer predisposition genes and inborn errors of immunity genes among individuals with Hodgkin lymphoma, and 2) evaluate differences in the germline genetic susceptibility across Hodgkin lymphoma disease characteristics. To accomplish these aims, the proposed study leverages the resources available in the Children’s Oncology Group, a cooperative group of more than 200 pediatric treatment centers in North America, to provide access 3,200 well-phenotyped cases of Hodgkin lymphoma with germline DNA samples available for whole genome sequencing. The investigative team, co-led by experts in genetic epidemiology, Hodgkin lymphoma biology, and bioinformatics, is uniquely positioned to accomplish the proposed study. This application has the potential to advance our understanding of the genetic etiology of Hodgkin lymphoma in children and adolescents. Ultimately, this work may guide clinical decision making regarding available treatment modalities, inform the development of targeted therapies, and assist with genetic counseling and screening strategies for patients and their families. PUBLIC HEALTH RELEVANCE: Hodgkin lymphoma is one of the most common malignancies in adolescents, but information on the inherited genetic landscape of Hodgkin lymphoma is limited. This study will: 1) evaluate the frequency of inherited variation in cancer predisposition genes and inborn errors of immunity among pediatric and adolescent patients with Hodgkin lymphoma, and 2) describe the distribution of Hodgkin lymphoma susceptibility variants across disease characteristics. The results of this work will lead to a better understanding of genetic risk for Hodgkin lymphoma and may inform the development of better treatment options and surveillance strategies in affected individuals. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Hakon Hakonarson | HD117371 | Children's Hospital of Philadelphia | Translation-Focused Discovery and Analysis Platform for Resolving Childhood Cancers | 2585 |
| Abstract: Building on previous success in the Kids First Program, The Children's Hospital of Philadelphia (CHOP) focuses on a novel discovery platform on over a thousand deeply-phenotyped pediatric cancer cases, leveraging the same resources and analytical pipeline that has yielded over 250 novel gene discoveries. All participants have broad-consented to ongoing genomic analyses. We hypothesize that the combination of deep phenotypes and innovative informatics analysis pipeline will accelerate disease gene discovery from sequencing datasets that will identify risk variants and help prioritize druggable targets. Three specific aims are outlined: Specific Aim 1 will apply a novel tool, Gene Disease Crossmatching (GDCross), a Python-based algorithm created to prioritize causal variants in rare disease cases. It allows us to efficiently and effectively filter known pathogenic/likely pathogenic variants in our pediatric cancer cases. In so doing, we can prioritize discover analyses to focus on cases where a likely-causal variant has not yet been identified, maximizing the likelihood of identifying novel biomarkers. GDCross will be implemented on 946 Cases with Childhood Cancer plus additional family members, all of whom will have whole genome sequence data through the Kids First X01 mechanism. The dataset is enriched for under-represented/minority participants, primarily African Americans, who constitute approximately 50% of the proposed cohort. Specific Aim 2, will leverage CHOP's robust analysis platform to identify causative variants in cases. CHOP's extensive experience in genomic discovery, backed by robust infrastructure and expertise, will facilitate a broad base of analyses, including the identification of single nucleotide variants (SNVs), structural variants (SVs), and copy number variants (CNVs) using advanced bioinformatics tools. These approaches, which yielded several high-impact findings in our previous Kids First cohort Analysis, will focus on shared disease pathways, enabling mutation burden determination across different cancer subgroups. Specific Aim 3 will align with Kids First best practices for sharing data, where the study team has a strong track record of data sharing, with tens of thousands of genotypes and genomes currently shared on platforms like AnVIL dbGaP. All data from this proposal will be shared openly and in adherence to NIH data-sharing regulations and timelines are ensured. Long-term objectives: We propose to develop and implement best practices for genomic discovery in pediatric cancer patients that will ultimately yield data to accelerate scientific breakthroughs that improve human health. Agency relevance: The program addresses NCI's mission to improve health by developing an open and scalable template for supporting cancer research across a diverse pediatric cohort. Identification of novel biomarkers advances scientific knowledge and contributes to novel therapies for improved health outcomes. PUBLIC HEALTH RELEVANCE: Although pediatric cancers only account for 1% of the cancers diagnosed each year, they constitute the second leading cause of death in children between the ages of 5 and 14 years, and survival rates remain low for several subtypes. To better understand genomic risk factors in pediatric cancer, we propose to sequence a large cohort of cancer cases and family members, prioritizing discovery analyses in individuals without known pathogenic or likely pathogenic variants. We anticipate that the information derived from this deep phenotype cohort will allow for an improved understanding of the pathophysiology and molecular mechanisms underlying pediatric cancer, which may inform new practices for treatment or innovative future therapies. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Thanh Thien Hoang | HD117372 | Baylor College of Medicine | Somatic and Germline Genomic Variations of Medulloblastoma | 420 |
| Abstract: Medulloblastoma is the most common, malignant brain tumor in children and adolescents. In 2016, the World Health Organization Classification of Tumors of the Central Nervous System began recognizing four molecular subgroups of medulloblastoma based on DNA methylation: Wnt, Shh, group 3, and group 4. Clinical studies have reported tremendous heterogeneity across these molecular subgroups from molecular to clinical characteristics. For example, the Wnt subgroup is the least common but has the best 5-year survival of 92-95%. Group 3 is observed in 25% of medulloblastoma cases and has the worst prognosis (5-year survival of 45-58%). While germline single nucleotide variants (SNVs) of cancer predisposition genes explains ~5% of all medulloblastomas, the causes of medulloblastoma for the remaining 95% of patients are unknown. Thus, there is an important need to identify other genomic variations that may contribute to the etiology of this disease. Evolutionary genetics may provide some novel insights into the development of medulloblastoma. One of the defining evolutionary characteristics of humans compared to other hominoids (i.e., erect bipedal primates) is their larger brain. When comparing hominoid genomes across different species, structural variation (e.g., duplications, copy number variants) contributes more to genetic differences than SNVs. Because structural variation at certain loci is highly repetitive, accurately genotyping those regions has been challenging. The advent of long-read sequencing has now allowed us to accurately sequence an individual’s complete genome, including copy number variants, to explore this novel research question. Our long-term goal is to understand the pathogenesis of medulloblastoma. The overall objective of this application is to understand how structural variation in tumor and germlinemay contribute to the development of medulloblastoma. We hypothesize that a higher copy number of certain genes willcorrelate to the risk of developing group 3 and group 4 medulloblastoma. We additionally hypothesize that other structuralvariation across the genome may impact medulloblastoma risk. Our results may ultimately pave the way for improved clinical care through (a) identifying a novel cancer predisposition gene which can be used to screen for high-risk children and (b) the development of more targeted drugs and precision of treatment plans. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| John R Shaffer | HD117346 | University of Pittsburgh at Pittsburgh | Expanding the orofacial cleft omics resources | 3530 |
| Abstract: Abstract Orofacial cleft (OFC) birth defects are one of the most common structural birth defects in humans, and the most common craniofacial anomalies, with worldwide incidence of approximately 1 per 700 newborns. OFCs represent a major public health problem due to the associated morbidity, mortality, and significant medical care expenditures. Based on structures affected, OFCs have been categorized as three subtypes: clefts affecting the lip only (cleft lip, CL), clefts affecting both the lip and the palate (cleft lip and palate, CLP), and clefts affecting the palate only (cleft palate, CP). Historically, CL and CLP have been considered variations of the same malformation that differ in severity, whereas the developmental origins of the affected structures, epidemiology, and familial patterns suggest that CP has a separate etiology than CL and CLP. Both genetic and environmental factors play important roles in the development of OFCs, although understanding of these risk factors is incomplete. The proposed project aims to expand the Gabriella Miller Kids First (GMKF) resource by collecting data to investigate the role of DNA methylation – an epigenomic marker of gene activity – on the development of clefts. We propose to collect genome-wide DNA methylation assays in a large cohort of affected children as well as DNA methylation and transcriptomics assays in a subset of children with available discarded surgical tissue. Ultimately, these data will contribute new and complementary types of omics data to the GMKF resource for participants with already-available whole-genome sequencing data. This resource will allow us and others to perform analyses to identify the differentially methylated regions of the genome associated with OFCs and subtypes, and explore the functional roles of previously identified OFC-associated genetic loci. Successful completion of this project will expand and deepen our understanding of the genetic architecture and regulatory landscape of OFCs including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. PUBLIC HEALTH RELEVANCE: This project will expand the Gabriella Miller Kids First resource and deepen our understanding of the genetic architecture and regulatory landscape of non-syndromic orofacial clefts including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. This knowledge may ultimately be useful for applications such as recurrence prediction or personalized therapeutic interventions. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Eric Chien-Wei Liao | HD117353 | Children's Hospital of Philadelphia | Craniosynostosis Tissue X01 | 1900 |
| Abstract: Abstract Syndromic and non-syndromic craniosynostosis (CS) are complex malformations of the cranial vault that result from premature or anomalous fusion of cranial sutures. The mainstay of treatment remains complex surgical operations with significant morbidity and risks to a newborn. Meanwhile, advances in fundamental understanding of craniosynostosis genetics stand in stark contrast to the persistent gap in translation to clinical impact. This proposal addresses critical unmet scientific and clinical need to analyze the direct pathologic suture and bone in order to understand CS pathogenesis. This project will generate genomic and transcriptome data from the pathologic fused suture and bone from over 385 CS cases, with normal bone tissue from a separate calvaria site as control. These pathogenic CS tissues span all craniosynostosis suture types, from both syndromic and non-syndromic CS cases. Additionally,143 of these pathogenic tissue cases are matched to CS trios that are currently undergoing whole genome sequence (WGS) data generation in the 2023 cycle of the Gabriella Miller Kids First (GMKF) X01 project. This unique CS tissue biobank and clinically annotated database enable us to address 2 key questions that were previously intractable. Reports from other groups and our preliminary data suggest that somatic mosaicism contributes to CS pathogenesis. A large scale study is necessary to determine whether somatic mutations cause CS in both syndromic and non-syndromic CS and across different suture types. Further animal model experimental evidence and clinical observations corroborate that post-natal suture and bone in many CS cases persist to impact natural history of disease and clinical outcomes. However, a direct comparison of anomalous CS synostotic suture and bone vs. normal bone has not been described across syndromic vs. non-syndromic CS and across suture types. To address these questions, Aim 1 will generate WGS data from the pathologic tissue and normal bone control, when integrated with germline WGS data from blood/saliva, will enable us to determine the role of somatic mosaicism in the pathogenesis of craniosynostosis. Aim 2 will generate RNAseq data from the pathologic and normal suture tissue, to enable comparison of the molecular differences. Successful completion of this project will yield genomic and transcriptome data that will address these questions and enrich the data available to the community through the GMKF projects, with overall impact of enhancing fundamental research and clinical translation. PUBLIC HEALTH RELEVANCE: Syndromic and non-syndromic craniosynostosis (CS) occur when the cranial sutures are aberrantly fused at birth, leading to significant neurological disability and craniofacial deformity if left untreated. This study will generate genomic and transcriptomic data from the direct pathogenic synostotic and normal bone tissue that will enable analysis of somatic mosaicism and identify molecular differences that enhance our understanding of CS pathogenesis and natural history of disease. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Philip F Giampietro | HD117362 | University of Illinois at Chicago | Whole genome analysis in patients with vertebral malformations and congenital scoliosis | 51 |
| Abstract: Vertebral malformations (VM) represent conditions that occur with an estimated incidence of 1/2000 and pose a significant public health impact due to their association with congenital scoliosis (CS) and other conditions. To better understand genetic variants that contribute to VM, we propose to perform whole genome sequencing (WGS) through Gabriella Miller Kids First on an existing vertebral malformation (VM) cohort of 69 probands and investigate their genetic etiology. We hypothesize the existence of novel genes, phenotypes, and mechanisms associated with these conditions. We propose to develop a pipeline from gene discovery and functional validation in zebrafish and mouse models. Our first aim is to perform WGS on a cohort of 69 probands with VM and 60 family members through Kids First. We collect detailed phenotyping data and maternal exposure data including diabetes and medications during pregnancy. This proposal will expand the range of pediatric disorders included within the Kids First Data Resource and downstream analyses will aid in the GMKF data sharing initiative within the pediatric research community. The identification of candidate genes for VM by rigorous bioinformatic analysis will serve as a focal point for the development of downstream efforts to develop animal models and functional assays to evaluate sequence variant pathogenicity (Aim 2 and Future Initiatives). Research in this field will be accelerated through the sharing of DNA sequence variants in publicly available databases. The ability to identify genes associated with VM will serve as a foundation for guiding prevention, therapeutic, and genetic counseling strategies for patients cared for by the clinical genetics and greater pediatric orthopedic community. PUBLIC HEALTH RELEVANCE: To better understand the pathogenetic mechanisms for the occurrence of vertebral malformations (VM) we will perform whole genome sequencing on a cohort of 69 probands and 60 parent samples through Gabriella Miller Kids First. This will build on our original VM cohort of 86 probands. We propose to use both mouse and zebrafish models downstream of analysis in order to validate the pathogenicity of VM and congenital scoliosis-associated sequence variants. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Wendy K Chung | HD117365 | Boston Children's Hospital | Genetic basis of laryngeal clefts | 376 |
| Abstract: Esophageal atresia/tracheoesophageal fistula/laryngeal clefts (EA/TEF/LC) are a group of rare and complex aerodigestive congenital anomalies with an estimated incidence of 1 in 2500 to 1 in 4000 live births. There is a 45% incidence of associated congenital malformations, most commonly digestive, cardiovascular, urogenital, and musculoskeletal, often part of a syndrome or complex association, with VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities) being most frequently recognized. Advanced surgical techniques and pre and post-operative care have improved the prognosis and survival of patients over the past decades. However, with improved survival, many of the long- term morbidities have been exposed. It is likely that patient outcomes are influenced by multiple genetic and clinical factors; however, determining which factors are critical has been limited by the lack of data, particularly genomic data. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of EA/TEF/LC and define new genes and conditions associated with EA/TEF/LC by performing whole genome sequencing on 200 probands with laryngeal clefts in a clinically well characterized cohort to identify rare variants and new genes for laryngeal cleft as we aggregate the data from these patients with our two prior EA/TEF cohorts in Gabrielle Miller Kids First. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions and improve outcomes. PUBLIC HEALTH RELEVANCE: Esophageal atresia/tracheoesophageal fistula/laryngeal clefts (EA/TEF/LC) are a group of rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. We propose to elucidate the underlying genomic architecture of these conditions by performing whole genome sequencing to characterize new clinical syndromes to provide more accurate clinical prognostic information. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Friedhelm Hildebrandt | HD117370 | Boston Children's Hospital | Genomic Landscape of Renal Developmental Disorders, Including Renal Ciliopathies and Congenital Anomalies of Kidneys and the Urinary Tract | 750 |
| Abstract: Genomic Landscape of Renal Developmental Disorders, Including Renal Ciliopathies and Congenital Anomalies of Kidneys and the Urinary Tract. Background. Structural Birth defects (SBD) account for the overwhelming majority (66%) of chronic kidney diseases (CKD) that manifest before 25 years of age and require dialysis or renal transplantation for survival. Two major groups of Structural BD that cause CKD are: Congenital anomalies of the kidneys and urinary tract (CAKUT) (45%), and nephronophthisis-related ciliopathies (NPHP-RC) (6%). CAKUT represents the most frequent birth defect in humans (23%). There is no prevention of CAKUT. NPHP-RC are genetically very heterogeneous, and, currently, mutations in more than 90 genes have been described as single-gene causes. Both the phenotypes of NPHP-RC and CAKUT are very diverse, and often part of multisystem syndromes that involve structural BDs in virtually any organ system. A strong genotype-phenotype overlap exists between NPHP-RC and CAKUT. Understanding this overlap is essential in understanding the specific molecular pathways, thereby understanding the genetic mechanisms influencing kidney development. Previous work. Our lab has made substantial contributions to the identification of novel genomic causes of both NPHP and CAKUT in the following ways: i. Identification of >60 novel monogenic causes of CAKUT and NPHP-RC. ii. Functional characterization of disease-causing alleles, employing cell-based and animal models. iii. Delineation of novel pathogenic pathways of CAKUT and NPHP-RC. iv. Demonstration in large cohorts that we can identify a causative monogenic mutation in 1 of 220 monogenic genes in a high fraction of cases with CAKUT (17%) and NPHP-RC (50%). v. Monogenic gene products that we identified in CAKUT, NPHP-RC converge onto protein interaction complexes and novel distinct pathogenic pathways. Proposed Research. We, therefore, propose to identify the missing genomic causes of CAKUT and NPHP-RC by WGS to further elucidate disease mechanisms of early-onset CKD caused by SBD- related extrarenal pathomechanisms. The work will be performed independently by the Hildebrandt lab at BCH or in collaboration with Dr. Simone Sanna Cherchi (Columbia University). PUBLIC HEALTH RELEVANCE: Structural Birth defects (SBD) account for the overwhelming majority (66%) of chronic kidney diseases (CKD) that manifest before 25 years of age and require dialysis or renal transplantation for survival. Two major groups of Structural BD causing CKD are Congenital anomalies of the kidneys and urinary tract (CAKUT) (45%), and Nephronophthisis-Related Ciliopathies (NPHP-RC) (6%).CAKUT represents the most frequent birth defect in humans (23%). There is no prevention of CAKUT. NPHP-RC are genetically very heterogeneous, and, currently, mutations in more than 90 genes have been described as single-gene causes. Both the phenotypes of NPHP-RC and CAKUT are very diverse, and often part of multisystem syndromes that involve structural BDs in virtually any organ system. A strong genotype-phenotype overlap exists between NPHP-RC and CAKUT. Understanding this overlap is essential in understanding the specific molecular pathways, thereby understanding the genetic mechanisms influencing kidney development. Our lab has made substantial contributions to the identification of novel genomic causes of both NPHP and CAKUT by establishing >60 novel monogenic causes of CAKUT and NPHP-RC. We propose to sequence 470 trios by WGS to strengthen genomic findings. We, therefore, propose to identify the missing genomic causes of CAKUT and NPHP-RC by WGS to further elucidate disease mechanisms of early-onset CKD caused by SBD-related extrarenal pathomechanisms. . Identification of the missing causes of early-onset CKD by WGS will reveal novel distinct pathogenic pathways. It will enable the development of functional assays in cell-based and animal models for deleterious effects of monogenic disease alleles, thereby enabling unequivocal diagnostics, small molecule screening for therapeutic compounds, and potentially enabling therapeutic opportunities to eventually prevent and treat these currently intractable structural BD. | ||||
*Sequencing of this project is supported by the NIH Childhood Cancer Data initiative and and the data will be shared through the NCI Cancer Data Service
2024 X01 Projects
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Austin L Brown | HD117364 | Baylor College of Medicine | Whole genome sequencing to characterize genetic susceptibility and variability in pediatric and AYA classic Hodgkin lymphoma | 1722 |
| Abstract: Hodgkin lymphoma is a lymphoproliferative malignancy and is the most common malignancy diagnosed in individuals between 15 and 20 years of age. Intensive treatment has contributed to five-year survival rates for Hodgkin lymphoma approaching 90%. Unfortunately, curate therapy is associated with profound short- and long- term adverse events. Our long-term goal is to maintain high progression free and overall survival for children and adolescents with Hodgkin lymphoma while reducing their risk of acute and late toxicity. Approaches to avert these adverse events without compromising treatment efficacy rely on a better understanding of the etiology of Hodgkin lymphoma. Two of the strongest risk factors for Hodgkin lymphoma appear to be a family history of disease and disrupted immune function, supporting a role for inherited genetics in the development of Hodgkin lymphoma. However, two questions remain unanswered: 1) what proportion of Hodgkin lymphoma cases may be attributed to inherited genetic variants in established cancer predisposition genes or inborn errors of immunity, and 2) to what extent do these susceptibility variants associated with etiologically distinct disease features. These gaps limit continued progress in the treatment of Hodgkin lymphoma and surveillance of adverse outcomes among affected individuals. This application pursued the central hypothesis that patients with Hodgkin lymphoma frequently harbor likely pathogenic variants in cancer predisposition genes and inborn errors of immunity and the frequency of these variants differ across patient and disease characteristics. Our proposed Kids First study will evaluate this hypothesis in two specific aims: 1) determine the frequency of pathogenic and likely pathogenetic variants in cancer predisposition genes and inborn errors of immunity genes among individuals with Hodgkin lymphoma, and 2) evaluate differences in the germline genetic susceptibility across Hodgkin lymphoma disease characteristics. To accomplish these aims, the proposed study leverages the resources available in the Children’s Oncology Group, a cooperative group of more than 200 pediatric treatment centers in North America, to provide access 3,200 well-phenotyped cases of Hodgkin lymphoma with germline DNA samples available for whole genome sequencing. The investigative team, co-led by experts in genetic epidemiology, Hodgkin lymphoma biology, and bioinformatics, is uniquely positioned to accomplish the proposed study. This application has the potential to advance our understanding of the genetic etiology of Hodgkin lymphoma in children and adolescents. Ultimately, this work may guide clinical decision making regarding available treatment modalities, inform the development of targeted therapies, and assist with genetic counseling and screening strategies for patients and their families. PUBLIC HEALTH RELEVANCE: Hodgkin lymphoma is one of the most common malignancies in adolescents, but information on the inherited genetic landscape of Hodgkin lymphoma is limited. This study will: 1) evaluate the frequency of inherited variation in cancer predisposition genes and inborn errors of immunity among pediatric and adolescent patients with Hodgkin lymphoma, and 2) describe the distribution of Hodgkin lymphoma susceptibility variants across disease characteristics. The results of this work will lead to a better understanding of genetic risk for Hodgkin lymphoma and may inform the development of better treatment options and surveillance strategies in affected individuals. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Hakon Hakonarson | HD117371 | Children's Hospital of Philadelphia | Translation-Focused Discovery and Analysis Platform for Resolving Childhood Cancers | 2585 |
| Abstract: Building on previous success in the Kids First Program, The Children's Hospital of Philadelphia (CHOP) focuses on a novel discovery platform on over a thousand deeply-phenotyped pediatric cancer cases, leveraging the same resources and analytical pipeline that has yielded over 250 novel gene discoveries. All participants have broad-consented to ongoing genomic analyses. We hypothesize that the combination of deep phenotypes and innovative informatics analysis pipeline will accelerate disease gene discovery from sequencing datasets that will identify risk variants and help prioritize druggable targets. Three specific aims are outlined: Specific Aim 1 will apply a novel tool, Gene Disease Crossmatching (GDCross), a Python-based algorithm created to prioritize causal variants in rare disease cases. It allows us to efficiently and effectively filter known pathogenic/likely pathogenic variants in our pediatric cancer cases. In so doing, we can prioritize discover analyses to focus on cases where a likely-causal variant has not yet been identified, maximizing the likelihood of identifying novel biomarkers. GDCross will be implemented on 946 Cases with Childhood Cancer plus additional family members, all of whom will have whole genome sequence data through the Kids First X01 mechanism. The dataset is enriched for under-represented/minority participants, primarily African Americans, who constitute approximately 50% of the proposed cohort. Specific Aim 2, will leverage CHOP's robust analysis platform to identify causative variants in cases. CHOP's extensive experience in genomic discovery, backed by robust infrastructure and expertise, will facilitate a broad base of analyses, including the identification of single nucleotide variants (SNVs), structural variants (SVs), and copy number variants (CNVs) using advanced bioinformatics tools. These approaches, which yielded several high-impact findings in our previous Kids First cohort Analysis, will focus on shared disease pathways, enabling mutation burden determination across different cancer subgroups. Specific Aim 3 will align with Kids First best practices for sharing data, where the study team has a strong track record of data sharing, with tens of thousands of genotypes and genomes currently shared on platforms like AnVIL dbGaP. All data from this proposal will be shared openly and in adherence to NIH data-sharing regulations and timelines are ensured. Long-term objectives: We propose to develop and implement best practices for genomic discovery in pediatric cancer patients that will ultimately yield data to accelerate scientific breakthroughs that improve human health. Agency relevance: The program addresses NCI's mission to improve health by developing an open and scalable template for supporting cancer research across a diverse pediatric cohort. Identification of novel biomarkers advances scientific knowledge and contributes to novel therapies for improved health outcomes. PUBLIC HEALTH RELEVANCE: Although pediatric cancers only account for 1% of the cancers diagnosed each year, they constitute the second leading cause of death in children between the ages of 5 and 14 years, and survival rates remain low for several subtypes. To better understand genomic risk factors in pediatric cancer, we propose to sequence a large cohort of cancer cases and family members, prioritizing discovery analyses in individuals without known pathogenic or likely pathogenic variants. We anticipate that the information derived from this deep phenotype cohort will allow for an improved understanding of the pathophysiology and molecular mechanisms underlying pediatric cancer, which may inform new practices for treatment or innovative future therapies. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Thanh Thien Hoang | HD117372 | Baylor College of Medicine | Somatic and Germline Genomic Variations of Medulloblastoma | 420 |
| Abstract: Medulloblastoma is the most common, malignant brain tumor in children and adolescents. In 2016, the World Health Organization Classification of Tumors of the Central Nervous System began recognizing four molecular subgroups of medulloblastoma based on DNA methylation: Wnt, Shh, group 3, and group 4. Clinical studies have reported tremendous heterogeneity across these molecular subgroups from molecular to clinical characteristics. For example, the Wnt subgroup is the least common but has the best 5-year survival of 92-95%. Group 3 is observed in 25% of medulloblastoma cases and has the worst prognosis (5-year survival of 45-58%). While germline single nucleotide variants (SNVs) of cancer predisposition genes explains ~5% of all medulloblastomas, the causes of medulloblastoma for the remaining 95% of patients are unknown. Thus, there is an important need to identify other genomic variations that may contribute to the etiology of this disease. Evolutionary genetics may provide some novel insights into the development of medulloblastoma. One of the defining evolutionary characteristics of humans compared to other hominoids (i.e., erect bipedal primates) is their larger brain. When comparing hominoid genomes across different species, structural variation (e.g., duplications, copy number variants) contributes more to genetic differences than SNVs. Because structural variation at certain loci is highly repetitive, accurately genotyping those regions has been challenging. The advent of long-read sequencing has now allowed us to accurately sequence an individual’s complete genome, including copy number variants, to explore this novel research question. Our long-term goal is to understand the pathogenesis of medulloblastoma. The overall objective of this application is to understand how structural variation in tumor and germlinemay contribute to the development of medulloblastoma. We hypothesize that a higher copy number of certain genes willcorrelate to the risk of developing group 3 and group 4 medulloblastoma. We additionally hypothesize that other structuralvariation across the genome may impact medulloblastoma risk. Our results may ultimately pave the way for improved clinical care through (a) identifying a novel cancer predisposition gene which can be used to screen for high-risk children and (b) the development of more targeted drugs and precision of treatment plans. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| John R Shaffer | HD117346 | University of Pittsburgh at Pittsburgh | Expanding the orofacial cleft omics resources | 3530 |
| Abstract: Abstract Orofacial cleft (OFC) birth defects are one of the most common structural birth defects in humans, and the most common craniofacial anomalies, with worldwide incidence of approximately 1 per 700 newborns. OFCs represent a major public health problem due to the associated morbidity, mortality, and significant medical care expenditures. Based on structures affected, OFCs have been categorized as three subtypes: clefts affecting the lip only (cleft lip, CL), clefts affecting both the lip and the palate (cleft lip and palate, CLP), and clefts affecting the palate only (cleft palate, CP). Historically, CL and CLP have been considered variations of the same malformation that differ in severity, whereas the developmental origins of the affected structures, epidemiology, and familial patterns suggest that CP has a separate etiology than CL and CLP. Both genetic and environmental factors play important roles in the development of OFCs, although understanding of these risk factors is incomplete. The proposed project aims to expand the Gabriella Miller Kids First (GMKF) resource by collecting data to investigate the role of DNA methylation – an epigenomic marker of gene activity – on the development of clefts. We propose to collect genome-wide DNA methylation assays in a large cohort of affected children as well as DNA methylation and transcriptomics assays in a subset of children with available discarded surgical tissue. Ultimately, these data will contribute new and complementary types of omics data to the GMKF resource for participants with already-available whole-genome sequencing data. This resource will allow us and others to perform analyses to identify the differentially methylated regions of the genome associated with OFCs and subtypes, and explore the functional roles of previously identified OFC-associated genetic loci. Successful completion of this project will expand and deepen our understanding of the genetic architecture and regulatory landscape of OFCs including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. PUBLIC HEALTH RELEVANCE: This project will expand the Gabriella Miller Kids First resource and deepen our understanding of the genetic architecture and regulatory landscape of non-syndromic orofacial clefts including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. This knowledge may ultimately be useful for applications such as recurrence prediction or personalized therapeutic interventions. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Eric Chien-Wei Liao | HD117353 | Children's Hospital of Philadelphia | Craniosynostosis Tissue X01 | 1900 |
| Abstract: Abstract Syndromic and non-syndromic craniosynostosis (CS) are complex malformations of the cranial vault that result from premature or anomalous fusion of cranial sutures. The mainstay of treatment remains complex surgical operations with significant morbidity and risks to a newborn. Meanwhile, advances in fundamental understanding of craniosynostosis genetics stand in stark contrast to the persistent gap in translation to clinical impact. This proposal addresses critical unmet scientific and clinical need to analyze the direct pathologic suture and bone in order to understand CS pathogenesis. This project will generate genomic and transcriptome data from the pathologic fused suture and bone from over 385 CS cases, with normal bone tissue from a separate calvaria site as control. These pathogenic CS tissues span all craniosynostosis suture types, from both syndromic and non-syndromic CS cases. Additionally,143 of these pathogenic tissue cases are matched to CS trios that are currently undergoing whole genome sequence (WGS) data generation in the 2023 cycle of the Gabriella Miller Kids First (GMKF) X01 project. This unique CS tissue biobank and clinically annotated database enable us to address 2 key questions that were previously intractable. Reports from other groups and our preliminary data suggest that somatic mosaicism contributes to CS pathogenesis. A large scale study is necessary to determine whether somatic mutations cause CS in both syndromic and non-syndromic CS and across different suture types. Further animal model experimental evidence and clinical observations corroborate that post-natal suture and bone in many CS cases persist to impact natural history of disease and clinical outcomes. However, a direct comparison of anomalous CS synostotic suture and bone vs. normal bone has not been described across syndromic vs. non-syndromic CS and across suture types. To address these questions, Aim 1 will generate WGS data from the pathologic tissue and normal bone control, when integrated with germline WGS data from blood/saliva, will enable us to determine the role of somatic mosaicism in the pathogenesis of craniosynostosis. Aim 2 will generate RNAseq data from the pathologic and normal suture tissue, to enable comparison of the molecular differences. Successful completion of this project will yield genomic and transcriptome data that will address these questions and enrich the data available to the community through the GMKF projects, with overall impact of enhancing fundamental research and clinical translation. PUBLIC HEALTH RELEVANCE: Syndromic and non-syndromic craniosynostosis (CS) occur when the cranial sutures are aberrantly fused at birth, leading to significant neurological disability and craniofacial deformity if left untreated. This study will generate genomic and transcriptomic data from the direct pathogenic synostotic and normal bone tissue that will enable analysis of somatic mosaicism and identify molecular differences that enhance our understanding of CS pathogenesis and natural history of disease. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Philip F Giampietro | HD117362 | University of Illinois at Chicago | Whole genome analysis in patients with vertebral malformations and congenital scoliosis | 51 |
| Abstract: Vertebral malformations (VM) represent conditions that occur with an estimated incidence of 1/2000 and pose a significant public health impact due to their association with congenital scoliosis (CS) and other conditions. To better understand genetic variants that contribute to VM, we propose to perform whole genome sequencing (WGS) through Gabriella Miller Kids First on an existing vertebral malformation (VM) cohort of 69 probands and investigate their genetic etiology. We hypothesize the existence of novel genes, phenotypes, and mechanisms associated with these conditions. We propose to develop a pipeline from gene discovery and functional validation in zebrafish and mouse models. Our first aim is to perform WGS on a cohort of 69 probands with VM and 60 family members through Kids First. We collect detailed phenotyping data and maternal exposure data including diabetes and medications during pregnancy. This proposal will expand the range of pediatric disorders included within the Kids First Data Resource and downstream analyses will aid in the GMKF data sharing initiative within the pediatric research community. The identification of candidate genes for VM by rigorous bioinformatic analysis will serve as a focal point for the development of downstream efforts to develop animal models and functional assays to evaluate sequence variant pathogenicity (Aim 2 and Future Initiatives). Research in this field will be accelerated through the sharing of DNA sequence variants in publicly available databases. The ability to identify genes associated with VM will serve as a foundation for guiding prevention, therapeutic, and genetic counseling strategies for patients cared for by the clinical genetics and greater pediatric orthopedic community. PUBLIC HEALTH RELEVANCE: To better understand the pathogenetic mechanisms for the occurrence of vertebral malformations (VM) we will perform whole genome sequencing on a cohort of 69 probands and 60 parent samples through Gabriella Miller Kids First. This will build on our original VM cohort of 86 probands. We propose to use both mouse and zebrafish models downstream of analysis in order to validate the pathogenicity of VM and congenital scoliosis-associated sequence variants. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Wendy K Chung | HD117365 | Boston Children's Hospital | Genetic basis of laryngeal clefts | 376 |
| Abstract: Esophageal atresia/tracheoesophageal fistula/laryngeal clefts (EA/TEF/LC) are a group of rare and complex aerodigestive congenital anomalies with an estimated incidence of 1 in 2500 to 1 in 4000 live births. There is a 45% incidence of associated congenital malformations, most commonly digestive, cardiovascular, urogenital, and musculoskeletal, often part of a syndrome or complex association, with VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities) being most frequently recognized. Advanced surgical techniques and pre and post-operative care have improved the prognosis and survival of patients over the past decades. However, with improved survival, many of the long- term morbidities have been exposed. It is likely that patient outcomes are influenced by multiple genetic and clinical factors; however, determining which factors are critical has been limited by the lack of data, particularly genomic data. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of EA/TEF/LC and define new genes and conditions associated with EA/TEF/LC by performing whole genome sequencing on 200 probands with laryngeal clefts in a clinically well characterized cohort to identify rare variants and new genes for laryngeal cleft as we aggregate the data from these patients with our two prior EA/TEF cohorts in Gabrielle Miller Kids First. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions and improve outcomes. PUBLIC HEALTH RELEVANCE: Esophageal atresia/tracheoesophageal fistula/laryngeal clefts (EA/TEF/LC) are a group of rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. We propose to elucidate the underlying genomic architecture of these conditions by performing whole genome sequencing to characterize new clinical syndromes to provide more accurate clinical prognostic information. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Friedhelm Hildebrandt | HD117370 | Boston Children's Hospital | Genomic Landscape of Renal Developmental Disorders, Including Renal Ciliopathies and Congenital Anomalies of Kidneys and the Urinary Tract | 750 |
| Abstract: Genomic Landscape of Renal Developmental Disorders, Including Renal Ciliopathies and Congenital Anomalies of Kidneys and the Urinary Tract. Background. Structural Birth defects (SBD) account for the overwhelming majority (66%) of chronic kidney diseases (CKD) that manifest before 25 years of age and require dialysis or renal transplantation for survival. Two major groups of Structural BD that cause CKD are: Congenital anomalies of the kidneys and urinary tract (CAKUT) (45%), and nephronophthisis-related ciliopathies (NPHP-RC) (6%). CAKUT represents the most frequent birth defect in humans (23%). There is no prevention of CAKUT. NPHP-RC are genetically very heterogeneous, and, currently, mutations in more than 90 genes have been described as single-gene causes. Both the phenotypes of NPHP-RC and CAKUT are very diverse, and often part of multisystem syndromes that involve structural BDs in virtually any organ system. A strong genotype-phenotype overlap exists between NPHP-RC and CAKUT. Understanding this overlap is essential in understanding the specific molecular pathways, thereby understanding the genetic mechanisms influencing kidney development. Previous work. Our lab has made substantial contributions to the identification of novel genomic causes of both NPHP and CAKUT in the following ways: i. Identification of >60 novel monogenic causes of CAKUT and NPHP-RC. ii. Functional characterization of disease-causing alleles, employing cell-based and animal models. iii. Delineation of novel pathogenic pathways of CAKUT and NPHP-RC. iv. Demonstration in large cohorts that we can identify a causative monogenic mutation in 1 of 220 monogenic genes in a high fraction of cases with CAKUT (17%) and NPHP-RC (50%). v. Monogenic gene products that we identified in CAKUT, NPHP-RC converge onto protein interaction complexes and novel distinct pathogenic pathways. Proposed Research. We, therefore, propose to identify the missing genomic causes of CAKUT and NPHP-RC by WGS to further elucidate disease mechanisms of early-onset CKD caused by SBD- related extrarenal pathomechanisms. The work will be performed independently by the Hildebrandt lab at BCH or in collaboration with Dr. Simone Sanna Cherchi (Columbia University). PUBLIC HEALTH RELEVANCE: Structural Birth defects (SBD) account for the overwhelming majority (66%) of chronic kidney diseases (CKD) that manifest before 25 years of age and require dialysis or renal transplantation for survival. Two major groups of Structural BD causing CKD are Congenital anomalies of the kidneys and urinary tract (CAKUT) (45%), and Nephronophthisis-Related Ciliopathies (NPHP-RC) (6%).CAKUT represents the most frequent birth defect in humans (23%). There is no prevention of CAKUT. NPHP-RC are genetically very heterogeneous, and, currently, mutations in more than 90 genes have been described as single-gene causes. Both the phenotypes of NPHP-RC and CAKUT are very diverse, and often part of multisystem syndromes that involve structural BDs in virtually any organ system. A strong genotype-phenotype overlap exists between NPHP-RC and CAKUT. Understanding this overlap is essential in understanding the specific molecular pathways, thereby understanding the genetic mechanisms influencing kidney development. Our lab has made substantial contributions to the identification of novel genomic causes of both NPHP and CAKUT by establishing >60 novel monogenic causes of CAKUT and NPHP-RC. We propose to sequence 470 trios by WGS to strengthen genomic findings. We, therefore, propose to identify the missing genomic causes of CAKUT and NPHP-RC by WGS to further elucidate disease mechanisms of early-onset CKD caused by SBD-related extrarenal pathomechanisms. . Identification of the missing causes of early-onset CKD by WGS will reveal novel distinct pathogenic pathways. It will enable the development of functional assays in cell-based and animal models for deleterious effects of monogenic disease alleles, thereby enabling unequivocal diagnostics, small molecule screening for therapeutic compounds, and potentially enabling therapeutic opportunities to eventually prevent and treat these currently intractable structural BD. | ||||
*Sequencing of this project is supported by the NIH Childhood Cancer Data initiative and and the data will be shared through the NCI Cancer Data Service
2023 X01 Projects
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Joseph G Gleeson | HD114132 | University of California, San Diego | Whole Genome Sequencing in Structural Defects of the Neural Tube | 1200 |
| Abstract: Myelomeningocele (aka meningomyelocele, MM) is the most severe form of spina bifida, a neural tube defect (NTD) in humans and the most common CNS birth defect. MM is considered a genetically complex disease, and occurs in 3.72/10,000 live US birth, and is partly preventable with prenatal folate, but the genetic basis and the mechanisms by which folate work to reduce disease incidence remain obscure. MM is associated nearly uniformly with prenatal hydrocephalus and the Arnold-Chiari malformation, as well as paraplegia and lifelong neuromotor disability. The genes for several rare syndromic forms of NTDs are known, but the causes for the majority with sporadic MM remain unknown. Despite the importance of MM, most previous research has been limited to targeted sequencing and association studies of folate metabolism genes, or very small-scale exome sequencing. We hypothesize that de novo mutations (DNMs) produce likely gene disrupting (LGD) events that contribution to MM risk. Using conservative estimates of between 50-100 recurrently mutated discoverable genes contributing to risk, and our preliminary data demonstrating an excess of LGD DNMs in MM compared with control individuals, we estimate that with a cohort size of 1000 trios, we should uncover between 5-20 new recurrently mutated genes underlying MM, with minimal false-discovery. With this in mind, we formed the Spina Bifida Sequencing Consortium, and established a platform for data and sample sharing. Preliminary analysis of our first batch of 100 trios analyzed by WGS from GMKF suggests a wealth of important gene mutations. We have embarked on a new recruitment effort of an additional cohort of 400 new simplex MM trios, in collaboration with the US Spina Bifida Association, consented trios to allow for data sharing, and have performed detailed sample quality control. We also have preliminary data that use of dried bloodspot DNA from trios performs comparably to whole blood DNA, so will be happy to swap saliva for bloodspot recruitment at NIH’s preference. This cohort is now half-way assembled, with the remaining cohort to be ascertained in the next 6 months. We have established a workflow for de novo SNP/INDEL/SV detection from WGS and have ample computer storage and nodes to see the project to completion. We also plan to continue recruitment into the future with the goal of 2000 trios in the next 5 years. We propose a detailed bioinformatics workflow to identify gene mutations within a statistical framework, considering detailed scRNA expression profiling from developing mammalian neural tube, and have developed a robust functional validation workflow using Xenopus and mouse gene targeting. Our project has the potential to uncover a host of causes for this most common of the CNS birth defects, paving the way for future breakthroughs in detection, treatment, and prevention. PUBLIC HEALTH RELEVANCE: This work will identify new genetic disease genes predisposing to myelomeningocele, the most common pediatric structural brain disease. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Andrew L Hong | HD114129 | Emory University | Basis of Childhood Kidney Cancers and Birth Defects | 1353 |
| Abstract: Wilms Tumor is the most common renal tumor of childhood. Although cure rates approach 90% after initial therapy that includes a combination of surgery, chemotherapy and radiation therapy, our understanding of the biology of how children develop this cancer remains limited due to small patient cohorts. Prior studies have uncovered a number of important genetic alterations associated with Wilms Tumor. However these studies are based on small cohorts. Here, we propose to advance our prior studies with a multi-decade effort to obtain high quality samples from over 200 pediatric institutions through Children’s Oncology Group Renal Tumor studies. With samples from approximately 2,946 patients, we propose to assess the whole genome, methylome and transcriptome of the patient’s germline, normal adjacent kidney and tumor kidney. Given the large sample size, we will be powered for the detection of rare variant alleles and validation of prior studies. Just as importantly, our patient cohort represents the diversity of the United States. The multi-PI team along with senior leadership of the COG Renal Tumor studies have deep expertise in the analyses of epidemiology, genetics, epigenetics and transcriptomics in childhood cancers along with decades experience with the care of children with renal tumors. This proposed study provides a timely opportunity to aid our understanding of cancer risk in children with genitourinary congenital anomalies and more broadly, our understanding of Wilms Tumor, from a diverse population. These data will provide a critical resource for cancer germline risk, congenital anomalies, developmental biology and cancer biology. PUBLIC HEALTH RELEVANCE: Wilms Tumor is the most common kidney cancer in children. Although some predisposition syndromes have been associated with Wilms Tumor (e.g., Beckwith Wiedemann Syndrome, Denys Drash Syndrome, Hemihypertrophy, WAGR Syndrome), recent studies suggest many more children with Wilms Tumor may have an underlying predisposition syndrome. This study will explore how these germline changes relate to the developing kidney or structural birth defects in addition to the development of kidney cancer which may lead to prevention strategies or enhance risk stratification and therapeutic target identification. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Soheil Meshinchi | HD114141 | Fred Hutchinson Cancer Research Center | Long-Read Sequencing of childhood AML, DS-AML, and TAM | 820 |
| Abstract: Advances in sequencing have allowed identification of somatic variants, gene fusions, and copy number variants as potential therapeutic targets. Although myeloid disorders in children may show morphologic similarities to that seen in adults, TARGET AML initiative (Meshinchi, PI) clearly demonstrated that somatic genomic and transcriptome variants are highly distinct in children and young adults. In fact, there are a number of variants that are uniquely restricted to younger children, some with high therapeutic potential. In addition to identification of somatic variants, analysis of the germline data provided a glimpse into the constitutional make-up of patients with AML. The identification of numerous “function altering” variants may provide an insight into possible interactions between the host and the disease, where these germline variants might alter AML risk (predisposition), response to therapy (altering target expression, drug metabolism), susceptibilities to short and long-term complications (including infectious and cardiac complications), or modify risk of secondary malignancies. Armed with data from initial sequencing efforts in AML (including prior GMKF awards), we are poised to take full advantage of the available sequencing technologies to conduct the most comprehensive genome and transcriptome interrogation of myeloid disorders in children with specimens we have amassed over the last decade. To this end, we have put in place unparalleled specimen resources from children with de novo AML treated on prior Children’s Oncology Group trials, (AAML1031), to create the most comprehensive genome, transcriptome and epigenome profiling in AML. Our original X01 applications providing funding support for whole genome sequencing patients treated on AAML1031. Given that transcriptome (mRNA, miRNA, LncRNA), whole genome, and methylation data are available for the entire AAML1031 cohort, the addition of long-read sequencing would provide the most comprehensive profiling effort in this single trial cohort. Additionally, through an INCLUDE project award and private foundation funding, we have completed sequencing of whole genome, transcriptome, and epigenomic analysis of two COG trials (AAML1531 and AAML08B1) that investigate individuals with Down Syndrome who develop AML (DS-AML), as well as infants with Down Syndrome that have transient abnormal myelopoiesis (TAM) which often transitions to myeloid disease. Recent advances in long read sequencing provide an opportunity to identify structural alterations that are not amenable to detection by other methods. We propose to interrogate the genomes and transcriptomes of a cohort of affected children from AAML1031, AAML1531, and AAML08B1 from a variety of pediatric AML subtypes to discover cancer predisposition variants or structural alterations not detected by short-read sequencing. In addition, long read RNA-seq could provide detailed knowledge of the splice isoform variants that may be linked to AML pathogenesis, both as a route to better diagnostics and also for discovery of new therapeutic targets. PUBLIC HEALTH RELEVANCE: Clinical outcome in children with AML, DS-AML and TAM have remained poor in part due to lack of deep understanding of the genomic makeup of the disease as well as the host. Comprehensive studies of the host and disease may enable more informed therapies in order to optimize targeting the leukemia while minimizing short and long term toxicities, leading to improved survival with minimal morbidities. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Simone Sanna-Cherchi | HD114139 | Columbia University Health Sciences | Large-scale Sequencing Studies in Congenital Anomalies of the Kidney and Urinary Tract (X01 HD114139-01) | 1260 |
| Abstract: Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) account for up to 50% of pediatric and 7% of adult end-stage kidney failure worldwide. The goal of this project is to apply genetic approaches to resolve the biological basis and clinical manifestations of CAKUT using three well-characterized cohorts with deep phenotypes and extensive longitudinal data. Here, we hypothesize that CAKUT is genetically heterogeneous, and caused by rare mutations with large effect on a background of polygenes with small effects that can be discovered by analysis of well phenotyped cohorts compared to genetically matched cohorts with WGS data available. We now propose to extend our prior studies by whole genome sequencing (WGS) in additional 500 trios with CAKUT as well as WES in 5,600 additional CAKUT singleton to achieve a total cohort of 1,160 WGS trios and 9,000 WES singletons. We expect that the proposed studies will provide new insight into urogenital development, clarify the clinical overlap with other syndromes and provide novel tools that can replace the current morphology-based diagnostic approaches. We will first perform annotation based on a standard ACMG guidelines to identify pathogenic variants diagnostic for known genetic disorders. In aim 2, we will perform comprehensive trios analysis of de novo mutations in coding and non-coding regions comparing data to the Simons Simplex Collection. In aim 3 we will combine all data in the largest sequencing effort to date by analysing WGS/WES in 10,160 independent CAKUT cases in order to provide a comprehensive catalogue of known and novel genetic variants for follow up clinical and functional studies. PUBLIC HEALTH RELEVANCE: Congenital defects of the kidney and urinary tract are a common cause of kidney failure in children and adults and elucidation of the genetics of these disorders will provide new opportunities for diagnosis, risk stratification and prevention of complications. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| John R Shaffer | HD114124 | University Of Pittsburgh at Pittsburgh | Epigenomics of Orofacial Clefts | 1465 |
| Abstract: Orofacial cleft (OFC) birth defects are one of the most common structural birth defects in humans, and the most common craniofacial anomalies, with worldwide incidence of approximately 1 per 700 newborns. OFCs represent a major public health problem due to the associated morbidity, mortality, and significant medical care expenditures. Based on structures affected, OFCs have been categorized as three subtypes: clefts affecting the lip only (cleft lip, CL), clefts affecting both the lip and the palate (cleft lip and palate, CLP), and clefts affecting the palate only (cleft palate, CP). Historically, CL and CLP have been considered variations of the same malformation that differ in severity, whereas the developmental origins of the affected structures, epidemiology, and familial patterns suggest that CP has a separate etiology than CL and CLP. Both genetic and environmental factors play important roles in the development of OFCs, although understanding of these risk factors is incomplete. The proposed project aims to expand the Gabriella Miller Kids First (GMKF) resource by collecting data to investigate the role of DNA methylation – an epigenomic marker of gene activity – on the development of clefts. We propose to collect genome-wide DNA methylation assays in a large cohort of affected children as well as DNA methylation and transcriptomics assays in a subset of children with available discarded surgical tissue. Ultimately, these data will contribute new and complementary types of omics data to the GMKF resource for participants with already-available whole-genome sequencing data. This resource will allow us and others to perform analyses to identify the differentially methylated regions of the genome associated with OFCs and subtypes, and explore the functional roles of previously identified OFC-associated genetic loci. Successful completion of this project will expand and deepen our understanding of the genetic architecture and regulatory landscape of OFCs including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. PUBLIC HEALTH RELEVANCE: This project will expand the Gabriella Miller Kids First resource and deepen our understanding of the genetic architecture and regulatory landscape of non-syndromic orofacial clefts including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. This knowledge may ultimately be useful for applications such as recurrence prediction or personalized therapeutic interventions. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Eric Chien-Wei Liao | HD114131 | Children's Hospital of Philadelphia | Genomic, somatic, transcriptional and epigenetic profiling of non-syndromic and syndromic craniosynostosis | 576 |
| Abstract: Syndromic and non-syndromic craniosynostosis (CS) are complex malformations of the cranial vault that result from premature or anomalous fusion of cranial sutures. The mainstay of treatment remains complex surgical operations with significant morbidity and risks to a newborn. Meanwhile, advances in fundamental understanding of craniosynostosis genetics stand in stark contrast to the persistent gap in translation to clinical impact. This proposal tests the central hypothesis that by integrating genomic, biological and clinical data and approaches, we can correlate genetic diagnosis to clinical course and treatment outcomes. In order to realize this genomic translation strategy, we carried out a multi-year effort to clinically phenotype, catalog, and collect trios and affected tissue in every consenting patient that presents to our center. As a leading craniofacial clinical program, we were able to collect over 438 cases of syndromic and non-syndromic CS over 5 years. This biorepository is unique compared to previously sequenced craniosynostosis cohorts, as these cases include specimen of the pathologic tissue from the anomalous fused craniosynostotic suture and normal bone as control. In Aim 1, we propose to comprehensively analyze germline, somatic, transcriptional and epigenetic contribution to syndromic and non-syndromic CS by: 1A) Whole genome sequencing of syndromic and non-syndromic craniosynostosis from trio blood and saliva, 1B) Somatic and transcriptional profiling of non-syndromic and syndromic craniosynostosis across subtypes, and 1C) Epigenetic analysis of pathologic craniosynostotic bone and normal bone. In Aim 2, we will characterize the longitudinal natural history of disease and clinical functional outcomes in syndromic and non-syndromic CS. This will be achieved by: 2A) integrating WGS, EMR and phenotype data to map genetic diagnosis to clinical course of disease, and 2B) integrating WGS, EMR and post-operative data to map genetic diagnosis to treatment outcomes. Successful completion of this project will yield genomic, epigenetic and transcriptional data that are integrated with clinical presentation, longitudinal natural history of disease, treatment and other functional outcomes. This resource will enable downstream genomic, developmental and clinical studies to address translation gaps in craniofacial biology and treatment, with the goal of delivering clinically actionable data to advance diagnosis and treatment of syndromic and non-syndromic craniosynostosis. PUBLIC HEALTH RELEVANCE: Syndromic and non-syndromic craniosynostosis occur when the cranial sutures are aberrantly fused at birth, leading to constrained cerebral growth, irreversible brain damage, blindness and significant craniofacial deformity if left untreated. This study proposes to carry out germline, somatic, transcriptomic and epigenetic sequencing, and to integrate this multi-omic data to clinical natural history of disease and functional treatment outcomes. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| David Teachey Charles G. Mullighan | HD114203 | Children's Hosp Of Philadelphia | Somatic and Germline Variants in Childhood T-cell acute lymphoblastic leukemia | 1185 |
| Abstract: The outcome for children with relapsed T-cell acute lymphoblastic leukemia (T-ALL) is dismal. Thus, the primary goal in treatment is to prevent relapse, which requires accurate risk stratification. Prior attempts to identify genetic aberrations that are prognostic independent of treatment response have failed. We recently performed comprehensive genomic profiling (whole genome sequencing (WGS), whole exome sequencing (WES), and whole transcriptome profiling (WTS) of tumor; WGS of germline) from >1300 patients with T-ALL treated on the AALL0434 clinical trial through a Gabriella Miller Kids First X01 award (X01HD100702) and made several novel, practice changing observations. We found T-ALL can be classified into 15 distinct groups, many of which are novel. We found that leukemic drivers were in non-coding regions in 60% of cases, highlighting the importance of WGS. We identified multiple subtypes that were predictive of favorable and unfavorable outcome. The successor trial to AALL0434 was AALL1231. On AALL1231, several changes were made to the backbone to eliminate cranial radiation in most patients and these changes had prognostic implications. Before we can prospectively incorporate genetic aberrations into risk stratification, we need to validate our results in an independent cohort treated with current therapy and identify genomic variants that are reproducibly prognostic irrespective of therapeutic backbone. In addition, we found the prognostic impact of some variants differed based on genetic ancestry; some genetic variants that were associated with higher cure rates in children of European ancestry were not associated with higher cure rates in children of African ancestry. We need to increase the number of patients studied from different racial and ethnic groups to ensure equity in future risk stratification. Finally, we were unable to identify the genomic driver in a small percentage of cases (5%) and long-read sequencing may be able to overcome this gap. We hypothesize that comprehensive genomic profiling will identify recurrent genetic alterations that can be used prospectively to risk classify patients with T-ALL. Genomic profiling of a large cohort of patients treated on the AALL1231 trial will serve as a natural extension of our initial X01 award, providing the power to assess the impact of genomic variants on outcome across genetic ancestral groups. We will test our hypothesis with the following specific aims: (1) validate prognostic variants in an independent cohort of patients with T-ALL; (2) identify novel genomic structural variants using long-read sequencing; and (3) determine the association between genetic ancestry, tumor biology and outcomes. The goal of the Kids First Program is to improve understanding of genetic mechanisms of disease, leading to improved diagnostic capabilities and ultimately more targeted therapies. Genomic profiling across two of the largest clinical trials ever performed in children with T-ALL will clearly meet these important goals. This work will not only fundamentally transform the understanding of T-ALL disease biology but also allow us to risk stratify patients accurately and equitably understand differences in tumor biology based on genetic ancestry. PUBLIC HEALTH RELEVANCE: Modern genetic tests have helped find better ways to identify children with T-cell acute lymphoblastic leukemia (T-ALL) who are less likely to be cured. Before we can use these tests in the clinic, we need to show they are helpful regardless of therapy used to treat the leukemia | ||||
*Sequencing of this project is supported by the NIH Childhood Cancer Data initiative and and the data will be shared through the NCI Cancer Data Service
2023 X01 Projects
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Joseph G Gleeson | HD114132 | University of California, San Diego | Whole Genome Sequencing in Structural Defects of the Neural Tube | 1200 |
| Abstract: Myelomeningocele (aka meningomyelocele, MM) is the most severe form of spina bifida, a neural tube defect (NTD) in humans and the most common CNS birth defect. MM is considered a genetically complex disease, and occurs in 3.72/10,000 live US birth, and is partly preventable with prenatal folate, but the genetic basis and the mechanisms by which folate work to reduce disease incidence remain obscure. MM is associated nearly uniformly with prenatal hydrocephalus and the Arnold-Chiari malformation, as well as paraplegia and lifelong neuromotor disability. The genes for several rare syndromic forms of NTDs are known, but the causes for the majority with sporadic MM remain unknown. Despite the importance of MM, most previous research has been limited to targeted sequencing and association studies of folate metabolism genes, or very small-scale exome sequencing. We hypothesize that de novo mutations (DNMs) produce likely gene disrupting (LGD) events that contribution to MM risk. Using conservative estimates of between 50-100 recurrently mutated discoverable genes contributing to risk, and our preliminary data demonstrating an excess of LGD DNMs in MM compared with control individuals, we estimate that with a cohort size of 1000 trios, we should uncover between 5-20 new recurrently mutated genes underlying MM, with minimal false-discovery. With this in mind, we formed the Spina Bifida Sequencing Consortium, and established a platform for data and sample sharing. Preliminary analysis of our first batch of 100 trios analyzed by WGS from GMKF suggests a wealth of important gene mutations. We have embarked on a new recruitment effort of an additional cohort of 400 new simplex MM trios, in collaboration with the US Spina Bifida Association, consented trios to allow for data sharing, and have performed detailed sample quality control. We also have preliminary data that use of dried bloodspot DNA from trios performs comparably to whole blood DNA, so will be happy to swap saliva for bloodspot recruitment at NIH’s preference. This cohort is now half-way assembled, with the remaining cohort to be ascertained in the next 6 months. We have established a workflow for de novo SNP/INDEL/SV detection from WGS and have ample computer storage and nodes to see the project to completion. We also plan to continue recruitment into the future with the goal of 2000 trios in the next 5 years. We propose a detailed bioinformatics workflow to identify gene mutations within a statistical framework, considering detailed scRNA expression profiling from developing mammalian neural tube, and have developed a robust functional validation workflow using Xenopus and mouse gene targeting. Our project has the potential to uncover a host of causes for this most common of the CNS birth defects, paving the way for future breakthroughs in detection, treatment, and prevention. PUBLIC HEALTH RELEVANCE: This work will identify new genetic disease genes predisposing to myelomeningocele, the most common pediatric structural brain disease. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Andrew L Hong | HD114129 | Emory University | Basis of Childhood Kidney Cancers and Birth Defects | 1353 |
| Abstract: Wilms Tumor is the most common renal tumor of childhood. Although cure rates approach 90% after initial therapy that includes a combination of surgery, chemotherapy and radiation therapy, our understanding of the biology of how children develop this cancer remains limited due to small patient cohorts. Prior studies have uncovered a number of important genetic alterations associated with Wilms Tumor. However these studies are based on small cohorts. Here, we propose to advance our prior studies with a multi-decade effort to obtain high quality samples from over 200 pediatric institutions through Children’s Oncology Group Renal Tumor studies. With samples from approximately 2,946 patients, we propose to assess the whole genome, methylome and transcriptome of the patient’s germline, normal adjacent kidney and tumor kidney. Given the large sample size, we will be powered for the detection of rare variant alleles and validation of prior studies. Just as importantly, our patient cohort represents the diversity of the United States. The multi-PI team along with senior leadership of the COG Renal Tumor studies have deep expertise in the analyses of epidemiology, genetics, epigenetics and transcriptomics in childhood cancers along with decades experience with the care of children with renal tumors. This proposed study provides a timely opportunity to aid our understanding of cancer risk in children with genitourinary congenital anomalies and more broadly, our understanding of Wilms Tumor, from a diverse population. These data will provide a critical resource for cancer germline risk, congenital anomalies, developmental biology and cancer biology. PUBLIC HEALTH RELEVANCE: Wilms Tumor is the most common kidney cancer in children. Although some predisposition syndromes have been associated with Wilms Tumor (e.g., Beckwith Wiedemann Syndrome, Denys Drash Syndrome, Hemihypertrophy, WAGR Syndrome), recent studies suggest many more children with Wilms Tumor may have an underlying predisposition syndrome. This study will explore how these germline changes relate to the developing kidney or structural birth defects in addition to the development of kidney cancer which may lead to prevention strategies or enhance risk stratification and therapeutic target identification. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Soheil Meshinchi | HD114141 | Fred Hutchinson Cancer Research Center | Long-Read Sequencing of childhood AML, DS-AML, and TAM | 820 |
| Abstract: Advances in sequencing have allowed identification of somatic variants, gene fusions, and copy number variants as potential therapeutic targets. Although myeloid disorders in children may show morphologic similarities to that seen in adults, TARGET AML initiative (Meshinchi, PI) clearly demonstrated that somatic genomic and transcriptome variants are highly distinct in children and young adults. In fact, there are a number of variants that are uniquely restricted to younger children, some with high therapeutic potential. In addition to identification of somatic variants, analysis of the germline data provided a glimpse into the constitutional make-up of patients with AML. The identification of numerous “function altering” variants may provide an insight into possible interactions between the host and the disease, where these germline variants might alter AML risk (predisposition), response to therapy (altering target expression, drug metabolism), susceptibilities to short and long-term complications (including infectious and cardiac complications), or modify risk of secondary malignancies. Armed with data from initial sequencing efforts in AML (including prior GMKF awards), we are poised to take full advantage of the available sequencing technologies to conduct the most comprehensive genome and transcriptome interrogation of myeloid disorders in children with specimens we have amassed over the last decade. To this end, we have put in place unparalleled specimen resources from children with de novo AML treated on prior Children’s Oncology Group trials, (AAML1031), to create the most comprehensive genome, transcriptome and epigenome profiling in AML. Our original X01 applications providing funding support for whole genome sequencing patients treated on AAML1031. Given that transcriptome (mRNA, miRNA, LncRNA), whole genome, and methylation data are available for the entire AAML1031 cohort, the addition of long-read sequencing would provide the most comprehensive profiling effort in this single trial cohort. Additionally, through an INCLUDE project award and private foundation funding, we have completed sequencing of whole genome, transcriptome, and epigenomic analysis of two COG trials (AAML1531 and AAML08B1) that investigate individuals with Down Syndrome who develop AML (DS-AML), as well as infants with Down Syndrome that have transient abnormal myelopoiesis (TAM) which often transitions to myeloid disease. Recent advances in long read sequencing provide an opportunity to identify structural alterations that are not amenable to detection by other methods. We propose to interrogate the genomes and transcriptomes of a cohort of affected children from AAML1031, AAML1531, and AAML08B1 from a variety of pediatric AML subtypes to discover cancer predisposition variants or structural alterations not detected by short-read sequencing. In addition, long read RNA-seq could provide detailed knowledge of the splice isoform variants that may be linked to AML pathogenesis, both as a route to better diagnostics and also for discovery of new therapeutic targets. PUBLIC HEALTH RELEVANCE: Clinical outcome in children with AML, DS-AML and TAM have remained poor in part due to lack of deep understanding of the genomic makeup of the disease as well as the host. Comprehensive studies of the host and disease may enable more informed therapies in order to optimize targeting the leukemia while minimizing short and long term toxicities, leading to improved survival with minimal morbidities. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Simone Sanna-Cherchi | HD114139 | Columbia University Health Sciences | Large-scale Sequencing Studies in Congenital Anomalies of the Kidney and Urinary Tract (X01 HD114139-01) | 1260 |
| Abstract: Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) account for up to 50% of pediatric and 7% of adult end-stage kidney failure worldwide. The goal of this project is to apply genetic approaches to resolve the biological basis and clinical manifestations of CAKUT using three well-characterized cohorts with deep phenotypes and extensive longitudinal data. Here, we hypothesize that CAKUT is genetically heterogeneous, and caused by rare mutations with large effect on a background of polygenes with small effects that can be discovered by analysis of well phenotyped cohorts compared to genetically matched cohorts with WGS data available. We now propose to extend our prior studies by whole genome sequencing (WGS) in additional 500 trios with CAKUT as well as WES in 5,600 additional CAKUT singleton to achieve a total cohort of 1,160 WGS trios and 9,000 WES singletons. We expect that the proposed studies will provide new insight into urogenital development, clarify the clinical overlap with other syndromes and provide novel tools that can replace the current morphology-based diagnostic approaches. We will first perform annotation based on a standard ACMG guidelines to identify pathogenic variants diagnostic for known genetic disorders. In aim 2, we will perform comprehensive trios analysis of de novo mutations in coding and non-coding regions comparing data to the Simons Simplex Collection. In aim 3 we will combine all data in the largest sequencing effort to date by analysing WGS/WES in 10,160 independent CAKUT cases in order to provide a comprehensive catalogue of known and novel genetic variants for follow up clinical and functional studies. PUBLIC HEALTH RELEVANCE: Congenital defects of the kidney and urinary tract are a common cause of kidney failure in children and adults and elucidation of the genetics of these disorders will provide new opportunities for diagnosis, risk stratification and prevention of complications. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| John R Shaffer | HD114124 | University Of Pittsburgh at Pittsburgh | Epigenomics of Orofacial Clefts | 1465 |
| Abstract: Orofacial cleft (OFC) birth defects are one of the most common structural birth defects in humans, and the most common craniofacial anomalies, with worldwide incidence of approximately 1 per 700 newborns. OFCs represent a major public health problem due to the associated morbidity, mortality, and significant medical care expenditures. Based on structures affected, OFCs have been categorized as three subtypes: clefts affecting the lip only (cleft lip, CL), clefts affecting both the lip and the palate (cleft lip and palate, CLP), and clefts affecting the palate only (cleft palate, CP). Historically, CL and CLP have been considered variations of the same malformation that differ in severity, whereas the developmental origins of the affected structures, epidemiology, and familial patterns suggest that CP has a separate etiology than CL and CLP. Both genetic and environmental factors play important roles in the development of OFCs, although understanding of these risk factors is incomplete. The proposed project aims to expand the Gabriella Miller Kids First (GMKF) resource by collecting data to investigate the role of DNA methylation – an epigenomic marker of gene activity – on the development of clefts. We propose to collect genome-wide DNA methylation assays in a large cohort of affected children as well as DNA methylation and transcriptomics assays in a subset of children with available discarded surgical tissue. Ultimately, these data will contribute new and complementary types of omics data to the GMKF resource for participants with already-available whole-genome sequencing data. This resource will allow us and others to perform analyses to identify the differentially methylated regions of the genome associated with OFCs and subtypes, and explore the functional roles of previously identified OFC-associated genetic loci. Successful completion of this project will expand and deepen our understanding of the genetic architecture and regulatory landscape of OFCs including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. PUBLIC HEALTH RELEVANCE: This project will expand the Gabriella Miller Kids First resource and deepen our understanding of the genetic architecture and regulatory landscape of non-syndromic orofacial clefts including identifying new risk loci and determining the mechanisms through which known risk loci influence the development of OFCs. This knowledge may ultimately be useful for applications such as recurrence prediction or personalized therapeutic interventions. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| Eric Chien-Wei Liao | HD114131 | Children's Hospital of Philadelphia | Genomic, somatic, transcriptional and epigenetic profiling of non-syndromic and syndromic craniosynostosis | 576 |
| Abstract: Syndromic and non-syndromic craniosynostosis (CS) are complex malformations of the cranial vault that result from premature or anomalous fusion of cranial sutures. The mainstay of treatment remains complex surgical operations with significant morbidity and risks to a newborn. Meanwhile, advances in fundamental understanding of craniosynostosis genetics stand in stark contrast to the persistent gap in translation to clinical impact. This proposal tests the central hypothesis that by integrating genomic, biological and clinical data and approaches, we can correlate genetic diagnosis to clinical course and treatment outcomes. In order to realize this genomic translation strategy, we carried out a multi-year effort to clinically phenotype, catalog, and collect trios and affected tissue in every consenting patient that presents to our center. As a leading craniofacial clinical program, we were able to collect over 438 cases of syndromic and non-syndromic CS over 5 years. This biorepository is unique compared to previously sequenced craniosynostosis cohorts, as these cases include specimen of the pathologic tissue from the anomalous fused craniosynostotic suture and normal bone as control. In Aim 1, we propose to comprehensively analyze germline, somatic, transcriptional and epigenetic contribution to syndromic and non-syndromic CS by: 1A) Whole genome sequencing of syndromic and non-syndromic craniosynostosis from trio blood and saliva, 1B) Somatic and transcriptional profiling of non-syndromic and syndromic craniosynostosis across subtypes, and 1C) Epigenetic analysis of pathologic craniosynostotic bone and normal bone. In Aim 2, we will characterize the longitudinal natural history of disease and clinical functional outcomes in syndromic and non-syndromic CS. This will be achieved by: 2A) integrating WGS, EMR and phenotype data to map genetic diagnosis to clinical course of disease, and 2B) integrating WGS, EMR and post-operative data to map genetic diagnosis to treatment outcomes. Successful completion of this project will yield genomic, epigenetic and transcriptional data that are integrated with clinical presentation, longitudinal natural history of disease, treatment and other functional outcomes. This resource will enable downstream genomic, developmental and clinical studies to address translation gaps in craniofacial biology and treatment, with the goal of delivering clinically actionable data to advance diagnosis and treatment of syndromic and non-syndromic craniosynostosis. PUBLIC HEALTH RELEVANCE: Syndromic and non-syndromic craniosynostosis occur when the cranial sutures are aberrantly fused at birth, leading to constrained cerebral growth, irreversible brain damage, blindness and significant craniofacial deformity if left untreated. This study proposes to carry out germline, somatic, transcriptomic and epigenetic sequencing, and to integrate this multi-omic data to clinical natural history of disease and functional treatment outcomes. | ||||
| Contact PI/Project Leader | Project Number | Awardee Organization | Title | Anticipated Number of Samples |
|---|---|---|---|---|
| David Teachey Charles G. Mullighan | HD114203 | Children's Hosp Of Philadelphia | Somatic and Germline Variants in Childhood T-cell acute lymphoblastic leukemia | 1185 |
| Abstract: The outcome for children with relapsed T-cell acute lymphoblastic leukemia (T-ALL) is dismal. Thus, the primary goal in treatment is to prevent relapse, which requires accurate risk stratification. Prior attempts to identify genetic aberrations that are prognostic independent of treatment response have failed. We recently performed comprehensive genomic profiling (whole genome sequencing (WGS), whole exome sequencing (WES), and whole transcriptome profiling (WTS) of tumor; WGS of germline) from >1300 patients with T-ALL treated on the AALL0434 clinical trial through a Gabriella Miller Kids First X01 award (X01HD100702) and made several novel, practice changing observations. We found T-ALL can be classified into 15 distinct groups, many of which are novel. We found that leukemic drivers were in non-coding regions in 60% of cases, highlighting the importance of WGS. We identified multiple subtypes that were predictive of favorable and unfavorable outcome. The successor trial to AALL0434 was AALL1231. On AALL1231, several changes were made to the backbone to eliminate cranial radiation in most patients and these changes had prognostic implications. Before we can prospectively incorporate genetic aberrations into risk stratification, we need to validate our results in an independent cohort treated with current therapy and identify genomic variants that are reproducibly prognostic irrespective of therapeutic backbone. In addition, we found the prognostic impact of some variants differed based on genetic ancestry; some genetic variants that were associated with higher cure rates in children of European ancestry were not associated with higher cure rates in children of African ancestry. We need to increase the number of patients studied from different racial and ethnic groups to ensure equity in future risk stratification. Finally, we were unable to identify the genomic driver in a small percentage of cases (5%) and long-read sequencing may be able to overcome this gap. We hypothesize that comprehensive genomic profiling will identify recurrent genetic alterations that can be used prospectively to risk classify patients with T-ALL. Genomic profiling of a large cohort of patients treated on the AALL1231 trial will serve as a natural extension of our initial X01 award, providing the power to assess the impact of genomic variants on outcome across genetic ancestral groups. We will test our hypothesis with the following specific aims: (1) validate prognostic variants in an independent cohort of patients with T-ALL; (2) identify novel genomic structural variants using long-read sequencing; and (3) determine the association between genetic ancestry, tumor biology and outcomes. The goal of the Kids First Program is to improve understanding of genetic mechanisms of disease, leading to improved diagnostic capabilities and ultimately more targeted therapies. Genomic profiling across two of the largest clinical trials ever performed in children with T-ALL will clearly meet these important goals. This work will not only fundamentally transform the understanding of T-ALL disease biology but also allow us to risk stratify patients accurately and equitably understand differences in tumor biology based on genetic ancestry. PUBLIC HEALTH RELEVANCE: Modern genetic tests have helped find better ways to identify children with T-cell acute lymphoblastic leukemia (T-ALL) who are less likely to be cured. Before we can use these tests in the clinic, we need to show they are helpful regardless of therapy used to treat the leukemia | ||||
*Sequencing of this project is supported by the NIH Childhood Cancer Data initiative and and the data will be shared through the NCI Cancer Data Service
2022 X01 Projects
| Project Number: | HD110884-01 | Contact PI / Project Leader: | Chakravarti, Aravinda |
| Title: | The genomic architecture of Hirschsprung Disease | Awardee Organization: | University Of Texas Health Science Center |
| Abstract: DESCRIPTION (provided by applicant): Hirschsprung disease (HSCR) is a male-biased developmental disorder associated with a lack of innervation of the gastrointestinal tract. Genetic studies have been instrumental in understanding its multifactorial inheritance, high heritability, syndromic associations, and genetic heterogeneity with variable penetrance and expressivity. 24 known genes and 9 loci with pathogenic alleles (PAs) underlie HSCR pathogenesis and explain 62% of its population attributable risk (PAR). Despite this heterogeneity, there is functional unity in HSCR: ~53% of HSCR PAs disrupt RET and EDNRB signaling in the developing enteric nervous system (ENS) with 11 HSCR genes comprising a gene regulatory network controlling RET and EDNRB gene expression. We propose to identify the remaining 30% PAR by studying 857 unrelated HSCR cases, their 125 affected and 1,446 unaffected first-degree relatives by whole genome sequencing to increase statistical power of gene discovery through improved detection of all types of coding and regulatory PAs. HSCR arises from cell autonomous defects in enteric neural crest cell precursors (ENCCs) affecting their proliferation, differentiation and migration in the ENS, functional studies that will guide our detection of novel genes. PUBLIC HEALTH RELEVANCE: Pathogenic allele (PA) diversity in HSCR is extensive and includes diverse molecular types of de novo mutations (DNMs) and segregating variants explaining 63% of its population attributable risk (PAR). We propose to identify the remaining 30% PAR by studying 857 unrelated HSCR cases, their 125 affected and 1,446 unaffected first-degree relatives by whole genome sequencing (WGS) by increasing statistical power of gene discovery through improved detection of SNVs, INDELs/CNVs and DNMs and coding and regulatory PAs. | |||
| Project Number: | HD110887-01 | Contact PI / Project Leader: | Chung, Wendy |
| Title: | Genomic Analysis of Esophageal Atresia and Tracheoesophageal Fistulas and Associated Congenital Anomalies | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Project Summary/Abstract Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. There is a 45% incidence of associated congenital malformations, most commonly digestive, cardiovascular, urogenital, and musculoskeletal, often part of a syndrome or complex association, with VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities) being most frequently recognized. Advanced surgical techniques and pre and post-operative care have improved the prognosis and survival of EA/TEF patients over the past decades. However, with improved survival, many of the long-term morbidities of EA/TEF have been exposed. It is likely that the outcome in EA/TEF patients is influenced by multiple genetic and clinical factors; however, determining which factors are critical has been limited by the lack of data, particularly genomic data. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of EA/TEF and define new genes and conditions associated with EA/TEF by performing whole genome sequencing on 100 parent child trios in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions and improve outcomes. PUBLIC HEALTH RELEVANCE: Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. We propose to elucidate the underlying genomic architecture of EA/TEF by performing whole genome sequencing to characterize new clinical syndromes associated with EA/TEF to provide more accurate clinical prognostic information. | |||
| Project Number: | HD110902-01 | Contact PI / Project Leader: | Espinosa, Joaquin M. |
| Title: | Epigenome analysis in the Human Trisome Project | Awardee Organization: | University of Colorado Denver |
| Abstract: DESCRIPTION (provided by applicant): Despite decades of research, the mechanisms by which trisomy 21 (T21) causes the myriad developmental and clinical hallmarks of Down syndrome (DS) are poorly understood, creating an obvious challenge in the clinical management of DS. T21 causes a different disease spectrum among those with DS, protecting these individuals from developing certain conditions, such as most solid malignancies, while strongly predisposing them to others, such as congenital heart disease, leukemias, and autoimmune disorders. Therefore, elucidating the mechanisms by which T21 causes this novel disease spectrum will greatly serve both people with DS and the general population affected by the numerous conditions modulated by T21. To accelerate research in this area, our team launched a pan-omics cohort study of people with DS known as the Crnic Institute Human Trisome Project (HTP). Supported by previous X01 awards, the HTP has become one of the deepest studies of people with DS to date, having completed matched analysis of the genome, transcriptome, proteome, metabolome, immune maps, and microbiome, along with deep clinical data annotation for hundreds of research participants. These efforts produced several discoveries about the impact of immune dysregulation in DS, leading to a novel clinical trial funded by the INCLUDE Project to test the safety and efficacy of a JAK inhibitor to improve health outcomes in DS. Now, we propose to complete a comprehensive analysis of epigenetic variation in DS with a focus on the immune system through the following Specific Aims: Aim 1. To complete a cross-sectional analysis of epigenetic variation in Down syndrome. We propose to complete DNA methylation analysis via bisulfite sequencing for 400+ participants with T21 versus 200+ age- and sex-matched euploid controls, most of whom have matched transcriptome and immune mapping data. Aim 2. To complete a longitudinal analysis of cell type-specific epigenetic variation in Down syndrome. We propose to complete an analysis of the epigenome of monocytes, a key immune cell type with major roles in inflammation in DS, via matched analysis of DNA methylation, chromatin accessibility (ATAC-seq), and transcriptome in a three-year longitudinal sample set. Aim 3. To complete a comprehensive analysis of the T and B cell receptor repertoires in Down syndrome. A key source of epigenetic variation highly relevant to the study of DS resides in the repertoire of rearranged genomic sequences encoding the T and B cell receptors (TCRs, BCRs). We propose to complete targeted long read sequencing to elucidate the TCR and BCR repertoires in 400+ participants with T21 versus 200+ controls. Altogether, this proposal is likely to generate the most comprehensive analysis of epigenetic variation in individuals with T21 to date, with a strong focus on the immune system, a key player in the etiology of many co- occurring conditions of DS. | |||
| Project Number: | HD110998-01 | Contact PI / Project Leader: | Gleeson, Joseph G |
| Title: | Whole Genome Sequencing in Structural Defects of the Neural Tube | Awardee Organization: | University of California, San Diego |
| Abstract: DESCRIPTION (provided by applicant): Myelomeningocele (aka meningomyelocele, MM) is the most severe form of spina bifida, a neural tube defect (NTD) in humans and the most common CNS birth defect. This defect occurs in 3.72/10,000 live US birth, and is partly preventable with prenatal folate, but the genetic basis and the mechanisms by which folate work to reduce disease incidence remain obscure. MM is associated nearly uniformly with prenatal hydrocephalus and the Arnold-Chiari malformation, as well as paraplegia and lifelong disability. The genes for several syndromic forms of NTDs are known, but the causes for the majority with sporadic clinical presentation remain unknown. Despite the importance of MM, previous research has been limited to targeted sequencing and association studies of folate metabolism genes, or very small-scale exome sequencing. We hypothesize that de novo mutations (DNMs) that produce likely gene disrupting (LGD) contribution to MM risk. Using conservative estimates of between 50-100 recurrently mutated discoverable genes, and given our preliminary data demonstrating an excess of LGD DNMs in MM compared with control individuals, we estimate that with a cohort size of 1000 trios, we should uncover between 5-20 new recurrently mutated genes underlying MM, with minimal false-discovery. With this in mind, we formed the Spina Bifida Sequencing Consortium, and established a platform for data and sample sharing. We recently completed submission of 333 trios for WGS at GMKF and are awaiting return of data. We have also more recently embarked on a new recruitment effort of an additional cohort of 400 new simplex MM trios, in collaboration with the US Spina Bifida Association, consented trios to allow for data sharing, and have performed detailed quality control on samples. To achieve recruitment success at this scale, we have had to emphasize saliva rather than blood sampling. This cohort in now half-way assembled and ready for sequencing, and the remaining cohort will be ascertained in the next 6 months. Here we propose to perform WGS the new 400 trios from saliva-derived DNA for this X01 effort to continue this discovery. We have established a workflow for de novo SNP/INDEL/SV detection from WGS and have ample computer storage and nodes to see the project to completion. We also plan to continue recruitment into the future with the goal of 2000 trios in the next 2 years. We propose a detailed bioinformatics workflow to identify gene mutations within a statistical framework, taking into account detailed RNA expression profiling from developing mouse neural tube, and have developed a robust functional validation workflow using Xenopus and mouse gene targeting. Our project has the potential to uncover a host of causes for this most common of the CNS birth defects, paving the way for future breakthroughs in detection, treatment and prevention. PUBLIC HEALTH RELEVANCE: This work will identify new genetic disease genes predisposing to myelomeningocele, the most common pediatric structural brain disease. | |||
| Project Number: | HD110886-01 | Contact PI / Project Leader: | Helbig, Ingo |
| Title: | The Genetic Basis of Structural Pediatric Epilepsies | Awardee Organization: | Children's Hospital Of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Childhood epilepsies are the most common neurological causes for hospital admissions in children. Gene identification has soared in the epilepsies over the last decade, and these discoveries have already led to novel therapies. In contrast, individuals with structural developmental brain anomalies who often benefit from epilepsy surgery are typically excluded from genetic testing. However, recent findings clearly suggest a strong genetic component. Accordingly, there is an essential need for a detailed understanding of the contributing genomic factors, which will be critical to improve patient care. We have recruited >700 patient-parent trios, 1,200 singleton, and 200 tissue samples derived from resective brain surgery. Our goal is to improve patient care by characterizing the genomic and transcriptional landscape of pediatric epilepsies. We hypothesize that known or presumed structural genetic epilepsies have a high frequency of disease-causing variants that can be identified through whole-genome sequencing and RNA sequencing and the analysis of longitudinal outcomes data through an established Electronic Medical Record (EMR) pipeline within the Kids First framework. Our study has two aims. First, we will analyze germline, somatic, and transcriptional contribution to structural pediatric epilepsies. We propose comprehensive profiling of 3,500 samples through Whole Genome Sequencing and 200 brain tissue samples derived from resective epilepsy surgery through parallel Whole Genome Sequencing and RNA Sequencing. We expect that this analysis will identify recurrent germline and somatic disease-causing variants, using the gene discovery expertise of our team to interpret identified genetic variants. Second, we aim to characterize the EMR-based longitudinal disease history of structural pediatric epilepsies. Our team has built frameworks and concepts for the use of longitudinal, de-identified EMR data. We will extract, de-identify, and map EMR data using the Human Phenotype Ontology (HPO) that we have been involved with for the last decade. We expect that implementing clinical data harmonization and analysis of complex phenotypic information will allow us to characterize the natural history and treatment response in known or presumed structural pediatric epilepsies which have not received attention in the past. In summary, our proposed project will have the possibility of systematically providing evidence for causative factors and impact on patient outcomes in known or presumed structural pediatric epilepsies, taking advantage of one of the largest pediatric epilepsy biobanks in conjunction with our expertise in cloud-based bioinformatic analysis and HPO-based data harmonization. The suggested datasets deposited within the Kids First Data Resource will help put structural epilepsies on similar footing to pediatric brain tumors and structural birth defects, enabling us to understand underlying disease mechanisms and allowing us to provide more targeted and improved treatments. PUBLIC HEALTH RELEVANCE: The proposed research is relevant to public health as more precise measurement of clinical and outcome data in structural childhood epilepsies is ultimately expected to translate into improved diagnostics and treatment of one of the most common structural disorders of the brain, allowing for greater personalized treatment choices. This project will address the significant unmet needs of children with structural epilepsies through the generation and integrative analysis of genomic data, including trio-based cohorts of longitudinally followed patients with deep clinical and phenotypic characterization. | |||
| Project Number: | DE032472-01 | Contact PI / Project Leader: | Marazita, Mary |
| Title: | Kids First: Genomics of Isolated Cleft Lip | Awardee Organization: | University of Pittsburgh |
| Abstract: DESCRIPTION (provided by applicant): Isolated Cleft Lip (CL) is one of three subtypes of nonsyndromic orofacial clefts (OFCs), a heterogeneous group of anomalies that also include cleft lip with cleft palate (CLP) and cleft palate alone (CP). Cumulatively, OFCs occur in about 1/700 live births worldwide, and thus comprise a significant proportion of human structural birth defects. Isolated CL (i.e. CL without CP) occurs in about 1 in every 2,800 babies in the U.S (1). Individuals with CL face feeding difficulties, speech, and dental problems and undergo multiple corrective surgeries and ongoing therapy that comes at a substantial personal and financial burden. Further, patients can experience lifelong psychosocial effects, increased mortality rates, and a higher risk of various cancer types. Because CL and CLP share a defect of the upper lip, these two OFC subtypes have historically been combined in genetic studies. However, most studies are dominated by CLP, the most common of all OFCs, and any contribution from the smaller CL sample alone is often undetectable. In recent years, increasing sample sizes afforded the ability to analyze CL and CLP as separate entities. There is now evidence that the subtypes of OFC have distinct differences in their genetic risk patterns. Isolated CL has not yet been investigated in detail as a separate sub-phenotype, with only a few GWAS reports and no reported whole genome sequencing (WGS) studies to date. Therefore, critical gaps in our understanding of CL persist. The major goal of this proposal is to investigate the genome in isolated CL trios to begin to fill this knowledge gap. To do so, we request WGS for 762 CL trios from our large collaborative resources. There is already WGS for a total of 2,078 OFC proband trios from multiple ethnicities (many from our research collaborations and funded mostly through the Gabriella Miller Kids First Consortium—GMKF). Of those trios, 272 have isolated CL; combined with the new trios we will have a total of 1,034 CL trios, a powerful sample size for CL risk variant discovery and equivalent to the discovery resources for CLP and CP. This larger resource of CL trios will fill a critical gap in data and resources necessary to deeply understand the genetic architectures of each OFC subtype. To accomplish the overall goal we will (i) identify risk variants for isolated CL by WGS of CL trios; (ii) compare and contrast the genetic architectures of CL to CLP and CP; and (iii) replicate variants/genes identified through (i) and (ii). PUBLIC HEALTH RELEVANCE: The goal of this project is to better understand the genetic architecture of isolated cleft lip (CL) birth defects by performing whole genome sequencing in multi-ethnic CL families. | |||
| Project Number: | HD110862-01 | Contact PI / Project Leader: | Rios, Jonathan |
| Title: | GMKF Project on Congenital Clubfoot | Awardee Organization: | University of Texas Southwestern Medical Center |
| Abstract: DESCRIPTION (provided by applicant): Talipes equinovarus (clubfoot) is a common congenital structural birth defect. Clubfoot occurs in ~1 in 1,000 live births in the United States, though the incidence varies in other worldwide populations. Clubfoot affects the structural components of the foot (tarsals), muscular and connective tissues including the Achilles and tibial tendons, and ligaments of the ankle. Males are affected twice as frequently as females, and at least half of patients present with bilateral disease. Surgical correction in infants requires tendoachilles lengthening, where the Achilles tendon is severed and the foot is casted to allow healing with the foot in a proper position. Although short-term success following clubfoot treatment is positive, long-term outcomes following surgical clubfoot correction are poor; complications include arthritis, reduced range of motion, weakness, pain and persistent deformity. Importantly, the number of surgical procedures required to produce a corrected clubfoot was significantly associated with poorer long-term outcomes. The pathogenesis of clubfoot remains largely unknown, though ~12% of patients report a family history. Targeted gene sequencing studies have failed to identify genetic loci associated with clubfoot. We recently reported FSTL5 as the first GWAS-associated locus associated with clubfoot, and we showed this gene was associated with sexually-dimorphic phenotypes in mice. Together with the Gabriella Miller Kids First Initiative (GMKF), we are poised to continue advancing the field’s understanding of the genetic causes of clubfoot. The GMKF provides comprehensive genome sequencing (GS) in individuals and families with congenital birth defects. However, no study of congenital limb malformations has yet been conducted as part of the GMKF; thus, our study will be the first GMKF study to investigate genetic causes of congenital limb defects. For the past several decades, we have collected DNA samples from families with multiple relatives affected with clubfoot. Similar to our previously-awarded GMKF studies (1X01HL132375 led by Dr. Rios and DE031445 co-led by Dr. Hecht), we will utilize the power of family-based inheritance mapping to discovery genetic causes of clubfoot. Using the comprehensive GS provided by the GMKF, we will discover sequence variants and copy number variants co-segregating with clubfoot in these families. We present a systematic approach to discover these clubfoot-causing variants, including an integrated approach to investigate variants impacting potential non-coding regulatory elements, which have previously been implicated in other limb malformations. At the completion of this study, we will provide the field with the most comprehensive genomic analysis of families with clubfoot, which will provide novel hypotheses regarding the genetic etiology of this complex congenital birth defect. PUBLIC HEALTH RELEVANCE: Clubfoot is a common birth defect affecting ~1 per 1,000 births, where infants and children are treated with various surgical and nonsurgical methods to correct the foot deformity. Our goal is to better understand the genetic factors contributing to clubfoot through family-based and population-based genetic studies, and our research team recently reported the first GWAS-associated clubfoot locus. Here, we propose to use genome sequencing and robust analytical approaches to systematically evaluate the causes of clubfoot in large multi- generational families. | |||
2022 X01 Projects
| Project Number: | HD110884-01 | Contact PI / Project Leader: | Chakravarti, Aravinda |
| Title: | The genomic architecture of Hirschsprung Disease | Awardee Organization: | University Of Texas Health Science Center |
| Abstract: DESCRIPTION (provided by applicant): Hirschsprung disease (HSCR) is a male-biased developmental disorder associated with a lack of innervation of the gastrointestinal tract. Genetic studies have been instrumental in understanding its multifactorial inheritance, high heritability, syndromic associations, and genetic heterogeneity with variable penetrance and expressivity. 24 known genes and 9 loci with pathogenic alleles (PAs) underlie HSCR pathogenesis and explain 62% of its population attributable risk (PAR). Despite this heterogeneity, there is functional unity in HSCR: ~53% of HSCR PAs disrupt RET and EDNRB signaling in the developing enteric nervous system (ENS) with 11 HSCR genes comprising a gene regulatory network controlling RET and EDNRB gene expression. We propose to identify the remaining 30% PAR by studying 857 unrelated HSCR cases, their 125 affected and 1,446 unaffected first-degree relatives by whole genome sequencing to increase statistical power of gene discovery through improved detection of all types of coding and regulatory PAs. HSCR arises from cell autonomous defects in enteric neural crest cell precursors (ENCCs) affecting their proliferation, differentiation and migration in the ENS, functional studies that will guide our detection of novel genes. PUBLIC HEALTH RELEVANCE: Pathogenic allele (PA) diversity in HSCR is extensive and includes diverse molecular types of de novo mutations (DNMs) and segregating variants explaining 63% of its population attributable risk (PAR). We propose to identify the remaining 30% PAR by studying 857 unrelated HSCR cases, their 125 affected and 1,446 unaffected first-degree relatives by whole genome sequencing (WGS) by increasing statistical power of gene discovery through improved detection of SNVs, INDELs/CNVs and DNMs and coding and regulatory PAs. | |||
| Project Number: | HD110887-01 | Contact PI / Project Leader: | Chung, Wendy |
| Title: | Genomic Analysis of Esophageal Atresia and Tracheoesophageal Fistulas and Associated Congenital Anomalies | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Project Summary/Abstract Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. There is a 45% incidence of associated congenital malformations, most commonly digestive, cardiovascular, urogenital, and musculoskeletal, often part of a syndrome or complex association, with VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities) being most frequently recognized. Advanced surgical techniques and pre and post-operative care have improved the prognosis and survival of EA/TEF patients over the past decades. However, with improved survival, many of the long-term morbidities of EA/TEF have been exposed. It is likely that the outcome in EA/TEF patients is influenced by multiple genetic and clinical factors; however, determining which factors are critical has been limited by the lack of data, particularly genomic data. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of EA/TEF and define new genes and conditions associated with EA/TEF by performing whole genome sequencing on 100 parent child trios in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions and improve outcomes. PUBLIC HEALTH RELEVANCE: Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. We propose to elucidate the underlying genomic architecture of EA/TEF by performing whole genome sequencing to characterize new clinical syndromes associated with EA/TEF to provide more accurate clinical prognostic information. | |||
| Project Number: | HD110902-01 | Contact PI / Project Leader: | Espinosa, Joaquin M. |
| Title: | Epigenome analysis in the Human Trisome Project | Awardee Organization: | University of Colorado Denver |
| Abstract: DESCRIPTION (provided by applicant): Despite decades of research, the mechanisms by which trisomy 21 (T21) causes the myriad developmental and clinical hallmarks of Down syndrome (DS) are poorly understood, creating an obvious challenge in the clinical management of DS. T21 causes a different disease spectrum among those with DS, protecting these individuals from developing certain conditions, such as most solid malignancies, while strongly predisposing them to others, such as congenital heart disease, leukemias, and autoimmune disorders. Therefore, elucidating the mechanisms by which T21 causes this novel disease spectrum will greatly serve both people with DS and the general population affected by the numerous conditions modulated by T21. To accelerate research in this area, our team launched a pan-omics cohort study of people with DS known as the Crnic Institute Human Trisome Project (HTP). Supported by previous X01 awards, the HTP has become one of the deepest studies of people with DS to date, having completed matched analysis of the genome, transcriptome, proteome, metabolome, immune maps, and microbiome, along with deep clinical data annotation for hundreds of research participants. These efforts produced several discoveries about the impact of immune dysregulation in DS, leading to a novel clinical trial funded by the INCLUDE Project to test the safety and efficacy of a JAK inhibitor to improve health outcomes in DS. Now, we propose to complete a comprehensive analysis of epigenetic variation in DS with a focus on the immune system through the following Specific Aims: Aim 1. To complete a cross-sectional analysis of epigenetic variation in Down syndrome. We propose to complete DNA methylation analysis via bisulfite sequencing for 400+ participants with T21 versus 200+ age- and sex-matched euploid controls, most of whom have matched transcriptome and immune mapping data. Aim 2. To complete a longitudinal analysis of cell type-specific epigenetic variation in Down syndrome. We propose to complete an analysis of the epigenome of monocytes, a key immune cell type with major roles in inflammation in DS, via matched analysis of DNA methylation, chromatin accessibility (ATAC-seq), and transcriptome in a three-year longitudinal sample set. Aim 3. To complete a comprehensive analysis of the T and B cell receptor repertoires in Down syndrome. A key source of epigenetic variation highly relevant to the study of DS resides in the repertoire of rearranged genomic sequences encoding the T and B cell receptors (TCRs, BCRs). We propose to complete targeted long read sequencing to elucidate the TCR and BCR repertoires in 400+ participants with T21 versus 200+ controls. Altogether, this proposal is likely to generate the most comprehensive analysis of epigenetic variation in individuals with T21 to date, with a strong focus on the immune system, a key player in the etiology of many co- occurring conditions of DS. | |||
| Project Number: | HD110998-01 | Contact PI / Project Leader: | Gleeson, Joseph G |
| Title: | Whole Genome Sequencing in Structural Defects of the Neural Tube | Awardee Organization: | University of California, San Diego |
| Abstract: DESCRIPTION (provided by applicant): Myelomeningocele (aka meningomyelocele, MM) is the most severe form of spina bifida, a neural tube defect (NTD) in humans and the most common CNS birth defect. This defect occurs in 3.72/10,000 live US birth, and is partly preventable with prenatal folate, but the genetic basis and the mechanisms by which folate work to reduce disease incidence remain obscure. MM is associated nearly uniformly with prenatal hydrocephalus and the Arnold-Chiari malformation, as well as paraplegia and lifelong disability. The genes for several syndromic forms of NTDs are known, but the causes for the majority with sporadic clinical presentation remain unknown. Despite the importance of MM, previous research has been limited to targeted sequencing and association studies of folate metabolism genes, or very small-scale exome sequencing. We hypothesize that de novo mutations (DNMs) that produce likely gene disrupting (LGD) contribution to MM risk. Using conservative estimates of between 50-100 recurrently mutated discoverable genes, and given our preliminary data demonstrating an excess of LGD DNMs in MM compared with control individuals, we estimate that with a cohort size of 1000 trios, we should uncover between 5-20 new recurrently mutated genes underlying MM, with minimal false-discovery. With this in mind, we formed the Spina Bifida Sequencing Consortium, and established a platform for data and sample sharing. We recently completed submission of 333 trios for WGS at GMKF and are awaiting return of data. We have also more recently embarked on a new recruitment effort of an additional cohort of 400 new simplex MM trios, in collaboration with the US Spina Bifida Association, consented trios to allow for data sharing, and have performed detailed quality control on samples. To achieve recruitment success at this scale, we have had to emphasize saliva rather than blood sampling. This cohort in now half-way assembled and ready for sequencing, and the remaining cohort will be ascertained in the next 6 months. Here we propose to perform WGS the new 400 trios from saliva-derived DNA for this X01 effort to continue this discovery. We have established a workflow for de novo SNP/INDEL/SV detection from WGS and have ample computer storage and nodes to see the project to completion. We also plan to continue recruitment into the future with the goal of 2000 trios in the next 2 years. We propose a detailed bioinformatics workflow to identify gene mutations within a statistical framework, taking into account detailed RNA expression profiling from developing mouse neural tube, and have developed a robust functional validation workflow using Xenopus and mouse gene targeting. Our project has the potential to uncover a host of causes for this most common of the CNS birth defects, paving the way for future breakthroughs in detection, treatment and prevention. PUBLIC HEALTH RELEVANCE: This work will identify new genetic disease genes predisposing to myelomeningocele, the most common pediatric structural brain disease. | |||
| Project Number: | HD110886-01 | Contact PI / Project Leader: | Helbig, Ingo |
| Title: | The Genetic Basis of Structural Pediatric Epilepsies | Awardee Organization: | Children's Hospital Of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Childhood epilepsies are the most common neurological causes for hospital admissions in children. Gene identification has soared in the epilepsies over the last decade, and these discoveries have already led to novel therapies. In contrast, individuals with structural developmental brain anomalies who often benefit from epilepsy surgery are typically excluded from genetic testing. However, recent findings clearly suggest a strong genetic component. Accordingly, there is an essential need for a detailed understanding of the contributing genomic factors, which will be critical to improve patient care. We have recruited >700 patient-parent trios, 1,200 singleton, and 200 tissue samples derived from resective brain surgery. Our goal is to improve patient care by characterizing the genomic and transcriptional landscape of pediatric epilepsies. We hypothesize that known or presumed structural genetic epilepsies have a high frequency of disease-causing variants that can be identified through whole-genome sequencing and RNA sequencing and the analysis of longitudinal outcomes data through an established Electronic Medical Record (EMR) pipeline within the Kids First framework. Our study has two aims. First, we will analyze germline, somatic, and transcriptional contribution to structural pediatric epilepsies. We propose comprehensive profiling of 3,500 samples through Whole Genome Sequencing and 200 brain tissue samples derived from resective epilepsy surgery through parallel Whole Genome Sequencing and RNA Sequencing. We expect that this analysis will identify recurrent germline and somatic disease-causing variants, using the gene discovery expertise of our team to interpret identified genetic variants. Second, we aim to characterize the EMR-based longitudinal disease history of structural pediatric epilepsies. Our team has built frameworks and concepts for the use of longitudinal, de-identified EMR data. We will extract, de-identify, and map EMR data using the Human Phenotype Ontology (HPO) that we have been involved with for the last decade. We expect that implementing clinical data harmonization and analysis of complex phenotypic information will allow us to characterize the natural history and treatment response in known or presumed structural pediatric epilepsies which have not received attention in the past. In summary, our proposed project will have the possibility of systematically providing evidence for causative factors and impact on patient outcomes in known or presumed structural pediatric epilepsies, taking advantage of one of the largest pediatric epilepsy biobanks in conjunction with our expertise in cloud-based bioinformatic analysis and HPO-based data harmonization. The suggested datasets deposited within the Kids First Data Resource will help put structural epilepsies on similar footing to pediatric brain tumors and structural birth defects, enabling us to understand underlying disease mechanisms and allowing us to provide more targeted and improved treatments. PUBLIC HEALTH RELEVANCE: The proposed research is relevant to public health as more precise measurement of clinical and outcome data in structural childhood epilepsies is ultimately expected to translate into improved diagnostics and treatment of one of the most common structural disorders of the brain, allowing for greater personalized treatment choices. This project will address the significant unmet needs of children with structural epilepsies through the generation and integrative analysis of genomic data, including trio-based cohorts of longitudinally followed patients with deep clinical and phenotypic characterization. | |||
| Project Number: | DE032472-01 | Contact PI / Project Leader: | Marazita, Mary |
| Title: | Kids First: Genomics of Isolated Cleft Lip | Awardee Organization: | University of Pittsburgh |
| Abstract: DESCRIPTION (provided by applicant): Isolated Cleft Lip (CL) is one of three subtypes of nonsyndromic orofacial clefts (OFCs), a heterogeneous group of anomalies that also include cleft lip with cleft palate (CLP) and cleft palate alone (CP). Cumulatively, OFCs occur in about 1/700 live births worldwide, and thus comprise a significant proportion of human structural birth defects. Isolated CL (i.e. CL without CP) occurs in about 1 in every 2,800 babies in the U.S (1). Individuals with CL face feeding difficulties, speech, and dental problems and undergo multiple corrective surgeries and ongoing therapy that comes at a substantial personal and financial burden. Further, patients can experience lifelong psychosocial effects, increased mortality rates, and a higher risk of various cancer types. Because CL and CLP share a defect of the upper lip, these two OFC subtypes have historically been combined in genetic studies. However, most studies are dominated by CLP, the most common of all OFCs, and any contribution from the smaller CL sample alone is often undetectable. In recent years, increasing sample sizes afforded the ability to analyze CL and CLP as separate entities. There is now evidence that the subtypes of OFC have distinct differences in their genetic risk patterns. Isolated CL has not yet been investigated in detail as a separate sub-phenotype, with only a few GWAS reports and no reported whole genome sequencing (WGS) studies to date. Therefore, critical gaps in our understanding of CL persist. The major goal of this proposal is to investigate the genome in isolated CL trios to begin to fill this knowledge gap. To do so, we request WGS for 762 CL trios from our large collaborative resources. There is already WGS for a total of 2,078 OFC proband trios from multiple ethnicities (many from our research collaborations and funded mostly through the Gabriella Miller Kids First Consortium—GMKF). Of those trios, 272 have isolated CL; combined with the new trios we will have a total of 1,034 CL trios, a powerful sample size for CL risk variant discovery and equivalent to the discovery resources for CLP and CP. This larger resource of CL trios will fill a critical gap in data and resources necessary to deeply understand the genetic architectures of each OFC subtype. To accomplish the overall goal we will (i) identify risk variants for isolated CL by WGS of CL trios; (ii) compare and contrast the genetic architectures of CL to CLP and CP; and (iii) replicate variants/genes identified through (i) and (ii). PUBLIC HEALTH RELEVANCE: The goal of this project is to better understand the genetic architecture of isolated cleft lip (CL) birth defects by performing whole genome sequencing in multi-ethnic CL families. | |||
| Project Number: | HD110862-01 | Contact PI / Project Leader: | Rios, Jonathan |
| Title: | GMKF Project on Congenital Clubfoot | Awardee Organization: | University of Texas Southwestern Medical Center |
| Abstract: DESCRIPTION (provided by applicant): Talipes equinovarus (clubfoot) is a common congenital structural birth defect. Clubfoot occurs in ~1 in 1,000 live births in the United States, though the incidence varies in other worldwide populations. Clubfoot affects the structural components of the foot (tarsals), muscular and connective tissues including the Achilles and tibial tendons, and ligaments of the ankle. Males are affected twice as frequently as females, and at least half of patients present with bilateral disease. Surgical correction in infants requires tendoachilles lengthening, where the Achilles tendon is severed and the foot is casted to allow healing with the foot in a proper position. Although short-term success following clubfoot treatment is positive, long-term outcomes following surgical clubfoot correction are poor; complications include arthritis, reduced range of motion, weakness, pain and persistent deformity. Importantly, the number of surgical procedures required to produce a corrected clubfoot was significantly associated with poorer long-term outcomes. The pathogenesis of clubfoot remains largely unknown, though ~12% of patients report a family history. Targeted gene sequencing studies have failed to identify genetic loci associated with clubfoot. We recently reported FSTL5 as the first GWAS-associated locus associated with clubfoot, and we showed this gene was associated with sexually-dimorphic phenotypes in mice. Together with the Gabriella Miller Kids First Initiative (GMKF), we are poised to continue advancing the field’s understanding of the genetic causes of clubfoot. The GMKF provides comprehensive genome sequencing (GS) in individuals and families with congenital birth defects. However, no study of congenital limb malformations has yet been conducted as part of the GMKF; thus, our study will be the first GMKF study to investigate genetic causes of congenital limb defects. For the past several decades, we have collected DNA samples from families with multiple relatives affected with clubfoot. Similar to our previously-awarded GMKF studies (1X01HL132375 led by Dr. Rios and DE031445 co-led by Dr. Hecht), we will utilize the power of family-based inheritance mapping to discovery genetic causes of clubfoot. Using the comprehensive GS provided by the GMKF, we will discover sequence variants and copy number variants co-segregating with clubfoot in these families. We present a systematic approach to discover these clubfoot-causing variants, including an integrated approach to investigate variants impacting potential non-coding regulatory elements, which have previously been implicated in other limb malformations. At the completion of this study, we will provide the field with the most comprehensive genomic analysis of families with clubfoot, which will provide novel hypotheses regarding the genetic etiology of this complex congenital birth defect. PUBLIC HEALTH RELEVANCE: Clubfoot is a common birth defect affecting ~1 per 1,000 births, where infants and children are treated with various surgical and nonsurgical methods to correct the foot deformity. Our goal is to better understand the genetic factors contributing to clubfoot through family-based and population-based genetic studies, and our research team recently reported the first GWAS-associated clubfoot locus. Here, we propose to use genome sequencing and robust analytical approaches to systematically evaluate the causes of clubfoot in large multi- generational families. | |||
2021 X01 Projects
| Project Number: | HD107271-01 | Contact PI / Project Leader: | Cody, Jannine De Mars |
| Title: | The genomic basis of structural birth defects associated with chromosome 18 copy number changes | Awardee Organization: | University Of Texas Health Science Center |
| Abstract: DESCRIPTION (provided by applicant): Chromosome abnormalities are a common cause of structural birth defects. However, because these genomic copy number changes involve multiple genes and because most of these conditions are individually rare defining the specific causative genes behind specific phenotypes has been a challenge. We met that challenge by spending the last 28 years enrolling and evaluating anyone with a chromosome 18 abnormality. The cohort now includes over 700 individuals with a wide variety of chromosome 18 copy number changes (CNV) as well as their parents. Because the vast majority of these participants have individually unique CNVs we have been able to perform extensive genotype phenotype correlations resulting in 58 publications. Of the 263 genes on chromosome 18, 28 are liked to specific hemizygous phenotypes. However, most have low penetrance. Genomic sequence data could identify variants in the extant allele that are hypermorphic and compensate for hemizygosity or are hypomorphic and exacerbate hemizygosity. Additionally, there are phenotypes within this cohort that are rare or an extreme version of one of the more common phenotypes. Genomic sequence data could help to discover new biallelic conditions by revealing functional sequence variants of the extant allele. In both of these cases there could also be variants in other genes on other chromosomes that may be associated with the phenotype that confer susceptibility or resilience. Inclusion of this unique cohort in the Gabriella Miller Kids First Pediatric Research Program can advance the goals of the program in several ways. First, by adding known susceptibility loci to the existing Kids First cohorts for the structural birth defects that are also found in our cohort. Second, for those structural birth defects known to be polygenetic, this cohort has a single defined risk factor which can simplify the search for secondary factors. Third, these studies can also bring clarity to people with chromosome 18 conditions and help to make the genotype more accurately predict phenotype. This approach could be a model for understanding the many other rare chromosome abnormalities which collectively are a common cause of structural birth defects. | |||
| Project Number: | CA268005-01 | Contact PI / Project Leader: | Diskin, Sharon |
| Title: | The Genetic Basis of Treatment Outcomes and Late Effects After High-Risk Neuroblastoma | Awardee Organization: | Children's Hospital Of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Children diagnosed with high-risk neuroblastoma receive intensive multi-modal therapy, yet 40-50% die of their primary cancer, and those who survive experience substantial treatment-related morbidities. There is no reliable way to identify those at greatest risk of treatment failure (death) or late effects, and only a nascent understanding of underlying genetic determinants. Our long term goal is to improve neuroblastoma outcomes by first characterizing the events driving tumorigenesis and treatment response so that evidence-based and less toxic therapies can be developed. We hypothesize that comprehensive whole genome sequencing (WGS) of high- risk neuroblastoma subjects treated with modern therapy and annotated with late effect phenotypes will identify genetic determinants of survival and treatment-related morbidities. Through an existing Gabriella Miller Kids First (GMKF) project, we performed WGS of neuroblastoma patient-parent triads/dyads (n=556) together with matched tumor DNA (n=336) and RNA-sequencing (n=207). These data have defined the heritable fraction of rare pathogenic variants in cancer predisposition genes and suggest carriers have worse survival. However, only a subset of cases (n=178) sequenced are high-risk and none include phenotyping of late effects. Here, we will build on existing GMKF profiling to generate germline WGS for 1,100 total children (n=922 new) who received modern high-risk neuroblastoma therapy, along with additional WGS of matched tumor DNA (n=553 new) and RNA-sequencing (n=461 new). All subjects participated in the Children’s Oncology Group (COG) neuroblastoma biology study (ANBL00B1). The entire cohort is annotated with demographic (age, sex, race, ethnicity), clinical (e.g. age at diagnosis, stage, risk group, survival), and tumor biological (e.g. MYCN status) co-variates. A subset (n=367) are 5+ year survivors enrolled in the COG ALTE15N2: Late Effects After High-Risk Neuroblastoma (LEAHRN) study and have undergone extensive clinical assessments, with excellent characterization of late toxicities. We will test our hypothesis through two Specific Aims: 1) Identify germline and somatic variants associated with high-risk neuroblastoma treatment failure. Using a phased approach, we will identify coding and non-coding germline variation, somatic alterations, and transcriptomic profiles predicting refractory disease and survival. 2) Discover genetic risk factors associated with late effects after high-risk neuroblastoma therapy. We will define the spectrum, prevalence, and association of rare pathogenic variants with respect to hearing loss, cardiomyopathy, growth impairment and primary gonadal failure in the LEAHRN subjects. Data from NCI- TARGET (n=1,108), our genome-wide association study (GWAS; n=6,202), and phenotyping in recent high-risk trials will be integrated to validate genetic associations with treatment outcomes. Sequencing of this unique and extensively phenotyped high-risk neuroblastoma cohort will provide an unparalleled opportunity to discover germline and somatic alterations that can be used to identify patients at risk for treatment failure and late effects. This will serve as rationale for the design of future trials aimed at improved survival and reduction in late effects. | |||
| Project Number: | HL161587-01 | Contact PI / Project Leader: | Gelb, Bruce D |
| Title: | Expanding our understanding of the role of noncoding variation causing congenital heart defects | Awardee Organization: | Icahn School Of Medicine At Mount Sinai |
| Abstract: DESCRIPTION (provided by applicant): The epidemiology of congenital heart defects (CHD) indicates that genetic variation is the overwhelmingly predominant cause of these commonest birth defects, but more than 50% of CHD cases remain unexplained even after trio exome sequencing (ES). The remaining large gap in genetic causality for CHD is what the Pediatric Cardiac Genomics Consortium (PCGC), a component of NHLBI’s Bench-to-Bassinet Program, seeks to address through the Gabriella Miller Kids First (GMKF) Pediatric Research Program. Under the auspices of prior GMKF awards for trio genome sequencing (GS), the PCGC began to elucidate the role of de novo noncoding damaging single nucleotide variants and small insertions and deletions (indels) in CHD causality . The cumulative mean attributed risk from noncoding de novo variants (DNVs) for exome-negative CHD was 17-45%. To further the understanding of the role of genetic variation in causing CHD, the PCGC is requesting GS to perform GS for 500 probands born with tetralogy of Fallot (ToF) or hypoplastic left heart syndrome (HLHS), unsolved after exome sequencing, and their unaffected parents. In addition to increasing cohort size to improve statistical power, we will use a new and larger control trio GS dataset available through TOPMed (n = 1,758) and generate an improved version of our neural network,HeartENN, which predicts functional impact of genetic variation, through incorporation of more-than-double cardiac noncoding regulatory feature data. Of note, the PCGC has the wherewithal to confirm relevant variants with other genomic methods as well as to perform functional cell-based assays to further support claims of pathogenicity. We will also use the GS data to expand our understanding of structural variation underlying CHD. We will use a best-of-class SV calling pipeline, developed by the Talkowski group at the Broad Institute. Analytic focus of SVs will include disruptions of known autosomal dominant CHD genes, 2nd hits in trans to damaging coding variants in known autosomal recessive CHD genes, and burden analysis for apparently damaging SVs combined with existing data about putatively damaging coding variants (SNVs and indels) from > 5000 CHD trios. Finally, in an exploratory portion of this aim, we will attempt calling of SVs such as repeat expansions that are difficult with short-read GS, focusing on a limited number of regions of potential interest based on our analysis of PacBio long-read GS from 200 CHD probands, currently being generated under the auspices of the GMKF pilot program. | |||
| Project Number: | HD107383-01 | Contact PI / Project Leader: | Krantz, Ian D |
| Title: | RNAseq in Cornelia de Lange Syndrome, Related Diagnoses and Structural Birth Defects | Awardee Organization: | Children's Hospital Of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Disorders of human morphogenesis are a major cause of human suffering for the affected individuals and their families. Congenital anomalies are identified in approximately 3% of term births, 10% of stillbirths, and in as many as 50% of first trimester spontaneous abortuses. While most, if not all, human structural birth defects have a significant genetic component, identification of genetic perturbations in isolated structural birth defects has been complicated by the complex nature of their underlying etiologies, likely involving disruption of regulatory elements that can act in a temporal and tissue specific manner, multi-gene, epigenetic and gene-environment interactions. Our approach to tease out genetic contributions to birth defects has been to identify the underlying causes of syndromic birth defects which are often Mendelian in nature and therefore lend themselves more readily to genetic causal identification. Once identified, these genetic causes of syndromic forms of birth defects can be leveraged to understand the genetic contributions to isolated birth defects seen in constellation in these syndromes. We propose to use Cornelia de Lange Syndrome (CdLS), a dominant multisystem developmental disorder consisting of a constellation of structural birth defects involving most body systems and significant growth and cognitive impairment as a prime example of this approach. We and others have shown that alterations in the cohesin and associated pathways are causative of CdLS and related diagnoses when disrupted and have more broadly been termed “cohesinopathies” or “disorders of transcriptional regulation (DTRs)”. In this proposal we outline an initial plan to perform RNA sequencing on a unique cohort of 77 probands with clinically confirmed CdLS or a related diagnosis (and 74 unaffected family members) in whom genome sequencing performed as part of previous XO1 project was non-diagnostic, but are strongly suspected of having an underlying genetic alteration to explain their clinical features. This work will lead to the identification of genes critical in human embryonic development, provide novel insights into transcriptional regulation and help to identify genetic causes and candidate genes for isolated birth defects seen in constellation in this group of diagnoses. Most critical developmental genes are also cancer genes and the genes known to cause CdLS are no exception. CdLS is not a cancer predisposition syndrome so understanding the mutational mechanisms in these genes that lead to structural birth defects when present in the germ line and result in cancer when mutated somatically is a fundamental aspect of this research. | |||
| Project Number: | DE031445-01 | Contact PI / Project Leader: | Letra, Ariadne M |
| Title: | Whole genome sequencing studies of multiplex nonsyndromic cleft lip/palate families | Awardee Organization: | University Of Texas Health Sci Ctr Houston |
| Abstract: DESCRIPTION (provided by applicant): In this proposal, we request whole genome sequencing (WGS) services of 923 individuals from our cohort of well-characterized, large multigenerational nonsyndromic cleft lip/palate (NSCLP) families of Hispanic and non-Hispanic white ethnicities. NSCLP is a common birth defect accounting for 65% of all birth defects and annually affecting approximately 135,000 newborns worldwide. Despite improvement in treatments, NSCLP imposes significant medical, psychosocial and financial burdens that affect quality of life of affected individuals and their families. NSCLP is complex, caused by genetic and environmental factors, and their interactions. Recent advances in genomic approaches have improved our knowledge of the genetic factors involved in NSCLP; however, most of the variants associated with NSCLP account for ~25% of the genetic liability and reflect common, modest risk-variants often located in noncoding regions of the genome. More recently, it has been suggested that some genetic risk for NSCLP lies in rare variants and this has contributed to the lack of consistent findings and difficulty in unraveling risk alleles. Further, it is likely that the missing heritability of NSCLP result in part due to interactions between common, modest risk variants and rare, high-risk variants. We will analyze WGS data and apply polygenic risk score analysis to identify novel, high-penetrance NSCLP variants and to systematically evaluate the contributions of both common and rare variants to NSCLP, and how they segregate individually and in concert within and between families. The results of this study will provide novel and important insights about the genetic architecture contributing to the complex etiology of NSCLP. Importantly, this proposal will translate into a rich and publicly available resource of NSCLP genotypic and phenotypic data that will be made available to the broader scientific community to foster additional studies on NSCLP, as well as other birth defects and/or associated co-morbidities. Further, this proposal will provide genotype and allele frequency data in Hispanics for which limited data is available on genetic databases. Additional follow-up studies proposed, although beyond the scope of this X01 application, include validating the variants identified in this study in our additional NSCLP trios as well as through joint analysis with data from additional existing Kids First datasets. Successful completion of this study will provide novel and important insights about the genetic architecture contributing to the complex etiology of NSCLP, and will translate into a large, rich resource for genetic and phenotypic information on NSCLP. | |||
| Project Number: | CA267638-01 | Contact PI / Project Leader: | Lupo, Philip J |
| Title: | Genetic Overlap Between Anomalies and Cancer in Kids in the Childrens Oncology Group: The COG GOBACK Study | Awardee Organization: | Baylor College Of Medicine |
| Abstract: DESCRIPTION (provided by applicant): One of the strongest risk factors for cancer in children and adolescents is being born with a congenital anomaly— this is true both for chromosomal abnormalities (e.g., Down syndrome) and non-chromosomal birth defects (e.g., non-syndromic congenital heart defects), as recently validated in our registry linkage study of over 10 million live births. Specifically, by linking data from population-based birth defects and cancer registries in four states included in the Genetic Overlap Between Anomalies and Cancer in Kids (GOBACK) Study, we identified multiple novel congenital anomaly-cancer associations that are not part of known cancer predisposition syndromes. We also observed increasing cancer risk with a corresponding increase in the number of non-chromosomal defects. Children with multiple congenital anomalies (MCAs) who develop cancer are likely a subset of individuals enriched for cancer predisposition syndromes that have yet to be identified. There are two unanswered questions that limit clinical translation of these findings. Specifically, it is not clear: 1) what proportion of these associations may be due to known cancer predisposition variants; and 2) if novel cancer predisposition syndromes might underlie these observed associations. These gaps limit genetic testing and counseling strategies for these families. Our central hypothesis is the co-occurrence of congenital anomalies and cancer results from molecular etiologies identifiable through genomic evaluation. Our hypothesis is built on rigorous prior research, including findings from the GOBACK Registry Linkage Cohort and whole-genome sequencing (WGS) on a subset of children enrolled in the GOBACK Family Cohort. Our proposed Kids First study leverages several robust and existing resources, including: 1) matched tumor-normal samples from children with congenital anomalies and cancer without a reported syndrome (N=500) enrolled as part of the Children's Oncology Group (COG) APEC14B1 protocol (Project: EveryChild or PEC); 2) an approved COG protocol that allows for WGS of these samples; 3) an ongoing study to recontact these families to obtain additional phenotypic data; 4) our established bioinformatic pipelines to evaluate the role of rare variants consistent with autosomal dominant, recessive, or X- linked disorders; and 5) the expanded GOBACK Registry Linkage Cohort representing >35% of the U.S. population, which can be used to evaluate associations and WGS findings observed in PEC. Our central hypothesis will be evaluated in two aims: 1) determine the frequency of known cancer predisposition variants among children with congenital anomalies and cancer; and 2) identify variants that underlie novel anomaly- cancer predisposition syndromes and describe the landscape of somatic alterations in these children. By extending our integrated population-based and genomic approach, this application has the potential to: 1) generate novel insights into the developmental pathways that lead to cancer; 2) identify new cancer susceptibility syndromes; and 3) subsequently lead to improved cancer surveillance strategies for children with congenital anomalies. | |||
| Project Number: | CA267576-01 | Contact PI / Project Leader: | Meshinchi, Soheil |
| Title: | Germline and Somatic Variants in Pediatric AML | Awardee Organization: | Fred Hutchinson Cancer Research Center |
| Abstract: DESCRIPTION (provided by applicant): Advances in genomic sequencing have allowed identification of somatic variants as potential therapeutic targets. Although myeloid disorders in children may show morphologic similarities to that seen in adults, TARGET AML initiative (Meshinchi, PI) clearly demonstrated that somatic genomic and transcriptome variants are highly distinct in children and young adults. In fact, there are a number of variants that are uniquely restricted to younger children. TARGET AML initiative, although modest in number, helped identify numerous somatic alterations with high therapeutic potential in younger AML patients. In addition to identification of somatic variants, analysis of the germline data provided a glimpse into the constitutional make-up of patients with AML. The identification of numerous “function altering” variants may provide an insight into possible interactions between the host and the disease, where these germline variants might alter AML risk (predisposition), response to therapy (altering target expression, drug metabolism), susceptibilities to short and long-term complications (including infectious and cardiac complications), or modify risk of secondary malignancies. Armed with data from initial sequencing efforts in AML, we are poised to take full advantage of the available sequencing technology to conduct the most comprehensive genome and transcriptome interrogation of myeloid disorders in children with specimens we have amassed over the last decade. To this end, we have put in place unparalleled specimen resources from children with de novo AML treated on COG AAML1031, to create the most comprehensive genome, transcriptome and epigenome profiling in AML. Our original X01 application providing funding support for whole genome sequencing of approximately half of the patients treated on AAML1031. Given that transcriptome (mRNA, miRNA, LncRNA) and methylation data is available for the entire AAML1031 cohort, completion of the genomic sequencing will provide completion of the profiling effort in this single trial cohort. The data provided by the prior X01 sequencing effort has yielded unparalleled data in defining novel therapeutic targets, prognostic biomarkers and have informed of germline variants that are associated with cancer predisposition. Also, germline variants can be exploited to identify those that might be at high risk of adverse events (cardiac complications, secondary malignancies, etc.) and their therapy tailored to minimize anticipated complications. Thus, we propose that the optimum outcome can only be obtained thru comprehensive interrogation of the somatic and germline genome to fully annotate the genomic makeup of the leukemia and its host. | |||
| Project Number: | CA267587-01 | Contact PI / Project Leader: | Resnick, Adam Cain |
| Title: | Germline and Somatic Disease Modifiers of Pediatric Brain Tumors | Awardee Organization: | Children's Hospital Of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Brain tumors are the most common form of cancer in children aged 0-19 in the United States, and are the largest cause of cancer-related deaths. The estimated number of new cases in 2019 is nearly 3,800 and thus brain tumors are a rare disease. Despite their relative rarity, the years of potential life lost due to brain tumors in 2009 was estimated at 47,631 years for children and adolescents aged 0-19 in the United States; this is a disproportionate amount of life lost compared to adult cancers and represents an unrecognized societal threat. There is an urgent need to improve therapies for these children. Most of the high-grade glial and embryonal brain cancers still remain largely incurable despite decades of clinical and laboratory research. Existing non-targeted chemotherapies and radiation, while at times effective, often represent pyrrhic victories, leaving behind life-long health burdens and causing a significant risk of secondary malignancies. NIH funded pediatric brain tumor cohort-based genomic dataset generation efforts have lagged behind other histologies and have yet to be included as part of large-scale sequencing efforts. However, consortia-based initiatives like those supported by the Children's Brain Tumor Network (CBTN) have demonstrated the early potential for clinically annotated genomic cohorts and their utility and interest by both the pediatric cancer and structural birth defect community with more than 130 data access requests for a non-embargoed cohort of tumor/normal whole genomes and paired tumor RNAseq. Indeed more than one quarter of this 800-subject initial sequencing cohort were identified to have birth-defect-associated clinical annotations in their clinical records, however, to our knowledge limited to no trio-based genomics cohort studies exist for any one pediatric brain tumor histology. The project's proposed sequencing cohort defines the largest, clinically annotated pediatric brain tumor cohort study to date and seeks to define the intersection of germline and somatic underpinnings of pediatric brain tumors across a shared developmental context of cancer and structural birth defects. | |||
| Project Number: | CA267639-01 | Contact PI / Project Leader: | Scheurer, Michael E |
| Title: | Genomic Analysis of Histiocytosis | Awardee Organization: | Baylor College Of Medicine |
| Abstract: DESCRIPTION (provided by applicant): Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasm characterized by lesions including pathogenic CD207+ dendritic cells among an inflammatory infiltrate. The median age at diagnosis is 30 months, and up-front chemotherapy fails in ~50% of patients resulting in multiple relapse events for 40-50% of cases, and long-term sequelae. Sequencing studies have found recurrent, mutually exclusive somatic activating mutations in MAPK pathway genes in ~85% of LCH lesions, including BRAF V600E in 50-65%. There is a “Misguided Myelomonocytic Precursor Model” in which specific somatic MAPK mutations at critical stages of myeloid differentiation determine extent of disease. However, this model fails to explain the significant differences in LCH risk across ethnicities. Despite advances to elucidate the somatic mutational landscape underlying LCH pathogenesis, germline risk factors remain largely unknown. Therefore, we conducted the first genome-wide association study of LCH and identified a SMAD6 variant associated with increased risk. SMAD6 inhibits bone morphogenetic protein and transforming growth factor-beta/activin signaling, which are determinants of Langerhans cell differentiation. This variant appears to suppress SMAD6 protein expression without a decrease in SMAD6 messenger RNA expression in patients carrying the risk allele. This risk allele is also more common in Hispanics who are at the highest risk of LCH, and absent in blacks who experience the lowest LCH incidence. Our preliminary data also support the emerging observation that LCH somatic activating mutations vary by race/ethnicity. Specifically, sequencing of tumors from black patients indicated that only 25% were BRAF V600E+ (compared to >60% in other populations), whereas 50% had mutations in MAP2K1 (compared to < 10% in other populations). Therefore, the objective of this Kids First X01 application is to more fully elucidate LCH etiology by defining the role of de novo mutations (DNMs) in established LCH genes and novel susceptibility genes, and by comprehensively assessing somatic variation in LCH. Our central hypothesis is that penetrant DNMs and novel germline and somatic variation may contribute to, or in some cases, drive LCH tumorigenesis. 1) We will leverage our ongoing Children's Oncology Group study, Genetic Epidemiology of Childhood Histiocytosis (GECHO), to sequence 300 LCH case-parent trios to evaluate the impact of recurrent DNMs on inherited susceptibility to LCH. 2) We will leverage paired germline-tumor samples from 200 patients enrolled to the Texas Children's Histiocytosis Program protocol or GECHO study to comprehensively assess the somatic landscape of LCH and identify germline variation contributing to somatic mutational profiles. Successful completion of the proposed aims may (1) improve genetic testing and counseling strategies in LCH patients and families; (2) advance surveillance and chemoprevention protocols; and (3) identify novel therapeutic targets. | |||
2021 X01 Projects
| Project Number: | HD107271-01 | Contact PI / Project Leader: | Cody, Jannine De Mars |
| Title: | The genomic basis of structural birth defects associated with chromosome 18 copy number changes | Awardee Organization: | University Of Texas Health Science Center |
| Abstract: DESCRIPTION (provided by applicant): Chromosome abnormalities are a common cause of structural birth defects. However, because these genomic copy number changes involve multiple genes and because most of these conditions are individually rare defining the specific causative genes behind specific phenotypes has been a challenge. We met that challenge by spending the last 28 years enrolling and evaluating anyone with a chromosome 18 abnormality. The cohort now includes over 700 individuals with a wide variety of chromosome 18 copy number changes (CNV) as well as their parents. Because the vast majority of these participants have individually unique CNVs we have been able to perform extensive genotype phenotype correlations resulting in 58 publications. Of the 263 genes on chromosome 18, 28 are liked to specific hemizygous phenotypes. However, most have low penetrance. Genomic sequence data could identify variants in the extant allele that are hypermorphic and compensate for hemizygosity or are hypomorphic and exacerbate hemizygosity. Additionally, there are phenotypes within this cohort that are rare or an extreme version of one of the more common phenotypes. Genomic sequence data could help to discover new biallelic conditions by revealing functional sequence variants of the extant allele. In both of these cases there could also be variants in other genes on other chromosomes that may be associated with the phenotype that confer susceptibility or resilience. Inclusion of this unique cohort in the Gabriella Miller Kids First Pediatric Research Program can advance the goals of the program in several ways. First, by adding known susceptibility loci to the existing Kids First cohorts for the structural birth defects that are also found in our cohort. Second, for those structural birth defects known to be polygenetic, this cohort has a single defined risk factor which can simplify the search for secondary factors. Third, these studies can also bring clarity to people with chromosome 18 conditions and help to make the genotype more accurately predict phenotype. This approach could be a model for understanding the many other rare chromosome abnormalities which collectively are a common cause of structural birth defects. | |||
| Project Number: | CA268005-01 | Contact PI / Project Leader: | Diskin, Sharon |
| Title: | The Genetic Basis of Treatment Outcomes and Late Effects After High-Risk Neuroblastoma | Awardee Organization: | Children's Hospital Of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Children diagnosed with high-risk neuroblastoma receive intensive multi-modal therapy, yet 40-50% die of their primary cancer, and those who survive experience substantial treatment-related morbidities. There is no reliable way to identify those at greatest risk of treatment failure (death) or late effects, and only a nascent understanding of underlying genetic determinants. Our long term goal is to improve neuroblastoma outcomes by first characterizing the events driving tumorigenesis and treatment response so that evidence-based and less toxic therapies can be developed. We hypothesize that comprehensive whole genome sequencing (WGS) of high- risk neuroblastoma subjects treated with modern therapy and annotated with late effect phenotypes will identify genetic determinants of survival and treatment-related morbidities. Through an existing Gabriella Miller Kids First (GMKF) project, we performed WGS of neuroblastoma patient-parent triads/dyads (n=556) together with matched tumor DNA (n=336) and RNA-sequencing (n=207). These data have defined the heritable fraction of rare pathogenic variants in cancer predisposition genes and suggest carriers have worse survival. However, only a subset of cases (n=178) sequenced are high-risk and none include phenotyping of late effects. Here, we will build on existing GMKF profiling to generate germline WGS for 1,100 total children (n=922 new) who received modern high-risk neuroblastoma therapy, along with additional WGS of matched tumor DNA (n=553 new) and RNA-sequencing (n=461 new). All subjects participated in the Children’s Oncology Group (COG) neuroblastoma biology study (ANBL00B1). The entire cohort is annotated with demographic (age, sex, race, ethnicity), clinical (e.g. age at diagnosis, stage, risk group, survival), and tumor biological (e.g. MYCN status) co-variates. A subset (n=367) are 5+ year survivors enrolled in the COG ALTE15N2: Late Effects After High-Risk Neuroblastoma (LEAHRN) study and have undergone extensive clinical assessments, with excellent characterization of late toxicities. We will test our hypothesis through two Specific Aims: 1) Identify germline and somatic variants associated with high-risk neuroblastoma treatment failure. Using a phased approach, we will identify coding and non-coding germline variation, somatic alterations, and transcriptomic profiles predicting refractory disease and survival. 2) Discover genetic risk factors associated with late effects after high-risk neuroblastoma therapy. We will define the spectrum, prevalence, and association of rare pathogenic variants with respect to hearing loss, cardiomyopathy, growth impairment and primary gonadal failure in the LEAHRN subjects. Data from NCI- TARGET (n=1,108), our genome-wide association study (GWAS; n=6,202), and phenotyping in recent high-risk trials will be integrated to validate genetic associations with treatment outcomes. Sequencing of this unique and extensively phenotyped high-risk neuroblastoma cohort will provide an unparalleled opportunity to discover germline and somatic alterations that can be used to identify patients at risk for treatment failure and late effects. This will serve as rationale for the design of future trials aimed at improved survival and reduction in late effects. | |||
| Project Number: | HL161587-01 | Contact PI / Project Leader: | Gelb, Bruce D |
| Title: | Expanding our understanding of the role of noncoding variation causing congenital heart defects | Awardee Organization: | Icahn School Of Medicine At Mount Sinai |
| Abstract: DESCRIPTION (provided by applicant): The epidemiology of congenital heart defects (CHD) indicates that genetic variation is the overwhelmingly predominant cause of these commonest birth defects, but more than 50% of CHD cases remain unexplained even after trio exome sequencing (ES). The remaining large gap in genetic causality for CHD is what the Pediatric Cardiac Genomics Consortium (PCGC), a component of NHLBI’s Bench-to-Bassinet Program, seeks to address through the Gabriella Miller Kids First (GMKF) Pediatric Research Program. Under the auspices of prior GMKF awards for trio genome sequencing (GS), the PCGC began to elucidate the role of de novo noncoding damaging single nucleotide variants and small insertions and deletions (indels) in CHD causality . The cumulative mean attributed risk from noncoding de novo variants (DNVs) for exome-negative CHD was 17-45%. To further the understanding of the role of genetic variation in causing CHD, the PCGC is requesting GS to perform GS for 500 probands born with tetralogy of Fallot (ToF) or hypoplastic left heart syndrome (HLHS), unsolved after exome sequencing, and their unaffected parents. In addition to increasing cohort size to improve statistical power, we will use a new and larger control trio GS dataset available through TOPMed (n = 1,758) and generate an improved version of our neural network,HeartENN, which predicts functional impact of genetic variation, through incorporation of more-than-double cardiac noncoding regulatory feature data. Of note, the PCGC has the wherewithal to confirm relevant variants with other genomic methods as well as to perform functional cell-based assays to further support claims of pathogenicity. We will also use the GS data to expand our understanding of structural variation underlying CHD. We will use a best-of-class SV calling pipeline, developed by the Talkowski group at the Broad Institute. Analytic focus of SVs will include disruptions of known autosomal dominant CHD genes, 2nd hits in trans to damaging coding variants in known autosomal recessive CHD genes, and burden analysis for apparently damaging SVs combined with existing data about putatively damaging coding variants (SNVs and indels) from > 5000 CHD trios. Finally, in an exploratory portion of this aim, we will attempt calling of SVs such as repeat expansions that are difficult with short-read GS, focusing on a limited number of regions of potential interest based on our analysis of PacBio long-read GS from 200 CHD probands, currently being generated under the auspices of the GMKF pilot program. | |||
| Project Number: | HD107383-01 | Contact PI / Project Leader: | Krantz, Ian D |
| Title: | RNAseq in Cornelia de Lange Syndrome, Related Diagnoses and Structural Birth Defects | Awardee Organization: | Children's Hospital Of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Disorders of human morphogenesis are a major cause of human suffering for the affected individuals and their families. Congenital anomalies are identified in approximately 3% of term births, 10% of stillbirths, and in as many as 50% of first trimester spontaneous abortuses. While most, if not all, human structural birth defects have a significant genetic component, identification of genetic perturbations in isolated structural birth defects has been complicated by the complex nature of their underlying etiologies, likely involving disruption of regulatory elements that can act in a temporal and tissue specific manner, multi-gene, epigenetic and gene-environment interactions. Our approach to tease out genetic contributions to birth defects has been to identify the underlying causes of syndromic birth defects which are often Mendelian in nature and therefore lend themselves more readily to genetic causal identification. Once identified, these genetic causes of syndromic forms of birth defects can be leveraged to understand the genetic contributions to isolated birth defects seen in constellation in these syndromes. We propose to use Cornelia de Lange Syndrome (CdLS), a dominant multisystem developmental disorder consisting of a constellation of structural birth defects involving most body systems and significant growth and cognitive impairment as a prime example of this approach. We and others have shown that alterations in the cohesin and associated pathways are causative of CdLS and related diagnoses when disrupted and have more broadly been termed “cohesinopathies” or “disorders of transcriptional regulation (DTRs)”. In this proposal we outline an initial plan to perform RNA sequencing on a unique cohort of 77 probands with clinically confirmed CdLS or a related diagnosis (and 74 unaffected family members) in whom genome sequencing performed as part of previous XO1 project was non-diagnostic, but are strongly suspected of having an underlying genetic alteration to explain their clinical features. This work will lead to the identification of genes critical in human embryonic development, provide novel insights into transcriptional regulation and help to identify genetic causes and candidate genes for isolated birth defects seen in constellation in this group of diagnoses. Most critical developmental genes are also cancer genes and the genes known to cause CdLS are no exception. CdLS is not a cancer predisposition syndrome so understanding the mutational mechanisms in these genes that lead to structural birth defects when present in the germ line and result in cancer when mutated somatically is a fundamental aspect of this research. | |||
| Project Number: | DE031445-01 | Contact PI / Project Leader: | Letra, Ariadne M |
| Title: | Whole genome sequencing studies of multiplex nonsyndromic cleft lip/palate families | Awardee Organization: | University Of Texas Health Sci Ctr Houston |
| Abstract: DESCRIPTION (provided by applicant): In this proposal, we request whole genome sequencing (WGS) services of 923 individuals from our cohort of well-characterized, large multigenerational nonsyndromic cleft lip/palate (NSCLP) families of Hispanic and non-Hispanic white ethnicities. NSCLP is a common birth defect accounting for 65% of all birth defects and annually affecting approximately 135,000 newborns worldwide. Despite improvement in treatments, NSCLP imposes significant medical, psychosocial and financial burdens that affect quality of life of affected individuals and their families. NSCLP is complex, caused by genetic and environmental factors, and their interactions. Recent advances in genomic approaches have improved our knowledge of the genetic factors involved in NSCLP; however, most of the variants associated with NSCLP account for ~25% of the genetic liability and reflect common, modest risk-variants often located in noncoding regions of the genome. More recently, it has been suggested that some genetic risk for NSCLP lies in rare variants and this has contributed to the lack of consistent findings and difficulty in unraveling risk alleles. Further, it is likely that the missing heritability of NSCLP result in part due to interactions between common, modest risk variants and rare, high-risk variants. We will analyze WGS data and apply polygenic risk score analysis to identify novel, high-penetrance NSCLP variants and to systematically evaluate the contributions of both common and rare variants to NSCLP, and how they segregate individually and in concert within and between families. The results of this study will provide novel and important insights about the genetic architecture contributing to the complex etiology of NSCLP. Importantly, this proposal will translate into a rich and publicly available resource of NSCLP genotypic and phenotypic data that will be made available to the broader scientific community to foster additional studies on NSCLP, as well as other birth defects and/or associated co-morbidities. Further, this proposal will provide genotype and allele frequency data in Hispanics for which limited data is available on genetic databases. Additional follow-up studies proposed, although beyond the scope of this X01 application, include validating the variants identified in this study in our additional NSCLP trios as well as through joint analysis with data from additional existing Kids First datasets. Successful completion of this study will provide novel and important insights about the genetic architecture contributing to the complex etiology of NSCLP, and will translate into a large, rich resource for genetic and phenotypic information on NSCLP. | |||
| Project Number: | CA267638-01 | Contact PI / Project Leader: | Lupo, Philip J |
| Title: | Genetic Overlap Between Anomalies and Cancer in Kids in the Childrens Oncology Group: The COG GOBACK Study | Awardee Organization: | Baylor College Of Medicine |
| Abstract: DESCRIPTION (provided by applicant): One of the strongest risk factors for cancer in children and adolescents is being born with a congenital anomaly— this is true both for chromosomal abnormalities (e.g., Down syndrome) and non-chromosomal birth defects (e.g., non-syndromic congenital heart defects), as recently validated in our registry linkage study of over 10 million live births. Specifically, by linking data from population-based birth defects and cancer registries in four states included in the Genetic Overlap Between Anomalies and Cancer in Kids (GOBACK) Study, we identified multiple novel congenital anomaly-cancer associations that are not part of known cancer predisposition syndromes. We also observed increasing cancer risk with a corresponding increase in the number of non-chromosomal defects. Children with multiple congenital anomalies (MCAs) who develop cancer are likely a subset of individuals enriched for cancer predisposition syndromes that have yet to be identified. There are two unanswered questions that limit clinical translation of these findings. Specifically, it is not clear: 1) what proportion of these associations may be due to known cancer predisposition variants; and 2) if novel cancer predisposition syndromes might underlie these observed associations. These gaps limit genetic testing and counseling strategies for these families. Our central hypothesis is the co-occurrence of congenital anomalies and cancer results from molecular etiologies identifiable through genomic evaluation. Our hypothesis is built on rigorous prior research, including findings from the GOBACK Registry Linkage Cohort and whole-genome sequencing (WGS) on a subset of children enrolled in the GOBACK Family Cohort. Our proposed Kids First study leverages several robust and existing resources, including: 1) matched tumor-normal samples from children with congenital anomalies and cancer without a reported syndrome (N=500) enrolled as part of the Children's Oncology Group (COG) APEC14B1 protocol (Project: EveryChild or PEC); 2) an approved COG protocol that allows for WGS of these samples; 3) an ongoing study to recontact these families to obtain additional phenotypic data; 4) our established bioinformatic pipelines to evaluate the role of rare variants consistent with autosomal dominant, recessive, or X- linked disorders; and 5) the expanded GOBACK Registry Linkage Cohort representing >35% of the U.S. population, which can be used to evaluate associations and WGS findings observed in PEC. Our central hypothesis will be evaluated in two aims: 1) determine the frequency of known cancer predisposition variants among children with congenital anomalies and cancer; and 2) identify variants that underlie novel anomaly- cancer predisposition syndromes and describe the landscape of somatic alterations in these children. By extending our integrated population-based and genomic approach, this application has the potential to: 1) generate novel insights into the developmental pathways that lead to cancer; 2) identify new cancer susceptibility syndromes; and 3) subsequently lead to improved cancer surveillance strategies for children with congenital anomalies. | |||
| Project Number: | CA267576-01 | Contact PI / Project Leader: | Meshinchi, Soheil |
| Title: | Germline and Somatic Variants in Pediatric AML | Awardee Organization: | Fred Hutchinson Cancer Research Center |
| Abstract: DESCRIPTION (provided by applicant): Advances in genomic sequencing have allowed identification of somatic variants as potential therapeutic targets. Although myeloid disorders in children may show morphologic similarities to that seen in adults, TARGET AML initiative (Meshinchi, PI) clearly demonstrated that somatic genomic and transcriptome variants are highly distinct in children and young adults. In fact, there are a number of variants that are uniquely restricted to younger children. TARGET AML initiative, although modest in number, helped identify numerous somatic alterations with high therapeutic potential in younger AML patients. In addition to identification of somatic variants, analysis of the germline data provided a glimpse into the constitutional make-up of patients with AML. The identification of numerous “function altering” variants may provide an insight into possible interactions between the host and the disease, where these germline variants might alter AML risk (predisposition), response to therapy (altering target expression, drug metabolism), susceptibilities to short and long-term complications (including infectious and cardiac complications), or modify risk of secondary malignancies. Armed with data from initial sequencing efforts in AML, we are poised to take full advantage of the available sequencing technology to conduct the most comprehensive genome and transcriptome interrogation of myeloid disorders in children with specimens we have amassed over the last decade. To this end, we have put in place unparalleled specimen resources from children with de novo AML treated on COG AAML1031, to create the most comprehensive genome, transcriptome and epigenome profiling in AML. Our original X01 application providing funding support for whole genome sequencing of approximately half of the patients treated on AAML1031. Given that transcriptome (mRNA, miRNA, LncRNA) and methylation data is available for the entire AAML1031 cohort, completion of the genomic sequencing will provide completion of the profiling effort in this single trial cohort. The data provided by the prior X01 sequencing effort has yielded unparalleled data in defining novel therapeutic targets, prognostic biomarkers and have informed of germline variants that are associated with cancer predisposition. Also, germline variants can be exploited to identify those that might be at high risk of adverse events (cardiac complications, secondary malignancies, etc.) and their therapy tailored to minimize anticipated complications. Thus, we propose that the optimum outcome can only be obtained thru comprehensive interrogation of the somatic and germline genome to fully annotate the genomic makeup of the leukemia and its host. | |||
| Project Number: | CA267587-01 | Contact PI / Project Leader: | Resnick, Adam Cain |
| Title: | Germline and Somatic Disease Modifiers of Pediatric Brain Tumors | Awardee Organization: | Children's Hospital Of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Brain tumors are the most common form of cancer in children aged 0-19 in the United States, and are the largest cause of cancer-related deaths. The estimated number of new cases in 2019 is nearly 3,800 and thus brain tumors are a rare disease. Despite their relative rarity, the years of potential life lost due to brain tumors in 2009 was estimated at 47,631 years for children and adolescents aged 0-19 in the United States; this is a disproportionate amount of life lost compared to adult cancers and represents an unrecognized societal threat. There is an urgent need to improve therapies for these children. Most of the high-grade glial and embryonal brain cancers still remain largely incurable despite decades of clinical and laboratory research. Existing non-targeted chemotherapies and radiation, while at times effective, often represent pyrrhic victories, leaving behind life-long health burdens and causing a significant risk of secondary malignancies. NIH funded pediatric brain tumor cohort-based genomic dataset generation efforts have lagged behind other histologies and have yet to be included as part of large-scale sequencing efforts. However, consortia-based initiatives like those supported by the Children's Brain Tumor Network (CBTN) have demonstrated the early potential for clinically annotated genomic cohorts and their utility and interest by both the pediatric cancer and structural birth defect community with more than 130 data access requests for a non-embargoed cohort of tumor/normal whole genomes and paired tumor RNAseq. Indeed more than one quarter of this 800-subject initial sequencing cohort were identified to have birth-defect-associated clinical annotations in their clinical records, however, to our knowledge limited to no trio-based genomics cohort studies exist for any one pediatric brain tumor histology. The project's proposed sequencing cohort defines the largest, clinically annotated pediatric brain tumor cohort study to date and seeks to define the intersection of germline and somatic underpinnings of pediatric brain tumors across a shared developmental context of cancer and structural birth defects. | |||
| Project Number: | CA267639-01 | Contact PI / Project Leader: | Scheurer, Michael E |
| Title: | Genomic Analysis of Histiocytosis | Awardee Organization: | Baylor College Of Medicine |
| Abstract: DESCRIPTION (provided by applicant): Langerhans cell histiocytosis (LCH) is an inflammatory myeloid neoplasm characterized by lesions including pathogenic CD207+ dendritic cells among an inflammatory infiltrate. The median age at diagnosis is 30 months, and up-front chemotherapy fails in ~50% of patients resulting in multiple relapse events for 40-50% of cases, and long-term sequelae. Sequencing studies have found recurrent, mutually exclusive somatic activating mutations in MAPK pathway genes in ~85% of LCH lesions, including BRAF V600E in 50-65%. There is a “Misguided Myelomonocytic Precursor Model” in which specific somatic MAPK mutations at critical stages of myeloid differentiation determine extent of disease. However, this model fails to explain the significant differences in LCH risk across ethnicities. Despite advances to elucidate the somatic mutational landscape underlying LCH pathogenesis, germline risk factors remain largely unknown. Therefore, we conducted the first genome-wide association study of LCH and identified a SMAD6 variant associated with increased risk. SMAD6 inhibits bone morphogenetic protein and transforming growth factor-beta/activin signaling, which are determinants of Langerhans cell differentiation. This variant appears to suppress SMAD6 protein expression without a decrease in SMAD6 messenger RNA expression in patients carrying the risk allele. This risk allele is also more common in Hispanics who are at the highest risk of LCH, and absent in blacks who experience the lowest LCH incidence. Our preliminary data also support the emerging observation that LCH somatic activating mutations vary by race/ethnicity. Specifically, sequencing of tumors from black patients indicated that only 25% were BRAF V600E+ (compared to >60% in other populations), whereas 50% had mutations in MAP2K1 (compared to < 10% in other populations). Therefore, the objective of this Kids First X01 application is to more fully elucidate LCH etiology by defining the role of de novo mutations (DNMs) in established LCH genes and novel susceptibility genes, and by comprehensively assessing somatic variation in LCH. Our central hypothesis is that penetrant DNMs and novel germline and somatic variation may contribute to, or in some cases, drive LCH tumorigenesis. 1) We will leverage our ongoing Children's Oncology Group study, Genetic Epidemiology of Childhood Histiocytosis (GECHO), to sequence 300 LCH case-parent trios to evaluate the impact of recurrent DNMs on inherited susceptibility to LCH. 2) We will leverage paired germline-tumor samples from 200 patients enrolled to the Texas Children's Histiocytosis Program protocol or GECHO study to comprehensively assess the somatic landscape of LCH and identify germline variation contributing to somatic mutational profiles. Successful completion of the proposed aims may (1) improve genetic testing and counseling strategies in LCH patients and families; (2) advance surveillance and chemoprevention protocols; and (3) identify novel therapeutic targets. | |||
2020 X01 Projects
| Project Number: | HL155060-01 | Contact PI / Project Leader: | Chung, Wendy K |
| Title: | Genomic Analysis of Congenital Diaphragmatic Hernia | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Congenital diaphragmatic hernia (CDH) is defined as a defect in the muscular or tendinous portion of diaphragm that results in antenatal herniation of the abdominal contents into the thoracic cavity and pulmonary hypoplasia due to compression of the lungs and/or primary abnormalities in lung development. The incidence of CDH is 1 in 3000 live births, accounting for 1-2% of infant mortality and 8% of all birth defects, making it one of the most common and lethal congenital anomalies. CDH is isolated in 50-60% of cases but is associated with other major anomalies, most commonly congenital heart disease or central nervous system malformations, in the remaining 40-50%. Historically CDH carried a grave prognosis with mortality of greater than 50%. However, with recent advances in the post-natal care of children with CDH, survival has improved significantly. However, with improved survival, many of the long-term morbidities of CDH have been exposed including pulmonary hypertension, the leading cause of CDH morbidity and mortality. In addition, a subset of children with CDH demonstrate significant developmental delay and intellectual disabilities. Many parents and prospective parents seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. The etiology of CDH is largely unknown. Many birth defects can result from rare de novo mutations and inherited rare variants. We propose to identify genes that increase the risk of CDH by performing whole genome sequencing on parent child trios and singletons and RNA sequencing of diaphragm tissue in a clinically well characterized cohort to identify de novo mutations and inherited rare variants. Our long-term goal is to define a set of genes important in the etiology of CDH and characterize new clinical syndromes associated with CDH. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information. PUBLIC HEALTH RELEVANCE: Congenital diaphragmatic hernia (CDH) is a serious birth defect accounting for 1-2% of infant mortality and 8% of all birth defects. We propose to elucidate the underlying genomic architecture of CDH by performing whole genome sequencing and RNA sequencing on diaphragm tissue to characterize new clinical syndromes associated with CDH to provide more accurate clinical prognostic information. | |||
| Project Number: | DE030062-01 | Contact PI / Project Leader: | Marazita, Mary |
| Title: | Kids First: Genomics of Orofacial Cleft Birth Defects in Families from Puerto Rico, Central and South America | Awardee Organization: | University of Pittsburgh |
| Abstract: DESCRIPTION (provided by applicant): Nonsyndromic orofacial clefts (OFCs) of the lip (CL), palate (CP), or both (CLP) occur in about 1/700 live births worldwide, and thus comprise a significant proportion of human structural birth defects. OFCs require surgical, nutritional, dental, speech, medical, and behavioral interventions, and thus impose substantial public health, economic, and personal burdens. On average a child with an OFC initially faces feeding difficulties, undergoes 6 surgeries, spends 30 days in hospital, receives 5 years of orthodontic treatment, and participates in ongoing speech therapy, leading to an estimated total lifetime treatment cost of about $200,000. Further, individuals born with an OFC have higher infant mortality, higher mortality rates at all other stages of life, increased incidence of mental health problems, and higher risk for other disorders (notably including breast, brain, and colon cancers). The etiology of OFCs is complex, and includes a major genetic component, with approximately 30 associated loci identified to date. However, critical gaps in our understanding persist, as previously discovered variants explain only a portion of the heritable risk for OFCs. Notably there are distinct ethnic differences in the epidemiological patterns of OFCs, which may reflect underlying genetic differences, such as different primary risk genes, or different frequencies of risk alleles. A major goal of our overall research strategy is to apply genomic approaches in families from multiple populations world-wide. Latin American families are at high risk for OFC birth defects and the goal of the current new project is to apply whole genome sequencing (WGS) to better understand the genetic architecture of OFCs in Latin America. Prior GMKF WGS of 276 Colombian trios from our study identified a novel locus on chromosome 21, illustrating the utility of analyses in Latin Americans which are one of the population groups at highest risk for OFC. The goal of this new study is to apply WGS in additional Latin American trios (available are 844 trios not overlapping previous WGS efforts), adding trios from Puerto Rico, Guatemala, Argentina and other sites to continue to seek Latin American specific OFC risk loci in these new trios, and for meta-analyses with the other existing GMKF OFC trios (including the prior 276 Colombian trios). PUBLIC HEALTH RELEVANCE: Latin American families are at high risk for orofacial cleft birth defects such as cleft lip and cleft palate. The goal of this project is to better understand the genetic architecture of these birth defects by performing whole genome sequencing in Latin American families. | |||
| Project Number: | HL155057-01 | Contact PI / Project Leader: | Weaver, Kathryn |
| Title: | Genetic diagnoses in a cohort of individuals with valvar pulmonary stenosis | Awardee Organization: | Cincinnati Children's Hospital Medical Center |
| Abstract: DESCRIPTION (provided by applicant): Congenital heart disease (CHD) affects 1% of live births and has both monogenic and multifactorial causes. There are multiple studies investigating genetic contribution to specific cardiac defects, e.g. left ventricular outflow tract obstruction and conotruncal defects. However, the prevalence of genetic diagnoses among individuals with vPS, which accounts for 8-12% of CHD, is unknown. Further, complex etiologies for vPS remain largely unexplored. This is despite studies of familial CHD which indicate that right ventricular outflow tract obstructive defects such as vPS are one of the more heritable forms of CHD. A diagnosis of vPS represents a significant healthcare burden: One quarter of individuals with vPS require invasive treatment with balloon valvuloplasty and/or open heart surgical repair, and a subset of these will require repeat intervention for recurrent valve stenosis, or due to interval development of valve insufficiency/regurgitation. Several genetic syndromes are associated with vPS, most commonly Noonan syndrome, but etiology is unknown in the majority of cases. Individuals with vPS due to Noonan syndrome are more likely to require intervention and re-intervention; however, many studies about vPS outcomes predated currently available genetic sequencing technology. We recently performed a retrospective analysis showing that 6% of 204 children (aged 0-4 years) with vPS have a Noonan syndrome spectrum diagnosis and 10% have a genetic diagnosis; however, only 18% of the cohort had a genetic evaluation. We subsequently analyzed a cohort of 105 probands with vPS in the Pediatric Cardiac Consortium (PCGC) cohort who had trio exome and phenotypic data available. Overall, 20 (19%) had a likely genetic etiology identified with exome sequencing, twice the incidence of genetic diagnosis in our cohort of 204, the majority of whom had not had a genetics evaluation. This suggests that genetic contribution to vPS may be under recognized. We propose whole genome sequencing (WGS) on a multi-institutional cohort of individuals with vPS. This includes 109 trios, 101 parent/proband duos, and 364 singletons, for a total of 574 probands, from two major children’s hospitals and the PCGC. Analysis of WGS data will accomplish the following three specific aims: 1) determine the prevalence of known genetic diagnoses among a cohort of individuals with vPS, 2) identify candidate genes for vPS, and 3) identify genes and pathways with high variant burden in individuals with vPS. Results of our study could impact genetic testing recommendations for infants and children with a new diagnosis of vPS. Earlier diagnosis of genetic disorders and understanding how genetic variants contribute to pathogenesis and ultimately outcomes of vPS can improve health and developmental outcomes by allowing anticipatory rather than reactionary guidance and management. PUBLIC HEALTH RELEVANCE: Congenital heart disease affects 1 in 100 live births and valvar pulmonary stenosis accounts for 8-10% of congenital heart disease. We propose whole genome sequencing in a large cohort of individuals with valvar PS in order to determine the prevalence of known genetic disorders, as well as identify candidate novel genes. This type of study and data is essential for being able to understand the genetic etiology of congenital heart disease. | |||
2020 X01 Projects
| Project Number: | HL155060-01 | Contact PI / Project Leader: | Chung, Wendy K |
| Title: | Genomic Analysis of Congenital Diaphragmatic Hernia | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Congenital diaphragmatic hernia (CDH) is defined as a defect in the muscular or tendinous portion of diaphragm that results in antenatal herniation of the abdominal contents into the thoracic cavity and pulmonary hypoplasia due to compression of the lungs and/or primary abnormalities in lung development. The incidence of CDH is 1 in 3000 live births, accounting for 1-2% of infant mortality and 8% of all birth defects, making it one of the most common and lethal congenital anomalies. CDH is isolated in 50-60% of cases but is associated with other major anomalies, most commonly congenital heart disease or central nervous system malformations, in the remaining 40-50%. Historically CDH carried a grave prognosis with mortality of greater than 50%. However, with recent advances in the post-natal care of children with CDH, survival has improved significantly. However, with improved survival, many of the long-term morbidities of CDH have been exposed including pulmonary hypertension, the leading cause of CDH morbidity and mortality. In addition, a subset of children with CDH demonstrate significant developmental delay and intellectual disabilities. Many parents and prospective parents seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. The etiology of CDH is largely unknown. Many birth defects can result from rare de novo mutations and inherited rare variants. We propose to identify genes that increase the risk of CDH by performing whole genome sequencing on parent child trios and singletons and RNA sequencing of diaphragm tissue in a clinically well characterized cohort to identify de novo mutations and inherited rare variants. Our long-term goal is to define a set of genes important in the etiology of CDH and characterize new clinical syndromes associated with CDH. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information. PUBLIC HEALTH RELEVANCE: Congenital diaphragmatic hernia (CDH) is a serious birth defect accounting for 1-2% of infant mortality and 8% of all birth defects. We propose to elucidate the underlying genomic architecture of CDH by performing whole genome sequencing and RNA sequencing on diaphragm tissue to characterize new clinical syndromes associated with CDH to provide more accurate clinical prognostic information. | |||
| Project Number: | DE030062-01 | Contact PI / Project Leader: | Marazita, Mary |
| Title: | Kids First: Genomics of Orofacial Cleft Birth Defects in Families from Puerto Rico, Central and South America | Awardee Organization: | University of Pittsburgh |
| Abstract: DESCRIPTION (provided by applicant): Nonsyndromic orofacial clefts (OFCs) of the lip (CL), palate (CP), or both (CLP) occur in about 1/700 live births worldwide, and thus comprise a significant proportion of human structural birth defects. OFCs require surgical, nutritional, dental, speech, medical, and behavioral interventions, and thus impose substantial public health, economic, and personal burdens. On average a child with an OFC initially faces feeding difficulties, undergoes 6 surgeries, spends 30 days in hospital, receives 5 years of orthodontic treatment, and participates in ongoing speech therapy, leading to an estimated total lifetime treatment cost of about $200,000. Further, individuals born with an OFC have higher infant mortality, higher mortality rates at all other stages of life, increased incidence of mental health problems, and higher risk for other disorders (notably including breast, brain, and colon cancers). The etiology of OFCs is complex, and includes a major genetic component, with approximately 30 associated loci identified to date. However, critical gaps in our understanding persist, as previously discovered variants explain only a portion of the heritable risk for OFCs. Notably there are distinct ethnic differences in the epidemiological patterns of OFCs, which may reflect underlying genetic differences, such as different primary risk genes, or different frequencies of risk alleles. A major goal of our overall research strategy is to apply genomic approaches in families from multiple populations world-wide. Latin American families are at high risk for OFC birth defects and the goal of the current new project is to apply whole genome sequencing (WGS) to better understand the genetic architecture of OFCs in Latin America. Prior GMKF WGS of 276 Colombian trios from our study identified a novel locus on chromosome 21, illustrating the utility of analyses in Latin Americans which are one of the population groups at highest risk for OFC. The goal of this new study is to apply WGS in additional Latin American trios (available are 844 trios not overlapping previous WGS efforts), adding trios from Puerto Rico, Guatemala, Argentina and other sites to continue to seek Latin American specific OFC risk loci in these new trios, and for meta-analyses with the other existing GMKF OFC trios (including the prior 276 Colombian trios). PUBLIC HEALTH RELEVANCE: Latin American families are at high risk for orofacial cleft birth defects such as cleft lip and cleft palate. The goal of this project is to better understand the genetic architecture of these birth defects by performing whole genome sequencing in Latin American families. | |||
| Project Number: | HL155057-01 | Contact PI / Project Leader: | Weaver, Kathryn |
| Title: | Genetic diagnoses in a cohort of individuals with valvar pulmonary stenosis | Awardee Organization: | Cincinnati Children's Hospital Medical Center |
| Abstract: DESCRIPTION (provided by applicant): Congenital heart disease (CHD) affects 1% of live births and has both monogenic and multifactorial causes. There are multiple studies investigating genetic contribution to specific cardiac defects, e.g. left ventricular outflow tract obstruction and conotruncal defects. However, the prevalence of genetic diagnoses among individuals with vPS, which accounts for 8-12% of CHD, is unknown. Further, complex etiologies for vPS remain largely unexplored. This is despite studies of familial CHD which indicate that right ventricular outflow tract obstructive defects such as vPS are one of the more heritable forms of CHD. A diagnosis of vPS represents a significant healthcare burden: One quarter of individuals with vPS require invasive treatment with balloon valvuloplasty and/or open heart surgical repair, and a subset of these will require repeat intervention for recurrent valve stenosis, or due to interval development of valve insufficiency/regurgitation. Several genetic syndromes are associated with vPS, most commonly Noonan syndrome, but etiology is unknown in the majority of cases. Individuals with vPS due to Noonan syndrome are more likely to require intervention and re-intervention; however, many studies about vPS outcomes predated currently available genetic sequencing technology. We recently performed a retrospective analysis showing that 6% of 204 children (aged 0-4 years) with vPS have a Noonan syndrome spectrum diagnosis and 10% have a genetic diagnosis; however, only 18% of the cohort had a genetic evaluation. We subsequently analyzed a cohort of 105 probands with vPS in the Pediatric Cardiac Consortium (PCGC) cohort who had trio exome and phenotypic data available. Overall, 20 (19%) had a likely genetic etiology identified with exome sequencing, twice the incidence of genetic diagnosis in our cohort of 204, the majority of whom had not had a genetics evaluation. This suggests that genetic contribution to vPS may be under recognized. We propose whole genome sequencing (WGS) on a multi-institutional cohort of individuals with vPS. This includes 109 trios, 101 parent/proband duos, and 364 singletons, for a total of 574 probands, from two major children’s hospitals and the PCGC. Analysis of WGS data will accomplish the following three specific aims: 1) determine the prevalence of known genetic diagnoses among a cohort of individuals with vPS, 2) identify candidate genes for vPS, and 3) identify genes and pathways with high variant burden in individuals with vPS. Results of our study could impact genetic testing recommendations for infants and children with a new diagnosis of vPS. Earlier diagnosis of genetic disorders and understanding how genetic variants contribute to pathogenesis and ultimately outcomes of vPS can improve health and developmental outcomes by allowing anticipatory rather than reactionary guidance and management. PUBLIC HEALTH RELEVANCE: Congenital heart disease affects 1 in 100 live births and valvar pulmonary stenosis accounts for 8-10% of congenital heart disease. We propose whole genome sequencing in a large cohort of individuals with valvar PS in order to determine the prevalence of known genetic disorders, as well as identify candidate novel genes. This type of study and data is essential for being able to understand the genetic etiology of congenital heart disease. | |||
2019 X01 Projects
| Project Number: | N/A | Contact PI / Project Leader: | Chung, Wendy K (Contact); Shen, Yufeng |
| Title: | Genomic Analysis of Esophageal Atresia and Tracheoesophageal Fistulas and Associated Congenital Anomalies | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. There is a 45% incidence of associated congenital malformations, most commonly digestive, cardiovascular, urogenital, and musculoskeletal, often part of a syndrome or complex association, with VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities) being most frequently recognized. Advanced surgical techniques and pre and post-operative care have improved the prognosis and survival of EA/TEF patients over the past decades. However, with improved survival, many of the long-term morbidities of EA/TEF have been exposed. It is likely that the outcome in EA/TEF patients is influenced by multiple genetic and clinical factors; however, determining which factors are critical has been limited by the lack of data, particularly genomic data. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of EA/TEF and define new genes and conditions associated with EA/TEF by performing whole genome sequencing (WGS) on 150 additional parent child trios to complement the 140 trios awaiting WGS in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions and improve outcomes and identify genes and pathways causing EA/TEF and other birth defect and neurodevelopmental disorders. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Gharavi, Ali G |
| Title: | Genetics of Structural Defects of the Kidney and Urinary Tract | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) account for up to 50% of pediatric and 7% of adult end-stage kidney failure worldwide. The goal of this project is to apply genetic approaches to resolve the biological basis and clinical manifestations of CAKUT using three well-characterized cohorts with deep phenotypes and extensive longitudinal data. Here, we hypothesize that CAKUT is genetically heterogeneous, and caused by rare mutations with large effect on a background of polygenes with small effects that can be discovered by analysis of well phenotyped cohorts compared to genetically matched cohorts with WGS data available. We now propose to extend our prior studies by whole genome sequencing (GWS) in 510 trios with CAKUT. We expect that the proposed studies will provide new insight into urogenital development, clarify the clinical overlap with other syndromes and provide novel tools that can replace the current morphology-based diagnostic approaches. We will first perform annotation based on a standard ACMG guidelines to identify pathogenic CNVs and single nucleotide variants diagnostic for known genetic disorders. In aim 2, we will perform analysis of de-novo mutations in coding and non-coding mutation to detect new genes for CAKUT. We will next replicate top signals in additional CAKUT cohorts available in our laboratory. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Gleeson, Joseph G |
| Title: | Whole Exome and Genome Sequencing in Structural Defects of The Neural Tube | Awardee Organization: | University of California, San Die |
| Abstract: DESCRIPTION (provided by applicant): Myelomeningocele (MM) is the most severe form of spina bifida (SB), a neural tube defect (NTD) in humans and the most common CNS birth defect. This defect occurs in 3.72/10,000 live US birth, and is partly preventable with prenatal folate, but the genetic basis and the mechanisms by which folate work remains obscure. MM is associated nearly uniformly with prenatal hydrocephalus and the Arnold-Chiari malformation, as well as paraplegia and lifelong disability. The genes for several syndromic forms of NTDs are known, but the causes for the majority with sporadic clinical presentation remain unknown. Despite the importance of MM, previous research has been limited to targeted sequencing and association studies of folate metabolism genes, or very small-scale exome sequencing. We hypothesize that de novo loss of function (LOF) mutations contribute to MM risk. Using conservative estimates of between 50-100 recurrently-mutated discoverable genes, and assuming a nominal elevation in the number of de novo LOF alleles in affecteds compared with controls, we estimate that with a cohort size of 500 trios, this effort should uncover between 4-16 new recurrently mutated genes underlying MM, with minimal false-discovery. We have recruited a cohort of 500 simplex MM trios, in collaboration with the US Spina Bifida Association, consented trios to allow for data sharing, and have performed detailed quality control on samples. We have partially sequenced this cohort using philanthropy funds. Here we propose to WGS 100 trios on whom blood-derived DNA is or will be available using, and to WES 150 trios on whom salivaderived DNA is or will be available for this X01 effort to continue this discovery. We have established a workflow for de novo SNP/INDEL/SV detection from WES and WGS, and have ample storage and computational resources to see the project to completion. We also plan to continue recruitment into the future with the goal of 1000 trios in the next 2 years. We propose a detailed bioinformatics workflow to identify gene mutations within a statistical framework, taking into account detailed RNA expression profiling from developing mouse neural tube, and have developed a robust functional validation workflow using Xenopus larvae. Our project has the potential to uncover a host of causes for this most common of the CNS birth defects, paving the way for future breakthroughs in detection, treatment and prevention. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Gleeson, Joseph G |
| Title: | Whole Exome, Genome, and RNA Sequencing in Recessive Structural Brain Defects in Children | Awardee Organization: | University Of California, San Diego |
| Abstract: DESCRIPTION (provided by applicant): Almost 5% of all live births in the US (1:20 births) display an inborn defect, including both structural and functional/metabolic abnormalities. These are among the most common causes of Infant mortality in the developed world and underlie nearly half of hospitalizations in the first 3 years of life. Of the 35 major defects observable at birth from the International Clearinghouse for Birth Defects Surveillance Program ( www.icbdsr.org ), about half involve the nervous system. Many of these result in lifelong neurodevelopmental disorders as a result. Structural Brain Defects (SBDs) result from errors in development of the central nervous system, including defects in the forebrain, midbrain and hindbrain. Many SBDs arise as the consequence of a single gene bi-allelic mutation, and for this reason occur more commonly in populations or communities with elevated consanguinity. Our lab has identified dozens of novel SBD genes using WES/WGS in consanguineous SBD families. Importantly, the genes that we and others have identified in these unique families are then used to advance diagnosis in pediatric SBDs around the world. We have built an enormous cohort of SBD families, including newly recruited families not yet studied genetically, and previous families that were negative for cause following WES analysis. Here we propose to collaborate with the Gabriella Miller Kids First Pediatric Research Program (X01) to have sequencing performed in individuals from a total of 200 families with genetically undiagnosed SBDs. The Gleeson Lab team of researchers is dedicated to the field of SBDs, with an outstanding track record of high-impact science, and a collaborative approach to discovery. We have 150 newly recruited families that we propose to study by WES by sequencing blood-derived DNA from two affected or the parents and one affected. We also have 50 families in which WES was negative, that we propose to study in a multi-omics approach combining WGS from blood-derived DNA and RNAseq from RNA extracted from primary dermal fibroblasts. We anticipate that this study will lead to the identification of many new molecular causes of SBDs, as well as uncover new genotype-phenotype correlations and new disease mechanisms, paving the way for future breakthroughs in detection, treatment and prevention. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Leslie, Elizabeth Jane (Contact); Marazita, Mary L.; Murray, Jeffrey C |
| Title: | Genomics of Orofacial Clefts in the Philippines | Awardee Organization: | Emory University |
| Abstract: DESCRIPTION (provided by applicant): Orofacial clefts (OFCs) are the most common craniofacial structural birth defect in humans caused by incomplete formation of the upper lip and/or the palate. During childhood, affected individuals suffer from feeding difficulties, speech, hearing, and dental problems, and require multiple craniofacial and dental surgeries and ongoing therapies. Although the long-term prognosis is excellent for most individuals with OFCs, they can experience lifelong psychosocial effects, increased mortality rates from all causes, and a higher risk of various cancer types 2,3. The worldwide prevalence of OFCs is approximately 1 in 1000 live births but the observed prevalence is highly variable among ancestry groups. Over 4,000 children in the Philippines are born with an OFC every year and the Filipino OFC birth prevalence rate of 1 in 500 live births is one of the highest in the world. Elucidating the etiology of OFCs is critical not only for our knowledge of developmental biology and for how clefts arise, but ultimately for improved prevention, treatment, and prognosis for individuals affected by this disorder. Genome-wide association studies support a multifactorial etiology for OFCs, but common variants only account for up to ~25% of the heritable risk in any one population. Sequencing studies in diverse populations is essential to fully understand the genetic architecture of OFCs. We propose whole genome sequencing a combination of well-phenotyped case-parent trios, dyads, and additional affected individuals from the Philippines as a discovery sample. We seek to identify de novo mutations and inherited rare variants and will replicate these findings in our larger resource of over 10,000 individuals from the Philippines. Finally, we will combine these data with other Kids First OFC cohorts to compare and contrast the architectures in this high-risk population and to enable discovery of novel risk loci in the combined set of more than 1,000 caseparent trios. Our long-term goals include validation of WGS variants in established functional pipelines. This project is poised to rapidly advance our understanding of the genetic etiology of OFCs in this high-risk population. | |||
| Project Number: | N/A | Contact PI / Project Leader: | upo, Philip J (contact); Plon, Sharon E. |
| Title: | Genomic Analysis of Pediatric Rhabdomyosarcoma | Awardee Organization: | Baylor College of Medicine |
| Abstract: DESCRIPTION (provided by applicant): Rhabdomyosarcoma (RMS) is a highly malignant tumor believed to arise from developing skeletal muscle cells (myoblasts). Relative to other childhood cancers, the prognosis for many children with RMS remains poor. In particular, for those children with high- or intermediate-risk disease, use of maximally intensive therapy and application of new agents since the 1970s has led to only modest improvements in 5-year survival rates, which is currently only 43% to 67%. Ultimately, sarcomas are understudied cancers, and RMS is by far the most common soft tissue sarcoma in children and adolescents. To make advances in this area, complementary and innovative approaches are needed to 1) understand the molecular signatures underlying susceptibility; 2) develop a foundation for improved genetic counseling and clinical surveillance protocols; and 3) discover new therapeutic targets. Very little is known in relation to germline genetic susceptibility to RMS. For instance, based on smaller clinic-based studies, about 5% of RMS cases are thought to be associated with known cancer predisposition genes. However, there have been no population-based assessments to support this estimate, and much work remains to be done to understand the causes of the other 95% which appear to be sporadic. Additionally, there is growing evidence of the importance of de novo germline mutations (DNMs) in the etiology of seemingly sporadic diseases. While there is epidemiologic evidence to support the role of DNMs on the etiology of RMS, there have been no efforts to explore the role of DNMs on this pediatric malignancy. An important and innovative goal of the Gabriella Miller Kids First Pediatric Research Program is to conduct large-scale germline sequencing of well-annotated pediatric cancer patient and parent trios to address important questions about the genetics of childhood cancers. Therefore, the objective of this Kids First X01 application is to address unanswered questions about RMS by determining the role of DNMs in known cancer predisposition genes and in novel susceptibility genes. Our central hypothesis is that highly penetrant DNMs may underlie several childhood cancers, including RMS. Our hypothesis has been formulated on the basis of our preliminary studies. We plan to test our central hypothesis and, thereby, accomplish the objective of this application by pursuing the following two specific aims: 1) identify recurrent DNMs among RMS case-parent trios; and 2) determine the prevalence of mutations in both well-established sarcoma genes and genes identified with recurrent DNMs among children with sporadic RMS. This study represents an important step toward a better understanding of the etiology of these malignancies by combining the study of previously described and newly discovered genes. Ultimately, the findings from this study could lead to 1) improved genetic testing and counseling strategies in RMS patients, 2) advanced surveillance and chemoprevention protocols, and 3) the identification of novel therapeutic targets for this highly fatal tumor. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Martin, Donna M. |
| Title: | Genomic Etiologies of CHARGE Syndrome, Related Conditions and Structural Anomalies | Awardee Organization: | University of Michigan at Ann Arbor |
| Abstract: DESCRIPTION (provided by applicant): Developmental disorders with structural birth defects account for the majority of morbidity and mortality in children’s hospitals, and the genetic bases of many clinical phenotypes remain unknown. Genetic testing for individuals with structural malformations has uncovered the basis of many such birth defects; however, many more cases remain unsolved, posing challenges for diagnosis, treatment, and prevention. Multiple anomaly conditions are particularly challenging to diagnose, since they often present with unique combinations of clinical features that vary widely between affected individuals, even in the same family. CHARGE Syndrome (Coloboma of the eye, Heart Defects, Atresia of the choanae, Retardation of growth and development, Genital abnormalities including pubertal delay and infertility, Ear abnormalities with deafness and vestibular disorders) is a multiple anomaly condition that affects a wide variety of organ systems. CHARGE Syndrome is caused in most cases by monoallelic pathogenic variants in CHD7, the gene encoding ATP-dependent helicase chromodomain DNA binding protein 7. Both de novo and inherited variants in CHD7 have been reported in CHARGE, and a growing number of families present with individuals who test positive for a pathogenic CHD7 variant yet exhibit only mild features. Similarly, individuals with CHARGE Syndrome often exhibit broad variability and reduced penetrance of clinical features, consistent with pleiotropic roles for CHD7 during development and/or additional genetic contributors or modifying alleles. We hypothesize that (1) some cases of CHARGE are due to other genetic etiologies including oligogenicity, and (2) genetic modifiers contribute to the broad clinical variability and reduced penetrance of CHARGE features. To address these hypotheses, we have generated a cohort of 100 deeply clinically phenotyped individuals with CHARGE Syndrome and related disorders and structural anomalies who tested negative by chromosomal microarray, single gene sequencing, next generation panel sequencing, or exome sequencing. These individuals exhibit clinical CHARGE-like features including structural birth defects affecting craniofacial, ocular, neurosensory, brain, heart, mediastinal, renal, genitourinary, and skeletal organs. Our cohort includes affected and unaffected family members who consented to clinical and research genetic testing and donated blood samples for DNA and RNA isolation and sequencing. Building on this valuable cohort, we propose to use exome and genome sequencing to identify novel genetic etiologies of CHARGE and related developmental disorders for which alternative genetic tests have been inconclusive. Identification of novel pathogenic genetic variants and contributing modifier alleles within the coding and non-coding portion of the genome of these individuals will improve genetic diagnosis and provide important insights toward understanding the developmental mechanisms of structural birth defects. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Poynter, Jenny N. |
| Title: | Genetic susceptibility of extracranial germ cell tumors | Awardee Organization: | University of Minnesota |
| Abstract: DESCRIPTION (provided by applicant): Pediatric malignant germ cell tumors (GCTs) represent approximately 6% of childhood cancers, including 3% of tumors in children aged 0-14 years and 15% of tumors in adolescents. GCTs are heterogeneous and grouped together due to the presumed common cell of origin, the primordial germ cell (PGC). GCTs typically occur in the testes or ovaries; however, extragonadal GCTs can occur and are likely a result of abnormal germ cell migration during development. Evidence suggests that GCTs, including those diagnosed in adults, are initiated in utero. Thus, alterations in normal embryonic development are likely to be especially relevant to GCT etiology. Germline susceptibility has not been evaluated in an agnostic fashion in GCT, mainly due to a lack of an adequate number of samples. However, we can gain some knowledge from studies of adult testicular GCT (TGCT), which also arise from the PGC. The high heritability of TGCT suggests a genetic etiology, and recent genomewide association studies support this through the discovery of multiple susceptibility loci. We recently confirmed a subset of these loci as susceptibility variants for pediatric GCT. Our overarching goal for the proposed study is to understand the genomics of pediatric GCT, including both germline and tumor samples. In our recently completed NIH-funded case parent triad study (“Molecular Epidemiology of Pediatric Germ Cell Tumors”; R01 CA151284), we recruited GCT cases and their parents through the Children’s Oncology Group (COG) Childhood Cancer Research Network. In this study, we collected germline DNA for 867 GCT patients between the ages of 0-19 years at diagnosis, including 677 families with DNA samples for the complete trio. The intracranial GCT cases from this study will be included in a project selected for funding by the Gabriela Miller Kids First Sequencing program in 2018 (X01 HL145700; PIs Lau and Poynter). In the current proposal, we are proposing to use WGS and WES to evaluate the following specific aims in the extracranial (testicular, ovarian, and extragonadal) GCTs recruited for this study. In this project, we will: 1) Evaluate the contribution of rare genetic variants in GCT through the use of aggregate burden tests, focusing on genes and established regulatory regions; 2) Identify de novo SNVs and CNVs in pediatric GCT using a case-parent triad design; and 3) Identify molecular signatures in GCT tumor specimens, overall and by age group and tumor characteristics. Whole Genome Sequencing data generated through the Gabriella Miller Kids First Pediatric Research Program will provide an opportunity to investigate the genetic origins of GCT in a diverse set of samples. Given the limited knowledge of GCT etiology and biology, the results of the proposed analyses are likely to have a big impact on the field. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Teachey, David T (Contact), Mullighan, Charles G |
| Title: | Comprehensive Genomic Profiling to Improve Prediction of Clinical Outcome for Children with T-cell Acute Lymphoblastic Leukemia | Awardee Organization: | Children's Hospital of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): The outcome for patients with relapsed T-ALL is dismal with 3-year event free survival of <15%. Thus, the primary goal in the treatment of T-ALL is to prevent relapse, which requires accurate risk stratification. Unfortunately, no genetic alterations have been identified to date that are reproducibly prognostic independent of minimal residual disease (MRD), making it difficult at diagnosis to identify which patients are more likely to relapse. AALL0434 was a Children’s Oncology Group-initiated phase 3 randomized clinical trial comparing Capizzi-style escalating methotrexate plus pegaspargase (CMTX) vs. high dose methotrexate (HDMTX), with/without six 5-day courses of nelarabine. Survival on this study was superior to any prior trial for de novo T-ALL, changing the standard of care. Yet, a substantial minority (~15%) of patients had relapsed or refractory (r/r) disease. We recently performed RNA sequencing, DNA copy number analysis, and whole-exome sequencing on 264 T-ALL patients treated on AALL0434, demonstrating recurrent alterations could be grouped into 10 different potentially targetable functional pathways. This analysis was not powered to examine associations between genetic lesions with outcome, because too few patients with r/r disease were included. We hypothesize that comprehensive genomic profiling of the entire AALL0434 cohort will identify recurrent genetic alterations that can be segregated into biologically relevant deregulated pathways that can be combined with MRD to identify patients at risk for poor outcomes before they relapse and provide rationale for treatment with alternative therapies. In addition, a number of small recent studies demonstrated that many of the biologically relevant alterations in T-ALL occur in non-coding regions of the genome, but no large studies have performed whole genome sequencing in T-ALL. We further hypothesize that whole genome sequencing of a large cohort of patients with T-ALL will identify novel lesions in coding and non-coding regions that will be highly impactful in the understanding of T-ALL pathogenesis. We will test our hypotheses by performing comprehensive genomic profiling (whole genome sequencing, whole exome sequencing, RNA sequencing, and copy number analysis) of the entire AALL0434 cohort (n = 1430) with the following specific aims: (1) identify recurrent genetic alterations that predict poor outcome in T-ALL; (2) identify novel alterations, including non-coding alterations in T-ALL; and (3) identify germline genetic variants that predispose to T-ALL and to increased toxicity to nelarabine. The goal of the Kids First Program is to improve understanding of genetic mechanisms of disease, leading to improved diagnostic capabilities and ultimately more targeted therapies or interventions. This proposal will meet that important goal through identification of germline and somatic alterations in T-ALL that can be used to identify patients that are likely to relapse before they relapse and can be treated with new therapies. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Ware, Stephanie |
| Title: | Genomic Analysis of Laterality Birth Defects | Awardee Organization: | Indiana Univ-Purdue Univ at Indianapolis |
| Abstract: DESCRIPTION (provided by applicant): Laterality defects occur in approximately 1:10,000 newborns and are associated with a range of structural birth defects and abnormalities of organ positioning. Gut malrotation, biliary atresia, asplenia or polysplenia, complex cardiovascular malformations, and midline defects such as neural tube defects, vertebral anomalies and rib fusions are found in various combinations in patients with laterality defects. In addition, a subset of laterality defects caused by abnormalities of cilia position or function are associated with additional medical problems such as chronic sinusitis and bronchiectasis that require specific preventive care; however these patients frequently are undiagnosed until late in disease course. The clinical picture firmly establishes laterality defects as not only diseases of significant phenotypic heterogeneity, but also ones of considerable medical and economic consequence. The goal of this project is to elucidate the genetic architecture of laterality defects in order to inform medical management and prevent complications. Laterality disorders are genetically heterogeneous and we and others have previously identified single nucleotide variants inherited in an X-linked or autosomal recessive manner as explanations for a minority of cases. In addition, we have demonstrated copy number variants (CNVs) as a mechanism of disease that requires additional investigation. We hypothesize that the majority of cases result from complex genetic inheritance. We propose to investigate this hypothesis using a multifaceted analysis approach in our extremely well phenotyped cohort of 550 probands with laterality disorders. Included within this cohort are 280 probands who had exome sequencing which was negative for pathogenic variants in 170 clinically relevant laterality genes. However, preliminary data demonstrate increased variant burden in these cases versus controls when interrogating 809 candidate genes important for left-right patterning and cilia function. These samples are excellent candidates for gene discovery and association analyses via whole genome sequencing (WGS) which will allow broader interrogation and expansion of analyses to include non-coding regions and CNVs. We will perform burden analyses to identify genes, gene interactions, and pathways important for susceptibility to laterality disorders. Also nested within our cohort of 550 probands are 105 trios that have not had previous sequencing. All trios will be analyzed by transmission disequilibrium test (TDT) including rare variant TDT. De novo mutations will also be identified from trios for potential gene discovery. This comprehensive genetic analysis in patients with laterality disorders is necessary to identify the appropriate clinical diagnostic testing for risk stratification, to elucidate underlying genetic architecture and facilitate novel gene discovery, and to provide essential knowledge about genes and pathways impacting the development of these birth defects. | |||
2019 X01 Projects
| Project Number: | N/A | Contact PI / Project Leader: | Chung, Wendy K (Contact); Shen, Yufeng |
| Title: | Genomic Analysis of Esophageal Atresia and Tracheoesophageal Fistulas and Associated Congenital Anomalies | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. There is a 45% incidence of associated congenital malformations, most commonly digestive, cardiovascular, urogenital, and musculoskeletal, often part of a syndrome or complex association, with VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities) being most frequently recognized. Advanced surgical techniques and pre and post-operative care have improved the prognosis and survival of EA/TEF patients over the past decades. However, with improved survival, many of the long-term morbidities of EA/TEF have been exposed. It is likely that the outcome in EA/TEF patients is influenced by multiple genetic and clinical factors; however, determining which factors are critical has been limited by the lack of data, particularly genomic data. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of EA/TEF and define new genes and conditions associated with EA/TEF by performing whole genome sequencing (WGS) on 150 additional parent child trios to complement the 140 trios awaiting WGS in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions and improve outcomes and identify genes and pathways causing EA/TEF and other birth defect and neurodevelopmental disorders. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Gharavi, Ali G |
| Title: | Genetics of Structural Defects of the Kidney and Urinary Tract | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) account for up to 50% of pediatric and 7% of adult end-stage kidney failure worldwide. The goal of this project is to apply genetic approaches to resolve the biological basis and clinical manifestations of CAKUT using three well-characterized cohorts with deep phenotypes and extensive longitudinal data. Here, we hypothesize that CAKUT is genetically heterogeneous, and caused by rare mutations with large effect on a background of polygenes with small effects that can be discovered by analysis of well phenotyped cohorts compared to genetically matched cohorts with WGS data available. We now propose to extend our prior studies by whole genome sequencing (GWS) in 510 trios with CAKUT. We expect that the proposed studies will provide new insight into urogenital development, clarify the clinical overlap with other syndromes and provide novel tools that can replace the current morphology-based diagnostic approaches. We will first perform annotation based on a standard ACMG guidelines to identify pathogenic CNVs and single nucleotide variants diagnostic for known genetic disorders. In aim 2, we will perform analysis of de-novo mutations in coding and non-coding mutation to detect new genes for CAKUT. We will next replicate top signals in additional CAKUT cohorts available in our laboratory. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Gleeson, Joseph G |
| Title: | Whole Exome and Genome Sequencing in Structural Defects of The Neural Tube | Awardee Organization: | University of California, San Die |
| Abstract: DESCRIPTION (provided by applicant): Myelomeningocele (MM) is the most severe form of spina bifida (SB), a neural tube defect (NTD) in humans and the most common CNS birth defect. This defect occurs in 3.72/10,000 live US birth, and is partly preventable with prenatal folate, but the genetic basis and the mechanisms by which folate work remains obscure. MM is associated nearly uniformly with prenatal hydrocephalus and the Arnold-Chiari malformation, as well as paraplegia and lifelong disability. The genes for several syndromic forms of NTDs are known, but the causes for the majority with sporadic clinical presentation remain unknown. Despite the importance of MM, previous research has been limited to targeted sequencing and association studies of folate metabolism genes, or very small-scale exome sequencing. We hypothesize that de novo loss of function (LOF) mutations contribute to MM risk. Using conservative estimates of between 50-100 recurrently-mutated discoverable genes, and assuming a nominal elevation in the number of de novo LOF alleles in affecteds compared with controls, we estimate that with a cohort size of 500 trios, this effort should uncover between 4-16 new recurrently mutated genes underlying MM, with minimal false-discovery. We have recruited a cohort of 500 simplex MM trios, in collaboration with the US Spina Bifida Association, consented trios to allow for data sharing, and have performed detailed quality control on samples. We have partially sequenced this cohort using philanthropy funds. Here we propose to WGS 100 trios on whom blood-derived DNA is or will be available using, and to WES 150 trios on whom salivaderived DNA is or will be available for this X01 effort to continue this discovery. We have established a workflow for de novo SNP/INDEL/SV detection from WES and WGS, and have ample storage and computational resources to see the project to completion. We also plan to continue recruitment into the future with the goal of 1000 trios in the next 2 years. We propose a detailed bioinformatics workflow to identify gene mutations within a statistical framework, taking into account detailed RNA expression profiling from developing mouse neural tube, and have developed a robust functional validation workflow using Xenopus larvae. Our project has the potential to uncover a host of causes for this most common of the CNS birth defects, paving the way for future breakthroughs in detection, treatment and prevention. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Gleeson, Joseph G |
| Title: | Whole Exome, Genome, and RNA Sequencing in Recessive Structural Brain Defects in Children | Awardee Organization: | University Of California, San Diego |
| Abstract: DESCRIPTION (provided by applicant): Almost 5% of all live births in the US (1:20 births) display an inborn defect, including both structural and functional/metabolic abnormalities. These are among the most common causes of Infant mortality in the developed world and underlie nearly half of hospitalizations in the first 3 years of life. Of the 35 major defects observable at birth from the International Clearinghouse for Birth Defects Surveillance Program ( www.icbdsr.org ), about half involve the nervous system. Many of these result in lifelong neurodevelopmental disorders as a result. Structural Brain Defects (SBDs) result from errors in development of the central nervous system, including defects in the forebrain, midbrain and hindbrain. Many SBDs arise as the consequence of a single gene bi-allelic mutation, and for this reason occur more commonly in populations or communities with elevated consanguinity. Our lab has identified dozens of novel SBD genes using WES/WGS in consanguineous SBD families. Importantly, the genes that we and others have identified in these unique families are then used to advance diagnosis in pediatric SBDs around the world. We have built an enormous cohort of SBD families, including newly recruited families not yet studied genetically, and previous families that were negative for cause following WES analysis. Here we propose to collaborate with the Gabriella Miller Kids First Pediatric Research Program (X01) to have sequencing performed in individuals from a total of 200 families with genetically undiagnosed SBDs. The Gleeson Lab team of researchers is dedicated to the field of SBDs, with an outstanding track record of high-impact science, and a collaborative approach to discovery. We have 150 newly recruited families that we propose to study by WES by sequencing blood-derived DNA from two affected or the parents and one affected. We also have 50 families in which WES was negative, that we propose to study in a multi-omics approach combining WGS from blood-derived DNA and RNAseq from RNA extracted from primary dermal fibroblasts. We anticipate that this study will lead to the identification of many new molecular causes of SBDs, as well as uncover new genotype-phenotype correlations and new disease mechanisms, paving the way for future breakthroughs in detection, treatment and prevention. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Leslie, Elizabeth Jane (Contact); Marazita, Mary L.; Murray, Jeffrey C |
| Title: | Genomics of Orofacial Clefts in the Philippines | Awardee Organization: | Emory University |
| Abstract: DESCRIPTION (provided by applicant): Orofacial clefts (OFCs) are the most common craniofacial structural birth defect in humans caused by incomplete formation of the upper lip and/or the palate. During childhood, affected individuals suffer from feeding difficulties, speech, hearing, and dental problems, and require multiple craniofacial and dental surgeries and ongoing therapies. Although the long-term prognosis is excellent for most individuals with OFCs, they can experience lifelong psychosocial effects, increased mortality rates from all causes, and a higher risk of various cancer types 2,3. The worldwide prevalence of OFCs is approximately 1 in 1000 live births but the observed prevalence is highly variable among ancestry groups. Over 4,000 children in the Philippines are born with an OFC every year and the Filipino OFC birth prevalence rate of 1 in 500 live births is one of the highest in the world. Elucidating the etiology of OFCs is critical not only for our knowledge of developmental biology and for how clefts arise, but ultimately for improved prevention, treatment, and prognosis for individuals affected by this disorder. Genome-wide association studies support a multifactorial etiology for OFCs, but common variants only account for up to ~25% of the heritable risk in any one population. Sequencing studies in diverse populations is essential to fully understand the genetic architecture of OFCs. We propose whole genome sequencing a combination of well-phenotyped case-parent trios, dyads, and additional affected individuals from the Philippines as a discovery sample. We seek to identify de novo mutations and inherited rare variants and will replicate these findings in our larger resource of over 10,000 individuals from the Philippines. Finally, we will combine these data with other Kids First OFC cohorts to compare and contrast the architectures in this high-risk population and to enable discovery of novel risk loci in the combined set of more than 1,000 caseparent trios. Our long-term goals include validation of WGS variants in established functional pipelines. This project is poised to rapidly advance our understanding of the genetic etiology of OFCs in this high-risk population. | |||
| Project Number: | N/A | Contact PI / Project Leader: | upo, Philip J (contact); Plon, Sharon E. |
| Title: | Genomic Analysis of Pediatric Rhabdomyosarcoma | Awardee Organization: | Baylor College of Medicine |
| Abstract: DESCRIPTION (provided by applicant): Rhabdomyosarcoma (RMS) is a highly malignant tumor believed to arise from developing skeletal muscle cells (myoblasts). Relative to other childhood cancers, the prognosis for many children with RMS remains poor. In particular, for those children with high- or intermediate-risk disease, use of maximally intensive therapy and application of new agents since the 1970s has led to only modest improvements in 5-year survival rates, which is currently only 43% to 67%. Ultimately, sarcomas are understudied cancers, and RMS is by far the most common soft tissue sarcoma in children and adolescents. To make advances in this area, complementary and innovative approaches are needed to 1) understand the molecular signatures underlying susceptibility; 2) develop a foundation for improved genetic counseling and clinical surveillance protocols; and 3) discover new therapeutic targets. Very little is known in relation to germline genetic susceptibility to RMS. For instance, based on smaller clinic-based studies, about 5% of RMS cases are thought to be associated with known cancer predisposition genes. However, there have been no population-based assessments to support this estimate, and much work remains to be done to understand the causes of the other 95% which appear to be sporadic. Additionally, there is growing evidence of the importance of de novo germline mutations (DNMs) in the etiology of seemingly sporadic diseases. While there is epidemiologic evidence to support the role of DNMs on the etiology of RMS, there have been no efforts to explore the role of DNMs on this pediatric malignancy. An important and innovative goal of the Gabriella Miller Kids First Pediatric Research Program is to conduct large-scale germline sequencing of well-annotated pediatric cancer patient and parent trios to address important questions about the genetics of childhood cancers. Therefore, the objective of this Kids First X01 application is to address unanswered questions about RMS by determining the role of DNMs in known cancer predisposition genes and in novel susceptibility genes. Our central hypothesis is that highly penetrant DNMs may underlie several childhood cancers, including RMS. Our hypothesis has been formulated on the basis of our preliminary studies. We plan to test our central hypothesis and, thereby, accomplish the objective of this application by pursuing the following two specific aims: 1) identify recurrent DNMs among RMS case-parent trios; and 2) determine the prevalence of mutations in both well-established sarcoma genes and genes identified with recurrent DNMs among children with sporadic RMS. This study represents an important step toward a better understanding of the etiology of these malignancies by combining the study of previously described and newly discovered genes. Ultimately, the findings from this study could lead to 1) improved genetic testing and counseling strategies in RMS patients, 2) advanced surveillance and chemoprevention protocols, and 3) the identification of novel therapeutic targets for this highly fatal tumor. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Martin, Donna M. |
| Title: | Genomic Etiologies of CHARGE Syndrome, Related Conditions and Structural Anomalies | Awardee Organization: | University of Michigan at Ann Arbor |
| Abstract: DESCRIPTION (provided by applicant): Developmental disorders with structural birth defects account for the majority of morbidity and mortality in children’s hospitals, and the genetic bases of many clinical phenotypes remain unknown. Genetic testing for individuals with structural malformations has uncovered the basis of many such birth defects; however, many more cases remain unsolved, posing challenges for diagnosis, treatment, and prevention. Multiple anomaly conditions are particularly challenging to diagnose, since they often present with unique combinations of clinical features that vary widely between affected individuals, even in the same family. CHARGE Syndrome (Coloboma of the eye, Heart Defects, Atresia of the choanae, Retardation of growth and development, Genital abnormalities including pubertal delay and infertility, Ear abnormalities with deafness and vestibular disorders) is a multiple anomaly condition that affects a wide variety of organ systems. CHARGE Syndrome is caused in most cases by monoallelic pathogenic variants in CHD7, the gene encoding ATP-dependent helicase chromodomain DNA binding protein 7. Both de novo and inherited variants in CHD7 have been reported in CHARGE, and a growing number of families present with individuals who test positive for a pathogenic CHD7 variant yet exhibit only mild features. Similarly, individuals with CHARGE Syndrome often exhibit broad variability and reduced penetrance of clinical features, consistent with pleiotropic roles for CHD7 during development and/or additional genetic contributors or modifying alleles. We hypothesize that (1) some cases of CHARGE are due to other genetic etiologies including oligogenicity, and (2) genetic modifiers contribute to the broad clinical variability and reduced penetrance of CHARGE features. To address these hypotheses, we have generated a cohort of 100 deeply clinically phenotyped individuals with CHARGE Syndrome and related disorders and structural anomalies who tested negative by chromosomal microarray, single gene sequencing, next generation panel sequencing, or exome sequencing. These individuals exhibit clinical CHARGE-like features including structural birth defects affecting craniofacial, ocular, neurosensory, brain, heart, mediastinal, renal, genitourinary, and skeletal organs. Our cohort includes affected and unaffected family members who consented to clinical and research genetic testing and donated blood samples for DNA and RNA isolation and sequencing. Building on this valuable cohort, we propose to use exome and genome sequencing to identify novel genetic etiologies of CHARGE and related developmental disorders for which alternative genetic tests have been inconclusive. Identification of novel pathogenic genetic variants and contributing modifier alleles within the coding and non-coding portion of the genome of these individuals will improve genetic diagnosis and provide important insights toward understanding the developmental mechanisms of structural birth defects. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Poynter, Jenny N. |
| Title: | Genetic susceptibility of extracranial germ cell tumors | Awardee Organization: | University of Minnesota |
| Abstract: DESCRIPTION (provided by applicant): Pediatric malignant germ cell tumors (GCTs) represent approximately 6% of childhood cancers, including 3% of tumors in children aged 0-14 years and 15% of tumors in adolescents. GCTs are heterogeneous and grouped together due to the presumed common cell of origin, the primordial germ cell (PGC). GCTs typically occur in the testes or ovaries; however, extragonadal GCTs can occur and are likely a result of abnormal germ cell migration during development. Evidence suggests that GCTs, including those diagnosed in adults, are initiated in utero. Thus, alterations in normal embryonic development are likely to be especially relevant to GCT etiology. Germline susceptibility has not been evaluated in an agnostic fashion in GCT, mainly due to a lack of an adequate number of samples. However, we can gain some knowledge from studies of adult testicular GCT (TGCT), which also arise from the PGC. The high heritability of TGCT suggests a genetic etiology, and recent genomewide association studies support this through the discovery of multiple susceptibility loci. We recently confirmed a subset of these loci as susceptibility variants for pediatric GCT. Our overarching goal for the proposed study is to understand the genomics of pediatric GCT, including both germline and tumor samples. In our recently completed NIH-funded case parent triad study (“Molecular Epidemiology of Pediatric Germ Cell Tumors”; R01 CA151284), we recruited GCT cases and their parents through the Children’s Oncology Group (COG) Childhood Cancer Research Network. In this study, we collected germline DNA for 867 GCT patients between the ages of 0-19 years at diagnosis, including 677 families with DNA samples for the complete trio. The intracranial GCT cases from this study will be included in a project selected for funding by the Gabriela Miller Kids First Sequencing program in 2018 (X01 HL145700; PIs Lau and Poynter). In the current proposal, we are proposing to use WGS and WES to evaluate the following specific aims in the extracranial (testicular, ovarian, and extragonadal) GCTs recruited for this study. In this project, we will: 1) Evaluate the contribution of rare genetic variants in GCT through the use of aggregate burden tests, focusing on genes and established regulatory regions; 2) Identify de novo SNVs and CNVs in pediatric GCT using a case-parent triad design; and 3) Identify molecular signatures in GCT tumor specimens, overall and by age group and tumor characteristics. Whole Genome Sequencing data generated through the Gabriella Miller Kids First Pediatric Research Program will provide an opportunity to investigate the genetic origins of GCT in a diverse set of samples. Given the limited knowledge of GCT etiology and biology, the results of the proposed analyses are likely to have a big impact on the field. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Teachey, David T (Contact), Mullighan, Charles G |
| Title: | Comprehensive Genomic Profiling to Improve Prediction of Clinical Outcome for Children with T-cell Acute Lymphoblastic Leukemia | Awardee Organization: | Children's Hospital of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): The outcome for patients with relapsed T-ALL is dismal with 3-year event free survival of <15%. Thus, the primary goal in the treatment of T-ALL is to prevent relapse, which requires accurate risk stratification. Unfortunately, no genetic alterations have been identified to date that are reproducibly prognostic independent of minimal residual disease (MRD), making it difficult at diagnosis to identify which patients are more likely to relapse. AALL0434 was a Children’s Oncology Group-initiated phase 3 randomized clinical trial comparing Capizzi-style escalating methotrexate plus pegaspargase (CMTX) vs. high dose methotrexate (HDMTX), with/without six 5-day courses of nelarabine. Survival on this study was superior to any prior trial for de novo T-ALL, changing the standard of care. Yet, a substantial minority (~15%) of patients had relapsed or refractory (r/r) disease. We recently performed RNA sequencing, DNA copy number analysis, and whole-exome sequencing on 264 T-ALL patients treated on AALL0434, demonstrating recurrent alterations could be grouped into 10 different potentially targetable functional pathways. This analysis was not powered to examine associations between genetic lesions with outcome, because too few patients with r/r disease were included. We hypothesize that comprehensive genomic profiling of the entire AALL0434 cohort will identify recurrent genetic alterations that can be segregated into biologically relevant deregulated pathways that can be combined with MRD to identify patients at risk for poor outcomes before they relapse and provide rationale for treatment with alternative therapies. In addition, a number of small recent studies demonstrated that many of the biologically relevant alterations in T-ALL occur in non-coding regions of the genome, but no large studies have performed whole genome sequencing in T-ALL. We further hypothesize that whole genome sequencing of a large cohort of patients with T-ALL will identify novel lesions in coding and non-coding regions that will be highly impactful in the understanding of T-ALL pathogenesis. We will test our hypotheses by performing comprehensive genomic profiling (whole genome sequencing, whole exome sequencing, RNA sequencing, and copy number analysis) of the entire AALL0434 cohort (n = 1430) with the following specific aims: (1) identify recurrent genetic alterations that predict poor outcome in T-ALL; (2) identify novel alterations, including non-coding alterations in T-ALL; and (3) identify germline genetic variants that predispose to T-ALL and to increased toxicity to nelarabine. The goal of the Kids First Program is to improve understanding of genetic mechanisms of disease, leading to improved diagnostic capabilities and ultimately more targeted therapies or interventions. This proposal will meet that important goal through identification of germline and somatic alterations in T-ALL that can be used to identify patients that are likely to relapse before they relapse and can be treated with new therapies. | |||
| Project Number: | N/A | Contact PI / Project Leader: | Ware, Stephanie |
| Title: | Genomic Analysis of Laterality Birth Defects | Awardee Organization: | Indiana Univ-Purdue Univ at Indianapolis |
| Abstract: DESCRIPTION (provided by applicant): Laterality defects occur in approximately 1:10,000 newborns and are associated with a range of structural birth defects and abnormalities of organ positioning. Gut malrotation, biliary atresia, asplenia or polysplenia, complex cardiovascular malformations, and midline defects such as neural tube defects, vertebral anomalies and rib fusions are found in various combinations in patients with laterality defects. In addition, a subset of laterality defects caused by abnormalities of cilia position or function are associated with additional medical problems such as chronic sinusitis and bronchiectasis that require specific preventive care; however these patients frequently are undiagnosed until late in disease course. The clinical picture firmly establishes laterality defects as not only diseases of significant phenotypic heterogeneity, but also ones of considerable medical and economic consequence. The goal of this project is to elucidate the genetic architecture of laterality defects in order to inform medical management and prevent complications. Laterality disorders are genetically heterogeneous and we and others have previously identified single nucleotide variants inherited in an X-linked or autosomal recessive manner as explanations for a minority of cases. In addition, we have demonstrated copy number variants (CNVs) as a mechanism of disease that requires additional investigation. We hypothesize that the majority of cases result from complex genetic inheritance. We propose to investigate this hypothesis using a multifaceted analysis approach in our extremely well phenotyped cohort of 550 probands with laterality disorders. Included within this cohort are 280 probands who had exome sequencing which was negative for pathogenic variants in 170 clinically relevant laterality genes. However, preliminary data demonstrate increased variant burden in these cases versus controls when interrogating 809 candidate genes important for left-right patterning and cilia function. These samples are excellent candidates for gene discovery and association analyses via whole genome sequencing (WGS) which will allow broader interrogation and expansion of analyses to include non-coding regions and CNVs. We will perform burden analyses to identify genes, gene interactions, and pathways important for susceptibility to laterality disorders. Also nested within our cohort of 550 probands are 105 trios that have not had previous sequencing. All trios will be analyzed by transmission disequilibrium test (TDT) including rare variant TDT. De novo mutations will also be identified from trios for potential gene discovery. This comprehensive genetic analysis in patients with laterality disorders is necessary to identify the appropriate clinical diagnostic testing for risk stratification, to elucidate underlying genetic architecture and facilitate novel gene discovery, and to provide essential knowledge about genes and pathways impacting the development of these birth defects. | |||
2018 X01 Projects
| Project Number: | 1 X01 HL145692-01 | Contact PI / Project Leader: | Chung, Wendy K (Contact); Shen, Yufeng |
| Title: | Genomic Analysis of Esophageal Atresia and Tracheoesophageal Fistulas and Associated Congenital Anomalies | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. There is a 45% incidence of associated congenital malformations, most commonly digestive, cardiovascular, urogenital, and musculoskeletal, often part of a syndrome or complex association, with VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities) being most frequently recognized. Advanced surgical techniques and pre and post-operative care have improved the prognosis and survival of EA/TEF patients over the past decades. However, with improved survival, many of the long-term morbidities of EA/TEF have been exposed. It is likely that the outcome in EA/TEF patients is influenced by multiple genetic and clinical factors; however, determining which factors are critical has been limited by the lack of data, particularly genomic data. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of EA/TEF and define new genes and conditions associated with EA/TEF by performing whole genome sequencing on 100 parent child trios in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions and improve outcomes. PUBLIC HEALTH RELEVANCE: Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. We propose to elucidate the underlying genomic architecture of EA/TEF by performing whole genome sequencing to characterize new clinical syndromes associated with EA/TEF to provide more accurate clinical prognostic information. | |||
| Project Number: | 1 X01 HL145691-01 | Contact PI / Project Leader: | Seidman, Christine E |
| Title: | Germline Mutations in CHD | Awardee Organization: | Harvard Medical School |
| Abstract: DESCRIPTION (provided by applicant): Congenital heart disease (CHD) is the most common birth defect and is often accompanied by another congenital anomaly (CHD±CA). The Pediatric Cardiovascular Genetics Consortium (PCGC) is committed to defining the molecular mechanisms for CHD±CA. We have recruited over 29,000 participants including over 6000 CHD probands and parents (CHD trios) with extensive clinical data. Whole exome sequence (WES) analyses in ~3300 CHD trios by the PCGC has defined likely genetic causes in ~40% probands. As part of the Gabriella Miller Kids First Pediatric Research Program, we propose WGS to enable the discovery of variants and mechanisms that contribute to unexplained CHD in ~60% of probands studied by the PCGC. To accomplish these goals we will capitalize on new insights into CHD genes, identified by WES, that indicate aberrant transcriptional regulation during development is a major cause of CHD. In this application we request WGS on 550 CHD trios so that by leveraging existing genomic datasets we will empower robust analyses of variants that alter noncoding regulatory elements of cardiac development genes in WES-negative trios. Nested within this trio group are 100 CHD trios comprised of a proband with one damaging variant in a recessive CHD gene. In addition to genome-wide studies, focused analyses in this trio subgroup will search for noncoding variants that impact the “normal” allele. The remaining 450 CHD trios include probands with tetralogy of Fallot (ToF), the most common form of cyanotic heart disease. We will harness WGS in ToF trios to inform variants within particular genome regions that are susceptible to recurrent copy number and structural variants - regions that are poorly interrogated by WES. While mutation in these several variant-susceptible genes and loci are often found in ToF patients, these are remarkably absent in many ToF probands studied by WES and CNV analyses. Finally, we request high-depth WGS of 200 discarded CHD tissues obtained during surgical repair, to explore novel genetic mechanisms in CHD, including somatic mosaicism, mitochondrial variants, and to provide initial evidence of prenatal infections that may contribute to CHD. In all of these studies we will use existing resources and capabilities of the PCGC and its companion consortium in the Bench to Bassinet Program, the Cardiovascular Development Consortium, to perform confirmatory functional genomics studies using cell and animal models outside of the GMKF program. We expect that these studies will provide novel insights into the molecular basis for birth defects and fundamental knowledge about genes and pathways involved in the development of the heart and other organs. We request: 1. WGS (90X coverage) on 200 CHD tissues. 2. WGS on 100 CHD trios comprised of a proband with a damaging variant in a recessive CHD gene. 3. WGS on 450 TOF trios. PUBLIC HEALTH RELEVANCE: Using whole genome sequencing, we aim to discover the genetic mechanisms for congenital heart disease, the most common human birth defect. We will identify sequence variants that alter regulatory elements involved in developmental transcription and consider the consequences of these on discarded heart tissues obtained during surgical repair of heart malformations. Through focused analyses of tetralogy of Fallot, we hope to better understand the processes that promote this complex and prevalent heart malformation. | |||
| Project Number: | 1 X01 HL145698-01 | Contact PI / Project Leader: | Gharavi, Ali G |
| Title: | Genetics of Structural Defects of the Kidney and Urinary Tract | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) account for up to 50% of pediatric and 7% of adult end-stage kidney failure worldwide. The goal of this project is to apply genetic approaches to resolve the biological basis and clinical manifestations of CAKUT using three well-characterized cohorts with deep phenotypes and extensive longitudinal data (the NIDDK sponsored CKiD and RIVUR studies, and the Columbia cohort). Here, we hypothesize that CAKUT is genetically heterogeneous, and caused by rare mutations with large effect on a background of polygenes with small effects that can be discovered by analysis of well phenotyped cohorts compared to genetically matched cohorts with WGS data available. We now propose to extend our prior studies by whole genome sequencing (GWS) in patients with CAKUT from 3 well-phenotyped cohorts. We expect that the proposed studies will provide new insight into urogenital development, clarify the clinical overlap with other syndromes and provide novel tools that can replace the current morphology-based diagnostic approaches. We will first perform annotation based on a standard ACMG guidelines to identify pathogenic CNVs and single nucleotide variants diagnostic for known genetic disorders. In aim 2, we will perform genome-wide analysis of common and rare variant burden combining a case-control and trio design to detect new genes for CAKUT. We will next replicate top signals in additional CAKUT cohorts available in our laboratory. Finally, we will per phenotype- genotype correlations with longitudinal clinical data such a kidney function, proteinuria or neurodevelopmental outcomes to gain insight into clinical impact of causal variants. PUBLIC HEALTH RELEVANCE: Congenital defects of the kidney and urinary tract are a common cause of kidney failure in children and adults and elucidation of the genetics of these disorders will provide new opportunities for diagnosis, risk stratification and prevention of complications. Sequence and clinical data released in dbGap:Accession Number:phs002162 | |||
| Project Number: | 1 X01 HL145697-01 | Contact PI / Project Leader: | Krantz, Ian |
| Title: | Genomic Diagnostics in Cornelia de Lange Syndrome, Related Diagnoses and Structural Birth Defects | Awardee Organization: | Children's Hospital Of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Disorders of human morphogenesis are a major cause of human suffering for the affected individuals and their families. Congenital anomalies are identified in approximately 3% of term births, 10% of stillbirths, and in as many as 50% of first trimester spontaneous abortuses. While most, if not all, human structural birth defects have a significant genetic component, identification of genetic perturbations in isolated structural birth defects has been complicated by the complex nature of their underlying etiologies, likely involving disruption of regulatory elements that can act in a temporal and tissue specific manner, multi-gene, epigenetic and gene-environment interactions. Our approach to tease out genetic contributions to birth defects has been to identify the underlying causes of syndromic birth defects which are often Mendelian in nature and therefore lend themselves more readily to genetic causal identification. Once identified, these genetic causes of syndromic forms of birth defects can be leveraged to understand the genetic contributions to isolated birth defects seen in constellation in these syndromes. We propose to use Cornelia de Lange Syndrome (CdLS), a dominant multisystem developmental disorder consisting of a constellation of structural birth defects involving most body systems and significant growth and cognitive impairment as a prime example of this approach. We and others have shown that alterations in the cohesin and associated pathways are causative of CdLS and related diagnoses when disrupted and have more broadly been termed “cohesinopathies” or “disorders of transcriptional regulation (DTRs)”. In this proposal we outline an initial plan to perform genome sequence (subsequently RNA sequencing will be considered) on a unique cohort of 501 probands and family members with clinically confirmed CdLS or a related diagnosis in whom molecular analysis by targeted gene sequencing, next generation sequencing (NGS) panels or exome sequencing have been negative but are strongly suspected of having an underlying genetic alteration to explain their clinical features. This work will lead to the identification of genes critical in human embryonic development, provide novel insights into transcriptional regulation and help to identify genetic causes and candidate genes for isolated birth defects seen in constellation in this group of diagnoses. Most critical developmental genes are also cancer genes and the genes known to cause CdLS are no exception. CdLS is not a cancer predisposition syndrome so understanding the mutational mechanisms in these genes that lead to structural birth defects when present in the germ line and result in cancer when mutated somatically is a fundamental aspect of this research. PUBLIC HEALTH RELEVANCE: The proposed research Program is relevant to public health as we are addressing a major gap in our understanding of the genetic basis of syndromic and non-syndromic structural birth defects (with a focus on Cornelia de Lange syndrome and related diagnoses and birth defects), a major cause of human suffering for the affected individuals and their families. The proposed research Program is highly relevant to the NIH mission of improving health outcomes as we expect that discoveries of the basic mechanisms of structural birth defects will lead to improved diagnostics, counseling, management and therapeutics for affected individuals and their families. | |||
| Project Number: | 1 X01 HL145690-01 | Contact PI / Project Leader: | Seidman, Jonathan G |
| Title: | The Genetics of Microtia in Hispanic Populations | Awardee Organization: | Harvard Medical School |
| Abstract: DESCRIPTION (provided by applicant): Microtia is a rare congenital deformity of the external ear, the pinna. The severity of microtia is variable and ranges from subtle deformities in the pinna to absence of the external ear. Microtia is often associated with closure of the external auditory ear canal causing significant hearing loss. Microtia can be an isolated, unilateral or bilateral malformation, or occur solely with ear canal deformities, or with additional craniofacial or syndromic manifestations. Our study of identical twins with microtia demonstrated a significant genetic contribution. The molecular pathogenesis for most microtia remains unknown. We propose to leverage our clinical acumen in diagnosis and treatment of microtia (R.E.), our relationship to the microtia community (M.T.) and our collected DNA samples from microtia patients to identify genetic variant(s) that contribute to this congenital malformation. Microtia prevalence is much higher among Native Americans and some Latin Americans (17 per 10000 Ecuadorian births) than among individuals of European-descent (0.6 -1.6 per 10,000 births). To capitalize on this epidemiologic data, we have recruited microtia cohorts from Latin America and the U.S, including clinical data and DNA samples. We propose whole genome sequence of existing samples from isolated cases, trios (proband and parents) and one large family we propose comprehensive genetic analyses to interrogate coding and non-coding sequence variants associated with microtia. We hypothesize that genetic variants that cause microtia and other less pathogenic conditions, which have relatively small impact on reproductive fitness, are likely to be tolerated and inherited, but cause malformations in only a fraction of variant carriers (i.e. reduced penetrance). We suggest that we have power to detect a variant that increases the relative risk of microtia by >2.5 (i.e. a penetrance of ~3%). We suggest that microtia likely reflects variants with low penetrance that impact genes that participate in the molecular pathways of ear development. Such variants may also contribute to other hearing and craniofacial malformations. We expect to harness the insights and reagents developed here to elucidate factors that impact the penetrance of variants. Because of the prevalence of microtia in Latin America there are microtia support groups in Mexico, Colombia, and Ecuador. We have formed alliances, through our collaborator Melissa Tumblin (Ear Community), with these microtia support groups. We anticipate that any associations detected in the preliminary whole genome sequence (WGS) cohort will be confirmed in a second cohort of microtia patients. We request that the Gabrielle-Miller Kids First program support WGS of 821 microtia subjects and their parents as follows: a) 200 microtia probands; b) 200 trios (proband and both parents) and c) 21 members of family 3Sz. PUBLIC HEALTH RELEVANCE: We request whole genome sequence of 821 Hispanic subjects who have at least one family member with microtia, or abnormal outer ear formation. There are 200 microtia probands without parents, and 200 microtia probands with parents (trios, n=400) and 21 from a large family with 6 cases of microtia. We expect that analysis of the WGS will identify a gene variant(s) that increases the risk of microtia in some Latin American populations by ~25 fold and will provide new insights into the development of the outer ear. Sequence and clinical data released in dbGap:Accession Number: phs002172 | |||
| Project Number: | 1 X01 HL145702-01 | Contact PI / Project Leader: | Chambers, Christina |
| Title: | Discovery of Genetic Basis of Fetal Alcohol Spectrum Disorders | Awardee Organization: | University Of California, San Diego |
| Abstract: DESCRIPTION (provided by applicant): Fetal Alcohol Spectrum Disorder (FASD) is the most common birth defect worldwide, and is estimated to occur in at least 1-5% of all children in the U.S. However, not all children with prenatal exposure are similarly affected, even among those born to heavy, chronic alcohol-consuming pregnant women. Recent research has focused on the susceptibility or protective factors that seem to influence the risk for FASD. However, very little is known about the genetic risk or protective factors that may interact with prenatal alcohol exposure leading to this variable risk. In this study, we will use whole genome sequencing of well-characterized mother-child pairs, including mothers with or without prenatal alcohol exposure and their children with or without FASD, to test the hypothesis that genomic alterations in either the mother or her fetus or both play a role in susceptibility to the effects of alcohol. This information will be of critical value in better understanding the pathogenetic mechanisms underlying FASD. In addition, the identification of maternal or fetal genetic susceptibility factors for FASD may inform future intervention strategies for this common congenital disorder. PUBLIC HEALTH RELEVANCE: Fetal Alcohol Spectrum Disorder (FASD) is estimated to occur in at least 1-5% of all children in the U.S. and is a major public health issue. However, in addition to alcohol, other susceptibility factors, such as maternal or fetal genetic variation, must play a role as not all children prenatally exposed to alcohol are similarly affected. The proposed study will examine the role of genetic susceptibility for FASD; this work will help to inform more effective intervention efforts for this common congenital disorder | |||
| Project Number: | 1 X01 HL145686-01 | Contact PI / Project Leader: | Lupo, Philip J (Contact); Rabin, Karen R; Sherman, Stephanie L.; Yang, Jun J |
| Title: | Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome | Awardee Organization: | Baylor College Of Medicine |
| Abstract: DESCRIPTION (provided by applicant): Down syndrome (DS), which occurs due to trisomy 21, is one of the strongest risk factors for both congenital disease (CHD) and acute leukemia. For instance, children with DS have a 2000-fold increased risk of atrioventricular septal defects (AVSD) and a 20-fold increased risk of acute lymphoblastic leukemia (ALL). An important and innovative aspect of the Kids First program is understanding the overlap between structural birth defects and childhood cancer. Notably, the background of DS predisposes children to both phenotypes, however, the genomic architecture of risk remains largely undiscovered. Therefore, we propose that our assembled cohort of children with: 1) DS alone (n=607) 2) DS with AVSD (DS-AVSD, n=623) 3) DS with other CHD (DS-oCHD, n=594) and 4) DS with ALL (DS-ALL, 370) will advance our understanding of the developmental pathways that may lead to both structural birth defects and childhood cancer. The objectives of this study are to determine the genetic variants underlying AVSD and ALL risk in children with DS. Our central hypothesis is that risk-associated genetic variants in the background of DS lead to a higher penetrance of AVSD and ALL. Our secondary hypothesis is that rare variants explain a significant proportion of the increased risk of AVSD and ALL in children with DS. Our hypotheses are supported by our previous work indicating: 1) previously identified susceptibility loci in ALL genes (e.g., IKZF1) have stronger effects in children with DS-ALL compared to non-DS-ALL 2) common genetic variants and copy number variants do not explain the increased risk of AVSD among those with DS and 3) there is an increased burden of rare variants among children with DS-AVSD compared to those with DS alone. Therefore, the aims of our study are: 1) compare whole-genome sequencing (WGS) data between children with documented DS-AVSD and children with DS who have structurally normal hearts to identify genetic variants that perturb heart development and 2) compare WGS data between children with documented DS-ALL and children (from Aim 1) with DS who do not have a known history of ALL. For the subset of DS-ALL cases with a paired tumor sample, we will examine associations between germline mutations and somatic genomic features. This study will address the fundamental question of why children with DS have an elevated risk of AVSD and ALL. Insights into the genes that drive DS-AVSD and DS-ALL may have implications for improved genetic counseling, surveillance, clinical management, and treatment strategies for these children. Additionally, our findings may inform targeted therapies or interventions for children without DS who are at risk for structural birth defects and cancer. PUBLIC HEALTH RELEVANCE: PROJECT Children with Down syndrome (DS), which occurs due to trisomy 21, have a 2000-fold increased risk of atrioventricular septal defects (AVSD) and a 20-fold increased risk of acute lymphoblastic leukemia (ALL), but it is not understood which genetic features of trisomy 21 are responsible for the increased risk. The objectives of this study are to determine the genetic variants underlying AVSD and ALL risk in children with DS, which builds upon our previous work suggesting having an extra copy of chromosome 21 may “move” the susceptibility threshold for disease in these children. Insights into the genes that drive DS-AVSD and DS-ALL may have implications for improved genetic counseling, surveillance, clinical management, and treatment strategies for these and other children who may develop AVSD or ALL. | |||
| Project Number: | 1 X01 HL145695-01 | Contact PI / Project Leader: | Drolet, Beth A |
| Title: | Analyzing the Genetic Spectrum of Vascular Anomalies, Overgrowth and Structural Birth Defects | Awardee Organization: | Medical College Of Wisconsin |
| Abstract: DESCRIPTION (provided by applicant): Vascular anomalies include a heterogeneous group of tumors and malformations characterized by the presence of abnormal vascular structures. Vascular anomalies most often occur in the skin and soft tissue; however, they can occur within any organ and present with a wide range of symptoms and complications, depending on type and location of the lesion. These disorders are remarkably variable ranging from simple staining of the skin with mild soft tissue overgrowth to debilitating tissue overgrowth and severe structural birth defects. We assembled a large vascular anomalies cohort recruited from a 20-institution network to discover genes related to vascular anomalies and structural birth defects. Using targeted next-generation sequencing, we and others, have detected postzygotic mosaic variants in affected tissue from several vascular anomalies. The causative variants almost entirely overlap with those variants observed in cancer. The preliminary data generated from this cohort reinforces the approach set forth by the Gabriella Miller Kids First Program by demonstrating a direct connection between cancer and structural birth defects. We hypothesize that vascular anomalies are caused by postzygotic somatic mutations and that the phenotype is further influenced by the mutational burden, the tissue distribution of mutation, and germline alterations, which establish a necessary context in which postzygotic alterations act. Improved understanding of the complex genetic landscape of vascular anomalies will be critical for accurate diagnosis, the development of care guidelines, consideration of therapeutic options, and planning of future clinical trials. Aim 1: Identify genomic alterations in vascular anomalies, Aim 2: Contribute the data generated in this project to the Kids First Data Resource and the National Center for Biotechnology Information’s (NCBI) Database of Genotypes and Phenotypes (dbGaP). PUBLIC HEALTH RELEVANCE: Genomic analysis of vascular anomalies will inform treatment and expand knowledge about the causes of birth defects affecting blood vessels, brain, eye, and bones. The knowledge gained in this study will be used to drive strategies for prevention and provide critical targets for treatments for vascular anomalies and related birth defects. | |||
| Project Number: | 1 X01 HL145696-01 | Contact PI / Project Leader: | Meshinchi, Soheil |
| Title: | Germline and Somatic Variants in Myeloid Malignancies in Children | Awardee Organization: | Fred Hutchinson Cancer Research Center |
| Abstract: DESCRIPTION (provided by applicant): Advances in genomic sequencing has allowed identification of somatic variants as potential therapeutic targets. Although myeloid disorders in children may show morphologic similarities to that seen in adults, TARGET AML initiative (Meshinchi, PI) clearly demonstrated that somatic genomic and transcriptome variants are highly distinct in children and young adults, and in fact there are variants that are uniquely restricted to younger children. TARGET AML initiative, although modest in number, helped identify numerous somatic alterations with high therapeutic potential in younger AML patients. In addition to identification of somatic variants, analysis of the germline data provided a glimpse into the constitutional make-up of patients with AML. The identification of numerous “function altering” variants may provide an insight into possible interactions between the host and the disease, where these germline variants might alter AML risk (predisposition), response to therapy (altering target expression, drug metabolism), susceptibilities to short and long term complications (including infectious and cardiac complications) or modify risk of secondary malignancies. Armed with data from initial sequencing efforts in AML, we are poised to take full advantage of the available sequencing technology to conduct the most comprehensive genome and transcriptome interrogation of myeloid disorders in children in specimens we have amassed over the last decade. To this end, we have put in place unparalleled specimen resources from children with de novo AML, Down Syndrome AML (DS-AML), and acute promyelocytic AML (APL) treated on COG trials. In addition, thru collaboration with Dr. Resar and Kucine, we will be able to conduct the first broad sequencing study in the rare entity of myeloproliferative neoplasms of childhood (MPN-c). Identification of the somatic variants will provide valuable data on the potential genes and pathways that can be targeted for therapeutic gains. In addition, interrogation of the host’s constitutional genome may yield valuable information about potential germline variants that, in combination with the somatic data, might provide a more informed approach to patient care. For those patients with predisposition mutations, chemotherapy alone might not be adequate for cure and stem cell transplantation might be required. Also, those who might be at high risk of adverse secondary events (cardiac complications, secondary malignancies, etc.) can be identified early and their therapy tailored to minimize anticipated complications. Thus, we propose that the optimum outcome can only be obtained thru comprehensive interrogation of the somatic and germline genome to fully annotate the genomic makeup of the leukemia and its host. OMB No. 0925-0001/0002 (Rev. 01/18 Approved Through 03/31/2020) Page Continuation Format Page PUBLIC HEALTH RELEVANCE: Clinical outcome in children with myeloid disorders have remained poor in part due to lack of deep understanding of the genomic makeup of the disease as well as the host. Comprehensive studies of the host and disease may enable more informed therapies in order to optimize targeting the leukemia while minimizing short and long term toxicities, leading to improved survival with minimal morbidities. | |||
| Project Number: | 1 X01 HL145700-01 | Contact PI / Project Leader: | Lau, Ching Ching (Contact); Poynter, Jenny N. |
| Title: | Genetic Predisposition to Intracranial Germ Cell Tumors | Awardee Organization: | The Jackson Laboratory |
| Abstract: DESCRIPTION (provided by applicant): Pediatric germ cell tumors (GCTs) are rare and heterogeneous tumors that most commonly occur in the gonads but also develop in other locations. Intracranial GCTs (IGCTs) account for approximately 3% of brain tumors in children in the U.S. but are far more prevalent in Japan and East Asian countries, where they account for up to 11% of brain neoplasms. These observations suggest that there is genetic predisposition to IGCT. Currently little is known about the etiology of IGCTs. Their incidence peaks in the second decade of life with rates that vary widely by geography and are higher in males than in females. Recent reports support familial aggregation of IGCT. Data from the PIs of this project support the hypothesis that genetic variants contribute to IGCT predisposition, as rare variants in the gene JMJD1C were identified among a Japanese patient population in strong association with IGCT. JMJD1C is a plausible susceptibility gene for IGCT given its role in sex steroid hormone regulation and maintenance of male germ cells in mice. Additionally, it has been hypothesized that intracranial and other GCTs both arise from primordial germ cells that migrated abnormally during development. Indeed, using case parent trios recruited for a Children’s Oncology Group (COG), the PIs of this project found that common genetic variants associated with adult testicular GCT are also associated with both intracranial and systemic GCT, suggesting that there may be common genetic risk factors for all GCT types. Identification of additional genetic variants for IGCT risk will require a larger study using whole-genome sequencing (WGS) data. To test the hypothesis that there are genetic variants that increase susceptibility to pediatric IGCT development, this project will carry out three Aims that focus on a cohort of more than 400 IGCT cases from the U.S., Japan, and Thailand. Aim 1 will validate the importance of JMJD1C as a susceptibility locus for IGCT in Japanese and non-Japanese populations by identifying additional rare and novel variants that are over-represented in IGCT, which are expected to occur at a much higher frequency in Japanese IGCT cases. Aim 2 will identify novel susceptibility variants for IGCT that are enriched in the Japanese population by applying a previously developed filtering approach. Aim 3 will identify novel variants associated with IGCT using aggregate burden tests, focusing on genes and established regulatory regions. This analysis will improve the power to identify novel variants associated with IGCT in the entire cohort of samples and is anticipated to enable identification of familial predisposition for IGCT in both known and unrecognized cancer susceptibility genes. The availability of IGCT whole-genome sequencing data through the Gabriella Miller Kids First Data Resource Center will offer the cancer research community an opportunity to investigate the genetic basis of IGCT and promote the clinical risk assessment and treatment of this cancer. Additionally, the identification of associated genetic variants is anticipated to inform the understanding of other forms of pediatric cancers. PUBLIC HEALTH RELEVANCE: / RELEVANCE TO PUBLIC HEALTH Pediatric intracranial germ cell tumors (IGCTs) account for approximately 3% of brain tumors in children in the U.S. but are far more prevalent in Japan and East Asian countries, where they account for up to 11% of brain neoplasms. To understand the genetic risks of developing this cancer type in childhood, we have gathered hundreds of cases from the U.S., Japan, and Thailand so that their genomes can be fully sequenced through the Gabriella Miller Kids First Pediatric Research Program and be made publicly available as part of the Kids First Data Resource. We will computationally analyze this sequencing data to identify those genetic variants that are associated with IGCT and determine which gene functions are perturbed by these variants to increase susceptibility to this disease. | |||
| Project Number: | 1 X01 HL140546-01A1 | Contact PI / Project Leader: | Jelin, Angie Child |
| Title: | Single gene pathogenic variants associated with BEEC (Bladder extrophy, Epispadias, Complex) | Awardee Organization: | Johns Hopkins University |
| Abstract: DESCRIPTION (provided by applicant): This X01 application is submitted by Angie C. Jelin, MD, Assistant Professor of Gynecology and Obstetrics/Genetics at the Johns Hopkins School of Medicine. Dr. Jelin’s long term goal is to become an independent investigator in fetal urinary tract anomalies. Towards this goal, she proposes whole genome sequencing (WGS of Bladder Exstrophy Epispadias Complex (BEEC). Urogenital anomalies account for 20-30% of prenatally detected structural defects. BEEC describes a subset of anomalies with a spectrum of developmental defects ranging from a mild form of epispadias, to classic bladder exstrophy, to omphalocele, exstrophy, imperforate anus, spinal anomalies (OEIS) complex. Patients with BEEC suffer substantial morbidity and mortality due to impaired genito-urinary dysfunction. The etiology of BEEC is largely unknown. Elucidating the underlying genetic component is critical to gaining a better understanding of the developmental signaling pathways and is likely the first step to developing targeted therapy. Variants in genes identified in other urogenital anomalies appear to be responsible for some cases of BEEC including IS, WNT3, WNT9b, PLAG1 and p63. We propose to take advantage of our extensive analytical experience in the Baylor Hopkins Center for Mendelian Genomics and perform WGS on parent-proband trios for whom the proband has BEEC. One study utilizing whole exome sequencing (WES), identified candidate genes (SLC20A1 and CELSR3) in 2 out of 8 affected patients, providing reassurance that our proposed strategy will be successful. Following WGS, we will explore the pathogenicity of genetic variants by employing a knockout mouse model using CRISPR/Cas9 technology via collaboration with the Jackson Laboratory. Final validation will include mouse phenotyping by dynamic contrast-enhanced MRI under the expertise of, Cory Brayton, mouse pathologist. Aim 1. To identify the genetic basis of BEEC through Whole Genome Sequencing (WGS) Aim 2a. To create the founder (F0) homozygous knockout mouse using CRISPR/Cas9. Aim 2b. To define the murine model phenotype using dynamic contrast enhanced MRI. PUBLIC HEALTH RELEVANCE: Patients with Bladder Exstrophy Epispadias Complex suffer substantial morbidity and mortality due to impaired genito-urinary dysfunction. The etiology of BEEC is largely unknown. Elucidating the underlying genetic component is critical to gaining a better understanding of the developmental signaling pathways and is likely the first step to developing targeted therapy. | |||
2018 X01 Projects
| Project Number: | 1 X01 HL145692-01 | Contact PI / Project Leader: | Chung, Wendy K (Contact); Shen, Yufeng |
| Title: | Genomic Analysis of Esophageal Atresia and Tracheoesophageal Fistulas and Associated Congenital Anomalies | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. There is a 45% incidence of associated congenital malformations, most commonly digestive, cardiovascular, urogenital, and musculoskeletal, often part of a syndrome or complex association, with VACTERL (vertebral defects, anal atresia, cardiac defects, tracheoesophageal fistula, renal anomalies, and limb abnormalities) being most frequently recognized. Advanced surgical techniques and pre and post-operative care have improved the prognosis and survival of EA/TEF patients over the past decades. However, with improved survival, many of the long-term morbidities of EA/TEF have been exposed. It is likely that the outcome in EA/TEF patients is influenced by multiple genetic and clinical factors; however, determining which factors are critical has been limited by the lack of data, particularly genomic data. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of EA/TEF and define new genes and conditions associated with EA/TEF by performing whole genome sequencing on 100 parent child trios in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions and improve outcomes. PUBLIC HEALTH RELEVANCE: Esophageal atresia/tracheoesophageal fistula (EA/TEF) is a rare and complex aerodigestive congenital anomaly with an estimated incidence of 1 in 2500 to 1 in 4000 live births. We propose to elucidate the underlying genomic architecture of EA/TEF by performing whole genome sequencing to characterize new clinical syndromes associated with EA/TEF to provide more accurate clinical prognostic information. | |||
| Project Number: | 1 X01 HL145691-01 | Contact PI / Project Leader: | Seidman, Christine E |
| Title: | Germline Mutations in CHD | Awardee Organization: | Harvard Medical School |
| Abstract: DESCRIPTION (provided by applicant): Congenital heart disease (CHD) is the most common birth defect and is often accompanied by another congenital anomaly (CHD±CA). The Pediatric Cardiovascular Genetics Consortium (PCGC) is committed to defining the molecular mechanisms for CHD±CA. We have recruited over 29,000 participants including over 6000 CHD probands and parents (CHD trios) with extensive clinical data. Whole exome sequence (WES) analyses in ~3300 CHD trios by the PCGC has defined likely genetic causes in ~40% probands. As part of the Gabriella Miller Kids First Pediatric Research Program, we propose WGS to enable the discovery of variants and mechanisms that contribute to unexplained CHD in ~60% of probands studied by the PCGC. To accomplish these goals we will capitalize on new insights into CHD genes, identified by WES, that indicate aberrant transcriptional regulation during development is a major cause of CHD. In this application we request WGS on 550 CHD trios so that by leveraging existing genomic datasets we will empower robust analyses of variants that alter noncoding regulatory elements of cardiac development genes in WES-negative trios. Nested within this trio group are 100 CHD trios comprised of a proband with one damaging variant in a recessive CHD gene. In addition to genome-wide studies, focused analyses in this trio subgroup will search for noncoding variants that impact the “normal” allele. The remaining 450 CHD trios include probands with tetralogy of Fallot (ToF), the most common form of cyanotic heart disease. We will harness WGS in ToF trios to inform variants within particular genome regions that are susceptible to recurrent copy number and structural variants - regions that are poorly interrogated by WES. While mutation in these several variant-susceptible genes and loci are often found in ToF patients, these are remarkably absent in many ToF probands studied by WES and CNV analyses. Finally, we request high-depth WGS of 200 discarded CHD tissues obtained during surgical repair, to explore novel genetic mechanisms in CHD, including somatic mosaicism, mitochondrial variants, and to provide initial evidence of prenatal infections that may contribute to CHD. In all of these studies we will use existing resources and capabilities of the PCGC and its companion consortium in the Bench to Bassinet Program, the Cardiovascular Development Consortium, to perform confirmatory functional genomics studies using cell and animal models outside of the GMKF program. We expect that these studies will provide novel insights into the molecular basis for birth defects and fundamental knowledge about genes and pathways involved in the development of the heart and other organs. We request: 1. WGS (90X coverage) on 200 CHD tissues. 2. WGS on 100 CHD trios comprised of a proband with a damaging variant in a recessive CHD gene. 3. WGS on 450 TOF trios. PUBLIC HEALTH RELEVANCE: Using whole genome sequencing, we aim to discover the genetic mechanisms for congenital heart disease, the most common human birth defect. We will identify sequence variants that alter regulatory elements involved in developmental transcription and consider the consequences of these on discarded heart tissues obtained during surgical repair of heart malformations. Through focused analyses of tetralogy of Fallot, we hope to better understand the processes that promote this complex and prevalent heart malformation. | |||
| Project Number: | 1 X01 HL145698-01 | Contact PI / Project Leader: | Gharavi, Ali G |
| Title: | Genetics of Structural Defects of the Kidney and Urinary Tract | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Congenital Anomalies of the Kidney and Urinary Tract (CAKUT) account for up to 50% of pediatric and 7% of adult end-stage kidney failure worldwide. The goal of this project is to apply genetic approaches to resolve the biological basis and clinical manifestations of CAKUT using three well-characterized cohorts with deep phenotypes and extensive longitudinal data (the NIDDK sponsored CKiD and RIVUR studies, and the Columbia cohort). Here, we hypothesize that CAKUT is genetically heterogeneous, and caused by rare mutations with large effect on a background of polygenes with small effects that can be discovered by analysis of well phenotyped cohorts compared to genetically matched cohorts with WGS data available. We now propose to extend our prior studies by whole genome sequencing (GWS) in patients with CAKUT from 3 well-phenotyped cohorts. We expect that the proposed studies will provide new insight into urogenital development, clarify the clinical overlap with other syndromes and provide novel tools that can replace the current morphology-based diagnostic approaches. We will first perform annotation based on a standard ACMG guidelines to identify pathogenic CNVs and single nucleotide variants diagnostic for known genetic disorders. In aim 2, we will perform genome-wide analysis of common and rare variant burden combining a case-control and trio design to detect new genes for CAKUT. We will next replicate top signals in additional CAKUT cohorts available in our laboratory. Finally, we will per phenotype- genotype correlations with longitudinal clinical data such a kidney function, proteinuria or neurodevelopmental outcomes to gain insight into clinical impact of causal variants. PUBLIC HEALTH RELEVANCE: Congenital defects of the kidney and urinary tract are a common cause of kidney failure in children and adults and elucidation of the genetics of these disorders will provide new opportunities for diagnosis, risk stratification and prevention of complications. Sequence and clinical data released in dbGap:Accession Number:phs002162 | |||
| Project Number: | 1 X01 HL145697-01 | Contact PI / Project Leader: | Krantz, Ian |
| Title: | Genomic Diagnostics in Cornelia de Lange Syndrome, Related Diagnoses and Structural Birth Defects | Awardee Organization: | Children's Hospital Of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Disorders of human morphogenesis are a major cause of human suffering for the affected individuals and their families. Congenital anomalies are identified in approximately 3% of term births, 10% of stillbirths, and in as many as 50% of first trimester spontaneous abortuses. While most, if not all, human structural birth defects have a significant genetic component, identification of genetic perturbations in isolated structural birth defects has been complicated by the complex nature of their underlying etiologies, likely involving disruption of regulatory elements that can act in a temporal and tissue specific manner, multi-gene, epigenetic and gene-environment interactions. Our approach to tease out genetic contributions to birth defects has been to identify the underlying causes of syndromic birth defects which are often Mendelian in nature and therefore lend themselves more readily to genetic causal identification. Once identified, these genetic causes of syndromic forms of birth defects can be leveraged to understand the genetic contributions to isolated birth defects seen in constellation in these syndromes. We propose to use Cornelia de Lange Syndrome (CdLS), a dominant multisystem developmental disorder consisting of a constellation of structural birth defects involving most body systems and significant growth and cognitive impairment as a prime example of this approach. We and others have shown that alterations in the cohesin and associated pathways are causative of CdLS and related diagnoses when disrupted and have more broadly been termed “cohesinopathies” or “disorders of transcriptional regulation (DTRs)”. In this proposal we outline an initial plan to perform genome sequence (subsequently RNA sequencing will be considered) on a unique cohort of 501 probands and family members with clinically confirmed CdLS or a related diagnosis in whom molecular analysis by targeted gene sequencing, next generation sequencing (NGS) panels or exome sequencing have been negative but are strongly suspected of having an underlying genetic alteration to explain their clinical features. This work will lead to the identification of genes critical in human embryonic development, provide novel insights into transcriptional regulation and help to identify genetic causes and candidate genes for isolated birth defects seen in constellation in this group of diagnoses. Most critical developmental genes are also cancer genes and the genes known to cause CdLS are no exception. CdLS is not a cancer predisposition syndrome so understanding the mutational mechanisms in these genes that lead to structural birth defects when present in the germ line and result in cancer when mutated somatically is a fundamental aspect of this research. PUBLIC HEALTH RELEVANCE: The proposed research Program is relevant to public health as we are addressing a major gap in our understanding of the genetic basis of syndromic and non-syndromic structural birth defects (with a focus on Cornelia de Lange syndrome and related diagnoses and birth defects), a major cause of human suffering for the affected individuals and their families. The proposed research Program is highly relevant to the NIH mission of improving health outcomes as we expect that discoveries of the basic mechanisms of structural birth defects will lead to improved diagnostics, counseling, management and therapeutics for affected individuals and their families. | |||
| Project Number: | 1 X01 HL145690-01 | Contact PI / Project Leader: | Seidman, Jonathan G |
| Title: | The Genetics of Microtia in Hispanic Populations | Awardee Organization: | Harvard Medical School |
| Abstract: DESCRIPTION (provided by applicant): Microtia is a rare congenital deformity of the external ear, the pinna. The severity of microtia is variable and ranges from subtle deformities in the pinna to absence of the external ear. Microtia is often associated with closure of the external auditory ear canal causing significant hearing loss. Microtia can be an isolated, unilateral or bilateral malformation, or occur solely with ear canal deformities, or with additional craniofacial or syndromic manifestations. Our study of identical twins with microtia demonstrated a significant genetic contribution. The molecular pathogenesis for most microtia remains unknown. We propose to leverage our clinical acumen in diagnosis and treatment of microtia (R.E.), our relationship to the microtia community (M.T.) and our collected DNA samples from microtia patients to identify genetic variant(s) that contribute to this congenital malformation. Microtia prevalence is much higher among Native Americans and some Latin Americans (17 per 10000 Ecuadorian births) than among individuals of European-descent (0.6 -1.6 per 10,000 births). To capitalize on this epidemiologic data, we have recruited microtia cohorts from Latin America and the U.S, including clinical data and DNA samples. We propose whole genome sequence of existing samples from isolated cases, trios (proband and parents) and one large family we propose comprehensive genetic analyses to interrogate coding and non-coding sequence variants associated with microtia. We hypothesize that genetic variants that cause microtia and other less pathogenic conditions, which have relatively small impact on reproductive fitness, are likely to be tolerated and inherited, but cause malformations in only a fraction of variant carriers (i.e. reduced penetrance). We suggest that we have power to detect a variant that increases the relative risk of microtia by >2.5 (i.e. a penetrance of ~3%). We suggest that microtia likely reflects variants with low penetrance that impact genes that participate in the molecular pathways of ear development. Such variants may also contribute to other hearing and craniofacial malformations. We expect to harness the insights and reagents developed here to elucidate factors that impact the penetrance of variants. Because of the prevalence of microtia in Latin America there are microtia support groups in Mexico, Colombia, and Ecuador. We have formed alliances, through our collaborator Melissa Tumblin (Ear Community), with these microtia support groups. We anticipate that any associations detected in the preliminary whole genome sequence (WGS) cohort will be confirmed in a second cohort of microtia patients. We request that the Gabrielle-Miller Kids First program support WGS of 821 microtia subjects and their parents as follows: a) 200 microtia probands; b) 200 trios (proband and both parents) and c) 21 members of family 3Sz. PUBLIC HEALTH RELEVANCE: We request whole genome sequence of 821 Hispanic subjects who have at least one family member with microtia, or abnormal outer ear formation. There are 200 microtia probands without parents, and 200 microtia probands with parents (trios, n=400) and 21 from a large family with 6 cases of microtia. We expect that analysis of the WGS will identify a gene variant(s) that increases the risk of microtia in some Latin American populations by ~25 fold and will provide new insights into the development of the outer ear. Sequence and clinical data released in dbGap:Accession Number: phs002172 | |||
| Project Number: | 1 X01 HL145702-01 | Contact PI / Project Leader: | Chambers, Christina |
| Title: | Discovery of Genetic Basis of Fetal Alcohol Spectrum Disorders | Awardee Organization: | University Of California, San Diego |
| Abstract: DESCRIPTION (provided by applicant): Fetal Alcohol Spectrum Disorder (FASD) is the most common birth defect worldwide, and is estimated to occur in at least 1-5% of all children in the U.S. However, not all children with prenatal exposure are similarly affected, even among those born to heavy, chronic alcohol-consuming pregnant women. Recent research has focused on the susceptibility or protective factors that seem to influence the risk for FASD. However, very little is known about the genetic risk or protective factors that may interact with prenatal alcohol exposure leading to this variable risk. In this study, we will use whole genome sequencing of well-characterized mother-child pairs, including mothers with or without prenatal alcohol exposure and their children with or without FASD, to test the hypothesis that genomic alterations in either the mother or her fetus or both play a role in susceptibility to the effects of alcohol. This information will be of critical value in better understanding the pathogenetic mechanisms underlying FASD. In addition, the identification of maternal or fetal genetic susceptibility factors for FASD may inform future intervention strategies for this common congenital disorder. PUBLIC HEALTH RELEVANCE: Fetal Alcohol Spectrum Disorder (FASD) is estimated to occur in at least 1-5% of all children in the U.S. and is a major public health issue. However, in addition to alcohol, other susceptibility factors, such as maternal or fetal genetic variation, must play a role as not all children prenatally exposed to alcohol are similarly affected. The proposed study will examine the role of genetic susceptibility for FASD; this work will help to inform more effective intervention efforts for this common congenital disorder | |||
| Project Number: | 1 X01 HL145686-01 | Contact PI / Project Leader: | Lupo, Philip J (Contact); Rabin, Karen R; Sherman, Stephanie L.; Yang, Jun J |
| Title: | Genomic Analysis of Congenital Heart Defects and Acute Lymphoblastic Leukemia in Children with Down Syndrome | Awardee Organization: | Baylor College Of Medicine |
| Abstract: DESCRIPTION (provided by applicant): Down syndrome (DS), which occurs due to trisomy 21, is one of the strongest risk factors for both congenital disease (CHD) and acute leukemia. For instance, children with DS have a 2000-fold increased risk of atrioventricular septal defects (AVSD) and a 20-fold increased risk of acute lymphoblastic leukemia (ALL). An important and innovative aspect of the Kids First program is understanding the overlap between structural birth defects and childhood cancer. Notably, the background of DS predisposes children to both phenotypes, however, the genomic architecture of risk remains largely undiscovered. Therefore, we propose that our assembled cohort of children with: 1) DS alone (n=607) 2) DS with AVSD (DS-AVSD, n=623) 3) DS with other CHD (DS-oCHD, n=594) and 4) DS with ALL (DS-ALL, 370) will advance our understanding of the developmental pathways that may lead to both structural birth defects and childhood cancer. The objectives of this study are to determine the genetic variants underlying AVSD and ALL risk in children with DS. Our central hypothesis is that risk-associated genetic variants in the background of DS lead to a higher penetrance of AVSD and ALL. Our secondary hypothesis is that rare variants explain a significant proportion of the increased risk of AVSD and ALL in children with DS. Our hypotheses are supported by our previous work indicating: 1) previously identified susceptibility loci in ALL genes (e.g., IKZF1) have stronger effects in children with DS-ALL compared to non-DS-ALL 2) common genetic variants and copy number variants do not explain the increased risk of AVSD among those with DS and 3) there is an increased burden of rare variants among children with DS-AVSD compared to those with DS alone. Therefore, the aims of our study are: 1) compare whole-genome sequencing (WGS) data between children with documented DS-AVSD and children with DS who have structurally normal hearts to identify genetic variants that perturb heart development and 2) compare WGS data between children with documented DS-ALL and children (from Aim 1) with DS who do not have a known history of ALL. For the subset of DS-ALL cases with a paired tumor sample, we will examine associations between germline mutations and somatic genomic features. This study will address the fundamental question of why children with DS have an elevated risk of AVSD and ALL. Insights into the genes that drive DS-AVSD and DS-ALL may have implications for improved genetic counseling, surveillance, clinical management, and treatment strategies for these children. Additionally, our findings may inform targeted therapies or interventions for children without DS who are at risk for structural birth defects and cancer. PUBLIC HEALTH RELEVANCE: PROJECT Children with Down syndrome (DS), which occurs due to trisomy 21, have a 2000-fold increased risk of atrioventricular septal defects (AVSD) and a 20-fold increased risk of acute lymphoblastic leukemia (ALL), but it is not understood which genetic features of trisomy 21 are responsible for the increased risk. The objectives of this study are to determine the genetic variants underlying AVSD and ALL risk in children with DS, which builds upon our previous work suggesting having an extra copy of chromosome 21 may “move” the susceptibility threshold for disease in these children. Insights into the genes that drive DS-AVSD and DS-ALL may have implications for improved genetic counseling, surveillance, clinical management, and treatment strategies for these and other children who may develop AVSD or ALL. | |||
| Project Number: | 1 X01 HL145695-01 | Contact PI / Project Leader: | Drolet, Beth A |
| Title: | Analyzing the Genetic Spectrum of Vascular Anomalies, Overgrowth and Structural Birth Defects | Awardee Organization: | Medical College Of Wisconsin |
| Abstract: DESCRIPTION (provided by applicant): Vascular anomalies include a heterogeneous group of tumors and malformations characterized by the presence of abnormal vascular structures. Vascular anomalies most often occur in the skin and soft tissue; however, they can occur within any organ and present with a wide range of symptoms and complications, depending on type and location of the lesion. These disorders are remarkably variable ranging from simple staining of the skin with mild soft tissue overgrowth to debilitating tissue overgrowth and severe structural birth defects. We assembled a large vascular anomalies cohort recruited from a 20-institution network to discover genes related to vascular anomalies and structural birth defects. Using targeted next-generation sequencing, we and others, have detected postzygotic mosaic variants in affected tissue from several vascular anomalies. The causative variants almost entirely overlap with those variants observed in cancer. The preliminary data generated from this cohort reinforces the approach set forth by the Gabriella Miller Kids First Program by demonstrating a direct connection between cancer and structural birth defects. We hypothesize that vascular anomalies are caused by postzygotic somatic mutations and that the phenotype is further influenced by the mutational burden, the tissue distribution of mutation, and germline alterations, which establish a necessary context in which postzygotic alterations act. Improved understanding of the complex genetic landscape of vascular anomalies will be critical for accurate diagnosis, the development of care guidelines, consideration of therapeutic options, and planning of future clinical trials. Aim 1: Identify genomic alterations in vascular anomalies, Aim 2: Contribute the data generated in this project to the Kids First Data Resource and the National Center for Biotechnology Information’s (NCBI) Database of Genotypes and Phenotypes (dbGaP). PUBLIC HEALTH RELEVANCE: Genomic analysis of vascular anomalies will inform treatment and expand knowledge about the causes of birth defects affecting blood vessels, brain, eye, and bones. The knowledge gained in this study will be used to drive strategies for prevention and provide critical targets for treatments for vascular anomalies and related birth defects. | |||
| Project Number: | 1 X01 HL145696-01 | Contact PI / Project Leader: | Meshinchi, Soheil |
| Title: | Germline and Somatic Variants in Myeloid Malignancies in Children | Awardee Organization: | Fred Hutchinson Cancer Research Center |
| Abstract: DESCRIPTION (provided by applicant): Advances in genomic sequencing has allowed identification of somatic variants as potential therapeutic targets. Although myeloid disorders in children may show morphologic similarities to that seen in adults, TARGET AML initiative (Meshinchi, PI) clearly demonstrated that somatic genomic and transcriptome variants are highly distinct in children and young adults, and in fact there are variants that are uniquely restricted to younger children. TARGET AML initiative, although modest in number, helped identify numerous somatic alterations with high therapeutic potential in younger AML patients. In addition to identification of somatic variants, analysis of the germline data provided a glimpse into the constitutional make-up of patients with AML. The identification of numerous “function altering” variants may provide an insight into possible interactions between the host and the disease, where these germline variants might alter AML risk (predisposition), response to therapy (altering target expression, drug metabolism), susceptibilities to short and long term complications (including infectious and cardiac complications) or modify risk of secondary malignancies. Armed with data from initial sequencing efforts in AML, we are poised to take full advantage of the available sequencing technology to conduct the most comprehensive genome and transcriptome interrogation of myeloid disorders in children in specimens we have amassed over the last decade. To this end, we have put in place unparalleled specimen resources from children with de novo AML, Down Syndrome AML (DS-AML), and acute promyelocytic AML (APL) treated on COG trials. In addition, thru collaboration with Dr. Resar and Kucine, we will be able to conduct the first broad sequencing study in the rare entity of myeloproliferative neoplasms of childhood (MPN-c). Identification of the somatic variants will provide valuable data on the potential genes and pathways that can be targeted for therapeutic gains. In addition, interrogation of the host’s constitutional genome may yield valuable information about potential germline variants that, in combination with the somatic data, might provide a more informed approach to patient care. For those patients with predisposition mutations, chemotherapy alone might not be adequate for cure and stem cell transplantation might be required. Also, those who might be at high risk of adverse secondary events (cardiac complications, secondary malignancies, etc.) can be identified early and their therapy tailored to minimize anticipated complications. Thus, we propose that the optimum outcome can only be obtained thru comprehensive interrogation of the somatic and germline genome to fully annotate the genomic makeup of the leukemia and its host. OMB No. 0925-0001/0002 (Rev. 01/18 Approved Through 03/31/2020) Page Continuation Format Page PUBLIC HEALTH RELEVANCE: Clinical outcome in children with myeloid disorders have remained poor in part due to lack of deep understanding of the genomic makeup of the disease as well as the host. Comprehensive studies of the host and disease may enable more informed therapies in order to optimize targeting the leukemia while minimizing short and long term toxicities, leading to improved survival with minimal morbidities. | |||
| Project Number: | 1 X01 HL145700-01 | Contact PI / Project Leader: | Lau, Ching Ching (Contact); Poynter, Jenny N. |
| Title: | Genetic Predisposition to Intracranial Germ Cell Tumors | Awardee Organization: | The Jackson Laboratory |
| Abstract: DESCRIPTION (provided by applicant): Pediatric germ cell tumors (GCTs) are rare and heterogeneous tumors that most commonly occur in the gonads but also develop in other locations. Intracranial GCTs (IGCTs) account for approximately 3% of brain tumors in children in the U.S. but are far more prevalent in Japan and East Asian countries, where they account for up to 11% of brain neoplasms. These observations suggest that there is genetic predisposition to IGCT. Currently little is known about the etiology of IGCTs. Their incidence peaks in the second decade of life with rates that vary widely by geography and are higher in males than in females. Recent reports support familial aggregation of IGCT. Data from the PIs of this project support the hypothesis that genetic variants contribute to IGCT predisposition, as rare variants in the gene JMJD1C were identified among a Japanese patient population in strong association with IGCT. JMJD1C is a plausible susceptibility gene for IGCT given its role in sex steroid hormone regulation and maintenance of male germ cells in mice. Additionally, it has been hypothesized that intracranial and other GCTs both arise from primordial germ cells that migrated abnormally during development. Indeed, using case parent trios recruited for a Children’s Oncology Group (COG), the PIs of this project found that common genetic variants associated with adult testicular GCT are also associated with both intracranial and systemic GCT, suggesting that there may be common genetic risk factors for all GCT types. Identification of additional genetic variants for IGCT risk will require a larger study using whole-genome sequencing (WGS) data. To test the hypothesis that there are genetic variants that increase susceptibility to pediatric IGCT development, this project will carry out three Aims that focus on a cohort of more than 400 IGCT cases from the U.S., Japan, and Thailand. Aim 1 will validate the importance of JMJD1C as a susceptibility locus for IGCT in Japanese and non-Japanese populations by identifying additional rare and novel variants that are over-represented in IGCT, which are expected to occur at a much higher frequency in Japanese IGCT cases. Aim 2 will identify novel susceptibility variants for IGCT that are enriched in the Japanese population by applying a previously developed filtering approach. Aim 3 will identify novel variants associated with IGCT using aggregate burden tests, focusing on genes and established regulatory regions. This analysis will improve the power to identify novel variants associated with IGCT in the entire cohort of samples and is anticipated to enable identification of familial predisposition for IGCT in both known and unrecognized cancer susceptibility genes. The availability of IGCT whole-genome sequencing data through the Gabriella Miller Kids First Data Resource Center will offer the cancer research community an opportunity to investigate the genetic basis of IGCT and promote the clinical risk assessment and treatment of this cancer. Additionally, the identification of associated genetic variants is anticipated to inform the understanding of other forms of pediatric cancers. PUBLIC HEALTH RELEVANCE: / RELEVANCE TO PUBLIC HEALTH Pediatric intracranial germ cell tumors (IGCTs) account for approximately 3% of brain tumors in children in the U.S. but are far more prevalent in Japan and East Asian countries, where they account for up to 11% of brain neoplasms. To understand the genetic risks of developing this cancer type in childhood, we have gathered hundreds of cases from the U.S., Japan, and Thailand so that their genomes can be fully sequenced through the Gabriella Miller Kids First Pediatric Research Program and be made publicly available as part of the Kids First Data Resource. We will computationally analyze this sequencing data to identify those genetic variants that are associated with IGCT and determine which gene functions are perturbed by these variants to increase susceptibility to this disease. | |||
| Project Number: | 1 X01 HL140546-01A1 | Contact PI / Project Leader: | Jelin, Angie Child |
| Title: | Single gene pathogenic variants associated with BEEC (Bladder extrophy, Epispadias, Complex) | Awardee Organization: | Johns Hopkins University |
| Abstract: DESCRIPTION (provided by applicant): This X01 application is submitted by Angie C. Jelin, MD, Assistant Professor of Gynecology and Obstetrics/Genetics at the Johns Hopkins School of Medicine. Dr. Jelin’s long term goal is to become an independent investigator in fetal urinary tract anomalies. Towards this goal, she proposes whole genome sequencing (WGS of Bladder Exstrophy Epispadias Complex (BEEC). Urogenital anomalies account for 20-30% of prenatally detected structural defects. BEEC describes a subset of anomalies with a spectrum of developmental defects ranging from a mild form of epispadias, to classic bladder exstrophy, to omphalocele, exstrophy, imperforate anus, spinal anomalies (OEIS) complex. Patients with BEEC suffer substantial morbidity and mortality due to impaired genito-urinary dysfunction. The etiology of BEEC is largely unknown. Elucidating the underlying genetic component is critical to gaining a better understanding of the developmental signaling pathways and is likely the first step to developing targeted therapy. Variants in genes identified in other urogenital anomalies appear to be responsible for some cases of BEEC including IS, WNT3, WNT9b, PLAG1 and p63. We propose to take advantage of our extensive analytical experience in the Baylor Hopkins Center for Mendelian Genomics and perform WGS on parent-proband trios for whom the proband has BEEC. One study utilizing whole exome sequencing (WES), identified candidate genes (SLC20A1 and CELSR3) in 2 out of 8 affected patients, providing reassurance that our proposed strategy will be successful. Following WGS, we will explore the pathogenicity of genetic variants by employing a knockout mouse model using CRISPR/Cas9 technology via collaboration with the Jackson Laboratory. Final validation will include mouse phenotyping by dynamic contrast-enhanced MRI under the expertise of, Cory Brayton, mouse pathologist. Aim 1. To identify the genetic basis of BEEC through Whole Genome Sequencing (WGS) Aim 2a. To create the founder (F0) homozygous knockout mouse using CRISPR/Cas9. Aim 2b. To define the murine model phenotype using dynamic contrast enhanced MRI. PUBLIC HEALTH RELEVANCE: Patients with Bladder Exstrophy Epispadias Complex suffer substantial morbidity and mortality due to impaired genito-urinary dysfunction. The etiology of BEEC is largely unknown. Elucidating the underlying genetic component is critical to gaining a better understanding of the developmental signaling pathways and is likely the first step to developing targeted therapy. | |||
2017 X01 Projects
| Project Number: | 1X01 HL 140535-01 | Contact PI / Project Leader: | Simeon Boyd |
| Title: | Whole genome sequencing of nonsyndromic craniosynostosis | Awardee Organization: | University of California Davis |
| Abstract: DESCRIPTION (provided by applicant): Craniosynostosis (CS), the premature fusion of one or more cranial sutures, is a common, major structural birth defect occurring in about 1 in 2,500 live births. About 85% of infants with CS present with nonsyndromic craniosynostosis (NCS) without associated birth defects or developmental delays. NCS is a heterogeneous condition with presumed multifactorial etiology and its causes remain largely unknown. Primary prevention strategies for NCS are limited. Our International Craniosynostosis Consortium (ICC) has advanced understanding of the genetic etiology for sagittal NCS (sNCS). Through our previous NIH-NIDCR funding (R01 DE016866), we successfully conducted the first genome-wide association study (GWAS) for sNCS and identified robust associations to loci near BMP2 and BBS9, both biologic plausible genes involved in skeletal development. A similar GWAS with 415 case-parent trios with metopic NCS (mNCS) is in progress, as is an additional GWAS of over 600 coronal NCS (cNCS) case-parent trios. Additionally, others reported that by whole exome sequencing (WES), SMAD6 mutations were found in 7% of probands in a cohort of sNCS, mNCS, or combined NCS cases. Importantly, among 17 NCS cases with SMAD6 mutations, 14 had T>C mutation (rs1884302) downstream of BMP2, suggesting a two-loci inheritance model. This discovery of an epistatic interaction between BMP2 and SMAD6 through use of GWAS and WES approaches explains only a small proportion of all NCS cases. Along with the data generated from the completed and ongoing GWAS’s, we believe that whole genome sequencing (WGS) is the next important step towards identifying causal variants in NCS cases, because it has the power to discover rare and common variants missed by other high- throughput technologies. We hypothesize that WGS will identify novel genetic factors beyond those identified with GWAS’s that contribute to the etiology of NCS. In this application, we propose to investigate 600 case- parent trios (200 cases each with sNCS, cNCS, and mNCS) and 20 multiplex families (11 with sNCS and 9 with mNCS) using WGS for discovery of all types of germline variants (de novo and inherited single nucleotide variants, insertions/deletions and structural variations). Somatic mutations contribute to the etiology of cancer and have been reported in some structural birth defects. Thus, we will perform WGS on 25 paired blood- derived and bone-derived DNA specimens obtained from sNCS probands for detection of somatic mutations. Our discovery specimen repository represents one of the largest collections compiled, and along with our extensive collection of independent specimens for future replication studies, represents an unparalleled resource for studying the genetic etiology of NCS. Given our past accomplishments, experienced interdisciplinary research team, and substantial resources, we are well-positioned to successfully complete the proposed research and provide critical insights into the multifactorial etiology of NCS. PUBLIC HEALTH RELEVANCE: Nonsyndromic craniosynostosis (NCS) is a common, major structural birth defect – due to the premature fusion of one or more cranial sutures – that requires extensive surgical correction and is associated with considerable ongoing medical problems and health care costs. Because little is known about the causes of NCS, whole genome sequencing will help advance knowledge of genetic factors contributing to the etiology of NCS. Sequencing data generated will lead to a better understanding of biological processes involved in the etiology of NCS and provide critical insights for development of early diagnostic tools and therapeutic strategies. | |||
| Project Number: | 1X01 HL 140516-01 | Contact PI / Project Leader: | Azeez, Butali |
| Title: | Whole Genome Sequencing of African and Asian Orofacial Clefts Case-Parent Triads | Awardee Organization: | University of Iowa |
| Abstract: DESCRIPTION (provided by applicant): Principal Investigators: Dr Azeez Butali is a tenure-track Assistant Professor at the Iowa Institute for Oral Health Research, College of Dentistry, and the University of Iowa. His primary research focus is on the genetics and epidemiology of complex traits including orofacial clefts. Dr Terri Beaty is a Professor at the John Hopkins University. Her research focus is on genetic epidemiology studies of several chronic diseases with complex etiologies, where both genetic and environmental risk factors control risk of disease. Co-investigators: Dr Adebowale Adeyemo is Deputy Director at the National Human Genome Research Institute. His focus is on the genetics and genomics of complex traits in African population. Dr Marazita is a Professor at the University of Pittsburgh. She is an expert in statistical genetics application for complex traits and identification of sub-clinical cleft phenotypes. Dr Cao is an Assistant Professor at the University of Iowa. He uses bioinformatics tools to interrogate the human genome and for analyses of gene-regulatory networks. Dr Ruczinski is a Professor at the John Hopkins University. His expertise is in statistical genetics, genomics and proteomics of complex traits. Dr Taub is an Assistant Scientist at the John Hopkins University. Her area of expertise is in genomics and statistical genetics for gene expression data, genotyping data and DNA methylation data Environment: The University of Iowa is a leading institution with a strong reputation for excellence in teaching, research and healthcare. The John Hopkins University is one of the leaders in the research, teaching and healthcare in the US. Both institutions are consistently amongst centers supported by NIH grants Research Study: The focus of this study is to identify novel risk variants for OFC in Africa and Asian OFC case-parent triads through analysis of Whole Genome Sequencing data. PUBLIC HEALTH RELEVANCE: TITLE: Whole Genome Sequencing of African and Asian Orofacial Case-Parent Triads The long term goal of this study is to identify specific genomic variants through WGS of OFC case-parent triads from African and Asian populations. The knowledge gained from these WGS studies will drive future research on OFC and should eventually lead to more effective interventions to reduce the risk of OFC. | |||
| Project Number: | 1X01 HL 140543-01 | Contact PI / Project Leader: | Wendy Chung |
| Title: | Genomic Analysis of Congenital Diaphragmatic Hernia and Associated Congenital Anomalies | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Abstract Congenital diaphragmatic hernia (CDH) is defined as a defect in the muscular or tendinous portion of diaphragm that results in antenatal herniation of the abdominal contents into the thoracic cavity and pulmonary hypoplasia due to compression of the lungs. The incidence of CDH is 1 in 3000 live births, accounting for 1- 2% of infant mortality and 8% of all birth defects, making it one of the most common and lethal congenital anomalies. CDH is isolated in 50-60% of cases but is associated with other major anomalies, most commonly congenital heart disease or central nervous system malformations, in the remaining 40-50%. Historically CDH carried a grave prognosis with mortality of greater than 50%. However, with recent advances in the post-natal care of children with CDH, survival has improved significantly. However, with improved survival, many of the long term morbidities of CDH have been exposed including pulmonary hypertension, the leading cause of CDH morbidity and mortality. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. The etiology of CDH is largely unknown. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of CDH and define new genes and conditions associated with CDH by performing whole genome sequencing on parent child trios and RNA sequencing of diaphragm tissue in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. Our long-term goal is to define a set of genes important in the etiology of CDH and characterize new clinical syndromes associated with CDH. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions. PUBLIC HEALTH RELEVANCE: Congenital diaphragmatic hernia (CDH) is a serious birth defect accounting for 1-2% of infant mortality and 8% of all birth defects. We propose to elucidate the underlying genomic architecture of CDH by performing whole genome sequencing and RNA sequencing on diaphragm tissue to characterize new clinical syndromes associated with CDH to provide more accurate clinical prognostic information. | |||
| Project Number: | 1X01 HL 140544-01 | Contact PI / Project Leader: | Hakon Hakonarson |
| Title: | Genetics at the Intersection of Childhood Cancer and Birth Defects | Awardee Organization: | The Children's Hospital of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Evidence of a connection between childhood cancers and birth defects comes from three major sources: clinical observations of syndromes, registry linkages, and case-control studies. These studies demonstrate that children with a variety of birth defects have a significantly increased risk of developing several types of childhood cancers. However, due to the sparsity of cases, few risk factors have been consistently confirmed for specific types of birth defects and childhood cancers, and the etiology of most of these entities remains unexplained. This proposal will leverage the unique resources of The Center for Applied Genomics (CAG) at The Children’s Hospital of Philadelphia (CHOP) which houses the largest genomic facility/pediatric biobank in the US. We have identified 1,205 pediatric cancer patients that were also diagnosed with a birth defect from the CAG biobank. All have banked DNA samples from peripheral blood that are ready for sequencing together with age, sex and ethnically matched controls. The patients are from diverse backgrounds and the majority of them authorize re-contact. This study will utilize two complementary analytical approaches to disease gene discovery. Patients with parental sequences will be analyzed as trios in a typical winnowing variant prioritization approach. We also propose to sequence matched controls for each of the cases allowing for powerful statistical case control approaches, namely burden tests, to be applied to the dataset. Two strengths of this study design are the large sample sizes for what are rare phenotypes and the combination of birth defects and childhood cancers in all cases which are more likely to be burdened with low frequency variants that confer risk and that more impactful variants are more likely to be discovered. PUBLIC HEALTH RELEVANCE: Birth defects and childhood cancer share biological pathways that are important for cell growth and division. We propose that sequencing pediatric patients suffering both conditions will allow us to discover the underlying genes and in turn advance our understanding of the causes of these devastating diseases. | |||
| Project Number: | 1X01 HL 140518-01 | Contact PI / Project Leader: | Daniela Luquetti |
| Title: | Craniofacial Microsomia: Genetic Causes and Pathway Discovery | Awardee Organization: | Seattle Children's Hospital |
| Abstract: DESCRIPTION (provided by applicant): Craniofacial microsomia (CFM), also termed hemifacial microsomia or oculo-auricular-vertebral spectrum, is the third most common congenital craniofacial condition. CFM has an estimated birth prevalence in the US of 1 in 3,500-5,600, which is similar to conditions such as cystic fibrosis (1 in 3,700) and neurofibromatosis (1 in 4,200). CFM comprises a variable phenotype, and the most common features include malformations of the ear (i.e. microtia) and lower jaw (i.e. mandibular hypoplasia) on one or both sides. The etiology of CFM is largely unknown; however the presence of multiple cases within families, mouse models with CFM malformations and the increased risk of CFM in some ethnicities suggest that genetic variants contribute to its occurrence. Although chromosomal abnormalities have been associated with CFM, only three causative genes have been identified in few cases: HOXA2, FGF3, and MYT1. Our goal in this proposal is to identify coding and non- coding variants that are genetic risk factors to CFM by performing whole-genome sequencing (WGS) of case- parent trios with CFM. We propose to perform whole genome sequencing on DNAs from 105 trios (individuals with CFM and their parents or affected relatives in multi-affected families) to identify candidate genes with rare de novo and inherited variants. Our hypothesis is that CFM is caused by rare new and inherited DNA variation in gene(s) related to the craniofacial development. We will analyze the data on rare de novo coding and non- coding variants. Recognizing reduced penetrance in CFM, our analysis will include analyses for variants in a dominant inheritance with incomplete penetrance model. Our approach incorporates detailed phenotype, clinical characterization, and family history for each individual. We will also integrate the WGS data with our data on gene expression from murine embryonic pharyngeal arch and external ear human embryonic tissue to ascertain tissue specific expression at the relevant time of the development of tissues in CFM. Our statistical power by sampling patients with familial and severe disease who are most likely to have a high genetic loading. CFM represents an ideal condition in which to identify susceptibility variants because it is (1) relatively rare and represents more extreme selection under a liability threshold model, (2) distinctive, (3) stable, and (4) This study will be conducted by an interdisciplinary team with complementary expertise in clinical aspects of CFM, clinical genetics, genomics, and bioinformatics. Successful completion of this proposal will advance knowledge in the genetic architecture of susceptibility to CFM and will provide insight about the biological mechanisms underlying craniofacial development. The phenotypic and genomic data will be fully integrated into the Kids First Data Resource and available to all qualified investigators. The long-term goal of this project is to identify specific genetic risk factors to improve genetic counseling, enable tailored clinical care, and to provide more accurate prognosis. often familial (20-40% of cases). PUBLIC HEALTH RELEVANCE: Craniofacial microsomia (CFM) is the third most prevalent condition that affects craniofacial development; however, the cause of CFM is unknown for most affected individuals. We have established a cohort through previous studies and collected DNA to identify the genetic contributions to CFM, which could facilitate diagnosis, tailored treatment and guide prevention strategies. The results from the proposed study have potential to further research on the etiology of other craniofacial disorders, and the pathogenesis of typical and atypical craniofacial development. Sequence and clinical data released in dbGap: Accession Number: phs002130 | |||
| Project Number: | 1X01 HL 140547-01 | Contact PI / Project Leader: | Joshua Schiffman |
| Title: | Expanded Ewing sarcoma cohort for tumor genomics and association with DNA repair deficiences, clinical presentation, and outcome | Awardee Organization: | University of Utah |
| Abstract: DESCRIPTION (provided by applicant): Expanded Ewing sarcoma cohort for tumor genomics and association with DNA repair deficiencies, clinical presentation, and outcome Ewing sarcoma (ES) is the second most common bone tumor in children and adolescents, but is still relatively rare without much known about genetic risk and only small cohort studies linking tumor genomics to clinical features. Our group was awarded an initial Gabriella Miller Kids First (GMKF) Pediatric Research Program (X01) to study a cohort of germline DNA samples from the Project GENESIS cancer epidemiology study (Genetics of Ewing Sarcoma International Study, COG AEPI10N5), which included whole genome sequencing (WGS) on 329 ES trios (patient-mother-father) plus 123 individual ES patients, with 327 ES patients from the Children’s Oncology Group (COG). The GMKF WGS germline data are now in the process of being returned for analysis. For this expanded study to explore ES tumor genomics, we have assembled a team of leading biologists and clinical scientists in the field of ES along with leaders in the field of genomic sequence analyses and data storage. Utilizing the COG ES Biobank, we will request and submit for sequence analysis the available tumor pairs to the 185 COG ES germline trios plus an additional set of paired COG germline-tumor samples (N=315) to analyze the largest cohort ever assembled of 500 ES germline-tumor pairs for deep sequencing. Using our teams combined expertise, this ES expanded GMKF X01 will test the hypothesis that germline DNA repair deficiencies (as determined by DNA repair gene variants and germline rates of de novo alterations) will contribute to specific tumor genomic features including burden of genomic instability, translocation subtype, transcription profiles, and tumor subclonal heterogeneity (Aim 1). We also will test the hypothesis that these DNA repair deficiencies reflected in the germline will correlate with clinical features of presentation including patient age, sex, tumor site, and tumor stage, as well as test for any correlation between our measured tumor genomic features and clinical presentation (Aim 2). Finally, we will test the hypothesis that the same germline and tumor genomic features will correlate with clinical outcome of the ES patients as reflected in event-free survival and overall survival (Aim 3). Importantly, this study will allow us to determine the prevalence and clinical significance of ES-like tumors that previously were included in ES biological and clinical trials. This expanded GMKF X01 study including ES tumor genomics represents the largest and most comprehensive ES genomic analysis of its kind, and builds upon the successful sequencing of previous ES germline samples through the GMKF X01 program. PUBLIC HEALTH RELEVANCE: Ewing sarcoma (ES) is the second most common bone tumor in children and adolescents, but previous genomic studies have been limited due to this tumor’s overall rarity and difficulty linking to clinical features. Building upon our previous success with sending ES germline samples for whole genome sequencing (WGS) through the Gabriella Miller Kids First (GMKF) Pediatric Research Program (X01), we now will expand our cohort to include tumor samples from within the Children’s Oncology Group (COG) ES Biobank that have been linked to COG clinical trials. We will explore the association between ES tumor genomics and underlying germline DNA repair deficiencies, clinical presentation, and clinical outcome. | |||
| Project Number: | 1X01 HL 140519-01 | Contact PI / Project Leader: | Dawn Siegel |
| Title: | Genomic analysis of a cohort with infantile hemangiomas associated with multi-organ structural birth defects | Awardee Organization: | Medical College of Wisconsin |
| Abstract: DESCRIPTION (provided by applicant): Infantile hemangiomas are the most common benign vascular tumor in infants, affecting 4-5% of children. Thirty percent of segmental infantile hemangiomas on the face and scalp are associated with birth defects of multiple organs. This condition is known as PHACE, an acronym for posterior fossa brain malformations, segmental facial hemangiomas, arterial anomalies, cardiac defects, eye anomalies, and sternal clefting. There is high morbidity associated with PHACE including risk to vision, congenital heart disease often requiring surgery, risk of stroke, deafness and neurodevelopmental delays. The hemangioma is a vascular tumor that requires treatment in infancy to prevent functional complications and disfigurement, but later undergoes involution. Our strategy is to use this highly valuable PHACE cohort to discover critical genes related to structural birth defects which will be a valuable resource to link multiple different projects in the Kids First Program. We hypothesize that PHACE is caused by variants that occur very early during development resulting in birth defects of multiple organs and infantile hemangiomas. Aim 1: Use a custom bioinformatics pipeline to detect candidate variants for PHACE, Aim 2: Contribute the data generated in this project to the Kids First Data Resource and the National Center for Biotechnology Information's (NCBI) and Database of Genotypes and Phenotypes (dbGaP). PUBLIC HEALTH RELEVANCE: Genomic analysis of PHACE will inform treatment and expand knowledge about the causes of birth defects affecting the brain, arteries, heart, eye, midline development and hearing. The knowledge gained in this study will be used to drive strategies for prevention and provide critical targets for treatments for a range of birth defects and infantile hemangiomas. | |||
| Project Number: | 1X01 HL 140517-01 | Contact PI / Project Leader: | Nara Sobreira |
| Title: | Genome-wide Sequencing to Identify the Genes Responsible for Enchondromatoses and Related Malignant Tumors | Awardee Organization: | Johns Hopkins University |
| Abstract: DESCRIPTION (provided by applicant): Chondrosarcoma is a malignant tumor that originates from cartilaginous cells. It is the third most common primary malignancy of bone after myeloma and osteosarcoma. It accounts for about 20% of bone tumors and is diagnosed in approximately 600 patients each year in the United States. Up to 40% of the chondrosarcomas arise from an enchondroma. Enchondromas are benign, intramedullary cartilaginous tumors of bone. They can be solitary or multiple and are present in >3% of the population. Enchondromatosis refers to a group of diseases characterized by multiple enchondromas including metachondromatosis (MC), Ollier disease (OD), and Maffucci syndrome (MS) among others. All have skeletal abnormalities with or without associated vascular anomalies that can cause severe limb deformities during early childhood. The risk for chondrosarcoma in OD is up to 45.8% and in MS up to 57.1%. Currently, the only treatment for patients with these disorders is surgical; there is no effective pharmacologic therapy. We identified heterozygous germline loss of function variants in PTPN11 (encoding a non-receptor protein tyrosine phosphatase SHP2) causing MC (Sobreira at al., 2010). In preliminary studies, we also identified the PTPN11 R138X variant in in a retiform hemangioendothelioma of a patient with MS and the germline PTPN11 L560F variant in a patient with OD. PTPN11 encodes SHP2, a cytosolic protein tyrosine phosphatase involved in an early step in RAS/MAPK signaling downstream of several receptor tyrosine kinases including EGFR and FGFR. Pansuriya et al. (2011) and Amary et al. (2011) identified heterozygous somatic variants of IDH1 (R132H, R132C, R132S) and IDH2 (R172S) in the tumors (enchondromas, chondrosarcoma, and hemangiomas) of a fraction of the patients with MS and OD. Neither variant was identified in the germline DNA of the affected individuals. On basis of these results, we hypothesize that OD and MS are tumor predisposition syndromes caused by germline variants. Moreover, these variants likely down-regulate the RAS/MAPK pathway or are in genes that interact with IDH1 or 2. Subsequent hits in the same or different genes such as IDH1 and IDH2 or other as yet identified genes are involved in the formation of enchondromas and chondrosarcomas. PUBLIC HEALTH RELEVANCE: : Ollier disease and Maffucci syndrome are characterized by multiple enchondromas that can cause multiple swellings on the extremity, deformity around the joints, Madelung deformity, angular deformity such as genu valgus, gene varum, cubitus valgus, coxa vara and coxa valga, limitations in joint mobility, scoliosis, bone shortening, leg-length discrepancy, gait disturbances, pain and loss of function, pathological fractures, facial asymmetry and cranial nerve palsies and the risk of developing a chondrosarcoma in patients with Ollier disease is up to 45.8% and up to 57.1% in patients with Maffucci syndrome. In addition, gliomas, acute myeloid leukemia, and juvenile granulosa cell tumors have been found in patients with OD and pancreatic and hepatic adenocarcinoma, mesenchymal ovarian tumors, brain tumors such as glioma and astrocytoma, and various kinds of sarcomas are observed in patients with MS (Verdegaal et al., 2011). The molecular basis of this two disorders is not completely understood and currently, there is no effective drug therapy for these disorders. | |||
2017 X01 Projects
| Project Number: | 1X01 HL 140535-01 | Contact PI / Project Leader: | Simeon Boyd |
| Title: | Whole genome sequencing of nonsyndromic craniosynostosis | Awardee Organization: | University of California Davis |
| Abstract: DESCRIPTION (provided by applicant): Craniosynostosis (CS), the premature fusion of one or more cranial sutures, is a common, major structural birth defect occurring in about 1 in 2,500 live births. About 85% of infants with CS present with nonsyndromic craniosynostosis (NCS) without associated birth defects or developmental delays. NCS is a heterogeneous condition with presumed multifactorial etiology and its causes remain largely unknown. Primary prevention strategies for NCS are limited. Our International Craniosynostosis Consortium (ICC) has advanced understanding of the genetic etiology for sagittal NCS (sNCS). Through our previous NIH-NIDCR funding (R01 DE016866), we successfully conducted the first genome-wide association study (GWAS) for sNCS and identified robust associations to loci near BMP2 and BBS9, both biologic plausible genes involved in skeletal development. A similar GWAS with 415 case-parent trios with metopic NCS (mNCS) is in progress, as is an additional GWAS of over 600 coronal NCS (cNCS) case-parent trios. Additionally, others reported that by whole exome sequencing (WES), SMAD6 mutations were found in 7% of probands in a cohort of sNCS, mNCS, or combined NCS cases. Importantly, among 17 NCS cases with SMAD6 mutations, 14 had T>C mutation (rs1884302) downstream of BMP2, suggesting a two-loci inheritance model. This discovery of an epistatic interaction between BMP2 and SMAD6 through use of GWAS and WES approaches explains only a small proportion of all NCS cases. Along with the data generated from the completed and ongoing GWAS’s, we believe that whole genome sequencing (WGS) is the next important step towards identifying causal variants in NCS cases, because it has the power to discover rare and common variants missed by other high- throughput technologies. We hypothesize that WGS will identify novel genetic factors beyond those identified with GWAS’s that contribute to the etiology of NCS. In this application, we propose to investigate 600 case- parent trios (200 cases each with sNCS, cNCS, and mNCS) and 20 multiplex families (11 with sNCS and 9 with mNCS) using WGS for discovery of all types of germline variants (de novo and inherited single nucleotide variants, insertions/deletions and structural variations). Somatic mutations contribute to the etiology of cancer and have been reported in some structural birth defects. Thus, we will perform WGS on 25 paired blood- derived and bone-derived DNA specimens obtained from sNCS probands for detection of somatic mutations. Our discovery specimen repository represents one of the largest collections compiled, and along with our extensive collection of independent specimens for future replication studies, represents an unparalleled resource for studying the genetic etiology of NCS. Given our past accomplishments, experienced interdisciplinary research team, and substantial resources, we are well-positioned to successfully complete the proposed research and provide critical insights into the multifactorial etiology of NCS. PUBLIC HEALTH RELEVANCE: Nonsyndromic craniosynostosis (NCS) is a common, major structural birth defect – due to the premature fusion of one or more cranial sutures – that requires extensive surgical correction and is associated with considerable ongoing medical problems and health care costs. Because little is known about the causes of NCS, whole genome sequencing will help advance knowledge of genetic factors contributing to the etiology of NCS. Sequencing data generated will lead to a better understanding of biological processes involved in the etiology of NCS and provide critical insights for development of early diagnostic tools and therapeutic strategies. | |||
| Project Number: | 1X01 HL 140516-01 | Contact PI / Project Leader: | Azeez, Butali |
| Title: | Whole Genome Sequencing of African and Asian Orofacial Clefts Case-Parent Triads | Awardee Organization: | University of Iowa |
| Abstract: DESCRIPTION (provided by applicant): Principal Investigators: Dr Azeez Butali is a tenure-track Assistant Professor at the Iowa Institute for Oral Health Research, College of Dentistry, and the University of Iowa. His primary research focus is on the genetics and epidemiology of complex traits including orofacial clefts. Dr Terri Beaty is a Professor at the John Hopkins University. Her research focus is on genetic epidemiology studies of several chronic diseases with complex etiologies, where both genetic and environmental risk factors control risk of disease. Co-investigators: Dr Adebowale Adeyemo is Deputy Director at the National Human Genome Research Institute. His focus is on the genetics and genomics of complex traits in African population. Dr Marazita is a Professor at the University of Pittsburgh. She is an expert in statistical genetics application for complex traits and identification of sub-clinical cleft phenotypes. Dr Cao is an Assistant Professor at the University of Iowa. He uses bioinformatics tools to interrogate the human genome and for analyses of gene-regulatory networks. Dr Ruczinski is a Professor at the John Hopkins University. His expertise is in statistical genetics, genomics and proteomics of complex traits. Dr Taub is an Assistant Scientist at the John Hopkins University. Her area of expertise is in genomics and statistical genetics for gene expression data, genotyping data and DNA methylation data Environment: The University of Iowa is a leading institution with a strong reputation for excellence in teaching, research and healthcare. The John Hopkins University is one of the leaders in the research, teaching and healthcare in the US. Both institutions are consistently amongst centers supported by NIH grants Research Study: The focus of this study is to identify novel risk variants for OFC in Africa and Asian OFC case-parent triads through analysis of Whole Genome Sequencing data. PUBLIC HEALTH RELEVANCE: TITLE: Whole Genome Sequencing of African and Asian Orofacial Case-Parent Triads The long term goal of this study is to identify specific genomic variants through WGS of OFC case-parent triads from African and Asian populations. The knowledge gained from these WGS studies will drive future research on OFC and should eventually lead to more effective interventions to reduce the risk of OFC. | |||
| Project Number: | 1X01 HL 140543-01 | Contact PI / Project Leader: | Wendy Chung |
| Title: | Genomic Analysis of Congenital Diaphragmatic Hernia and Associated Congenital Anomalies | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Abstract Congenital diaphragmatic hernia (CDH) is defined as a defect in the muscular or tendinous portion of diaphragm that results in antenatal herniation of the abdominal contents into the thoracic cavity and pulmonary hypoplasia due to compression of the lungs. The incidence of CDH is 1 in 3000 live births, accounting for 1- 2% of infant mortality and 8% of all birth defects, making it one of the most common and lethal congenital anomalies. CDH is isolated in 50-60% of cases but is associated with other major anomalies, most commonly congenital heart disease or central nervous system malformations, in the remaining 40-50%. Historically CDH carried a grave prognosis with mortality of greater than 50%. However, with recent advances in the post-natal care of children with CDH, survival has improved significantly. However, with improved survival, many of the long term morbidities of CDH have been exposed including pulmonary hypertension, the leading cause of CDH morbidity and mortality. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. The etiology of CDH is largely unknown. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of CDH and define new genes and conditions associated with CDH by performing whole genome sequencing on parent child trios and RNA sequencing of diaphragm tissue in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. Our long-term goal is to define a set of genes important in the etiology of CDH and characterize new clinical syndromes associated with CDH. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions. PUBLIC HEALTH RELEVANCE: Congenital diaphragmatic hernia (CDH) is a serious birth defect accounting for 1-2% of infant mortality and 8% of all birth defects. We propose to elucidate the underlying genomic architecture of CDH by performing whole genome sequencing and RNA sequencing on diaphragm tissue to characterize new clinical syndromes associated with CDH to provide more accurate clinical prognostic information. | |||
| Project Number: | 1X01 HL 140544-01 | Contact PI / Project Leader: | Hakon Hakonarson |
| Title: | Genetics at the Intersection of Childhood Cancer and Birth Defects | Awardee Organization: | The Children's Hospital of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Evidence of a connection between childhood cancers and birth defects comes from three major sources: clinical observations of syndromes, registry linkages, and case-control studies. These studies demonstrate that children with a variety of birth defects have a significantly increased risk of developing several types of childhood cancers. However, due to the sparsity of cases, few risk factors have been consistently confirmed for specific types of birth defects and childhood cancers, and the etiology of most of these entities remains unexplained. This proposal will leverage the unique resources of The Center for Applied Genomics (CAG) at The Children’s Hospital of Philadelphia (CHOP) which houses the largest genomic facility/pediatric biobank in the US. We have identified 1,205 pediatric cancer patients that were also diagnosed with a birth defect from the CAG biobank. All have banked DNA samples from peripheral blood that are ready for sequencing together with age, sex and ethnically matched controls. The patients are from diverse backgrounds and the majority of them authorize re-contact. This study will utilize two complementary analytical approaches to disease gene discovery. Patients with parental sequences will be analyzed as trios in a typical winnowing variant prioritization approach. We also propose to sequence matched controls for each of the cases allowing for powerful statistical case control approaches, namely burden tests, to be applied to the dataset. Two strengths of this study design are the large sample sizes for what are rare phenotypes and the combination of birth defects and childhood cancers in all cases which are more likely to be burdened with low frequency variants that confer risk and that more impactful variants are more likely to be discovered. PUBLIC HEALTH RELEVANCE: Birth defects and childhood cancer share biological pathways that are important for cell growth and division. We propose that sequencing pediatric patients suffering both conditions will allow us to discover the underlying genes and in turn advance our understanding of the causes of these devastating diseases. | |||
| Project Number: | 1X01 HL 140518-01 | Contact PI / Project Leader: | Daniela Luquetti |
| Title: | Craniofacial Microsomia: Genetic Causes and Pathway Discovery | Awardee Organization: | Seattle Children's Hospital |
| Abstract: DESCRIPTION (provided by applicant): Craniofacial microsomia (CFM), also termed hemifacial microsomia or oculo-auricular-vertebral spectrum, is the third most common congenital craniofacial condition. CFM has an estimated birth prevalence in the US of 1 in 3,500-5,600, which is similar to conditions such as cystic fibrosis (1 in 3,700) and neurofibromatosis (1 in 4,200). CFM comprises a variable phenotype, and the most common features include malformations of the ear (i.e. microtia) and lower jaw (i.e. mandibular hypoplasia) on one or both sides. The etiology of CFM is largely unknown; however the presence of multiple cases within families, mouse models with CFM malformations and the increased risk of CFM in some ethnicities suggest that genetic variants contribute to its occurrence. Although chromosomal abnormalities have been associated with CFM, only three causative genes have been identified in few cases: HOXA2, FGF3, and MYT1. Our goal in this proposal is to identify coding and non- coding variants that are genetic risk factors to CFM by performing whole-genome sequencing (WGS) of case- parent trios with CFM. We propose to perform whole genome sequencing on DNAs from 105 trios (individuals with CFM and their parents or affected relatives in multi-affected families) to identify candidate genes with rare de novo and inherited variants. Our hypothesis is that CFM is caused by rare new and inherited DNA variation in gene(s) related to the craniofacial development. We will analyze the data on rare de novo coding and non- coding variants. Recognizing reduced penetrance in CFM, our analysis will include analyses for variants in a dominant inheritance with incomplete penetrance model. Our approach incorporates detailed phenotype, clinical characterization, and family history for each individual. We will also integrate the WGS data with our data on gene expression from murine embryonic pharyngeal arch and external ear human embryonic tissue to ascertain tissue specific expression at the relevant time of the development of tissues in CFM. Our statistical power by sampling patients with familial and severe disease who are most likely to have a high genetic loading. CFM represents an ideal condition in which to identify susceptibility variants because it is (1) relatively rare and represents more extreme selection under a liability threshold model, (2) distinctive, (3) stable, and (4) This study will be conducted by an interdisciplinary team with complementary expertise in clinical aspects of CFM, clinical genetics, genomics, and bioinformatics. Successful completion of this proposal will advance knowledge in the genetic architecture of susceptibility to CFM and will provide insight about the biological mechanisms underlying craniofacial development. The phenotypic and genomic data will be fully integrated into the Kids First Data Resource and available to all qualified investigators. The long-term goal of this project is to identify specific genetic risk factors to improve genetic counseling, enable tailored clinical care, and to provide more accurate prognosis. often familial (20-40% of cases). PUBLIC HEALTH RELEVANCE: Craniofacial microsomia (CFM) is the third most prevalent condition that affects craniofacial development; however, the cause of CFM is unknown for most affected individuals. We have established a cohort through previous studies and collected DNA to identify the genetic contributions to CFM, which could facilitate diagnosis, tailored treatment and guide prevention strategies. The results from the proposed study have potential to further research on the etiology of other craniofacial disorders, and the pathogenesis of typical and atypical craniofacial development. Sequence and clinical data released in dbGap: Accession Number: phs002130 | |||
| Project Number: | 1X01 HL 140547-01 | Contact PI / Project Leader: | Joshua Schiffman |
| Title: | Expanded Ewing sarcoma cohort for tumor genomics and association with DNA repair deficiences, clinical presentation, and outcome | Awardee Organization: | University of Utah |
| Abstract: DESCRIPTION (provided by applicant): Expanded Ewing sarcoma cohort for tumor genomics and association with DNA repair deficiencies, clinical presentation, and outcome Ewing sarcoma (ES) is the second most common bone tumor in children and adolescents, but is still relatively rare without much known about genetic risk and only small cohort studies linking tumor genomics to clinical features. Our group was awarded an initial Gabriella Miller Kids First (GMKF) Pediatric Research Program (X01) to study a cohort of germline DNA samples from the Project GENESIS cancer epidemiology study (Genetics of Ewing Sarcoma International Study, COG AEPI10N5), which included whole genome sequencing (WGS) on 329 ES trios (patient-mother-father) plus 123 individual ES patients, with 327 ES patients from the Children’s Oncology Group (COG). The GMKF WGS germline data are now in the process of being returned for analysis. For this expanded study to explore ES tumor genomics, we have assembled a team of leading biologists and clinical scientists in the field of ES along with leaders in the field of genomic sequence analyses and data storage. Utilizing the COG ES Biobank, we will request and submit for sequence analysis the available tumor pairs to the 185 COG ES germline trios plus an additional set of paired COG germline-tumor samples (N=315) to analyze the largest cohort ever assembled of 500 ES germline-tumor pairs for deep sequencing. Using our teams combined expertise, this ES expanded GMKF X01 will test the hypothesis that germline DNA repair deficiencies (as determined by DNA repair gene variants and germline rates of de novo alterations) will contribute to specific tumor genomic features including burden of genomic instability, translocation subtype, transcription profiles, and tumor subclonal heterogeneity (Aim 1). We also will test the hypothesis that these DNA repair deficiencies reflected in the germline will correlate with clinical features of presentation including patient age, sex, tumor site, and tumor stage, as well as test for any correlation between our measured tumor genomic features and clinical presentation (Aim 2). Finally, we will test the hypothesis that the same germline and tumor genomic features will correlate with clinical outcome of the ES patients as reflected in event-free survival and overall survival (Aim 3). Importantly, this study will allow us to determine the prevalence and clinical significance of ES-like tumors that previously were included in ES biological and clinical trials. This expanded GMKF X01 study including ES tumor genomics represents the largest and most comprehensive ES genomic analysis of its kind, and builds upon the successful sequencing of previous ES germline samples through the GMKF X01 program. PUBLIC HEALTH RELEVANCE: Ewing sarcoma (ES) is the second most common bone tumor in children and adolescents, but previous genomic studies have been limited due to this tumor’s overall rarity and difficulty linking to clinical features. Building upon our previous success with sending ES germline samples for whole genome sequencing (WGS) through the Gabriella Miller Kids First (GMKF) Pediatric Research Program (X01), we now will expand our cohort to include tumor samples from within the Children’s Oncology Group (COG) ES Biobank that have been linked to COG clinical trials. We will explore the association between ES tumor genomics and underlying germline DNA repair deficiencies, clinical presentation, and clinical outcome. | |||
| Project Number: | 1X01 HL 140519-01 | Contact PI / Project Leader: | Dawn Siegel |
| Title: | Genomic analysis of a cohort with infantile hemangiomas associated with multi-organ structural birth defects | Awardee Organization: | Medical College of Wisconsin |
| Abstract: DESCRIPTION (provided by applicant): Infantile hemangiomas are the most common benign vascular tumor in infants, affecting 4-5% of children. Thirty percent of segmental infantile hemangiomas on the face and scalp are associated with birth defects of multiple organs. This condition is known as PHACE, an acronym for posterior fossa brain malformations, segmental facial hemangiomas, arterial anomalies, cardiac defects, eye anomalies, and sternal clefting. There is high morbidity associated with PHACE including risk to vision, congenital heart disease often requiring surgery, risk of stroke, deafness and neurodevelopmental delays. The hemangioma is a vascular tumor that requires treatment in infancy to prevent functional complications and disfigurement, but later undergoes involution. Our strategy is to use this highly valuable PHACE cohort to discover critical genes related to structural birth defects which will be a valuable resource to link multiple different projects in the Kids First Program. We hypothesize that PHACE is caused by variants that occur very early during development resulting in birth defects of multiple organs and infantile hemangiomas. Aim 1: Use a custom bioinformatics pipeline to detect candidate variants for PHACE, Aim 2: Contribute the data generated in this project to the Kids First Data Resource and the National Center for Biotechnology Information's (NCBI) and Database of Genotypes and Phenotypes (dbGaP). PUBLIC HEALTH RELEVANCE: Genomic analysis of PHACE will inform treatment and expand knowledge about the causes of birth defects affecting the brain, arteries, heart, eye, midline development and hearing. The knowledge gained in this study will be used to drive strategies for prevention and provide critical targets for treatments for a range of birth defects and infantile hemangiomas. | |||
| Project Number: | 1X01 HL 140517-01 | Contact PI / Project Leader: | Nara Sobreira |
| Title: | Genome-wide Sequencing to Identify the Genes Responsible for Enchondromatoses and Related Malignant Tumors | Awardee Organization: | Johns Hopkins University |
| Abstract: DESCRIPTION (provided by applicant): Chondrosarcoma is a malignant tumor that originates from cartilaginous cells. It is the third most common primary malignancy of bone after myeloma and osteosarcoma. It accounts for about 20% of bone tumors and is diagnosed in approximately 600 patients each year in the United States. Up to 40% of the chondrosarcomas arise from an enchondroma. Enchondromas are benign, intramedullary cartilaginous tumors of bone. They can be solitary or multiple and are present in >3% of the population. Enchondromatosis refers to a group of diseases characterized by multiple enchondromas including metachondromatosis (MC), Ollier disease (OD), and Maffucci syndrome (MS) among others. All have skeletal abnormalities with or without associated vascular anomalies that can cause severe limb deformities during early childhood. The risk for chondrosarcoma in OD is up to 45.8% and in MS up to 57.1%. Currently, the only treatment for patients with these disorders is surgical; there is no effective pharmacologic therapy. We identified heterozygous germline loss of function variants in PTPN11 (encoding a non-receptor protein tyrosine phosphatase SHP2) causing MC (Sobreira at al., 2010). In preliminary studies, we also identified the PTPN11 R138X variant in in a retiform hemangioendothelioma of a patient with MS and the germline PTPN11 L560F variant in a patient with OD. PTPN11 encodes SHP2, a cytosolic protein tyrosine phosphatase involved in an early step in RAS/MAPK signaling downstream of several receptor tyrosine kinases including EGFR and FGFR. Pansuriya et al. (2011) and Amary et al. (2011) identified heterozygous somatic variants of IDH1 (R132H, R132C, R132S) and IDH2 (R172S) in the tumors (enchondromas, chondrosarcoma, and hemangiomas) of a fraction of the patients with MS and OD. Neither variant was identified in the germline DNA of the affected individuals. On basis of these results, we hypothesize that OD and MS are tumor predisposition syndromes caused by germline variants. Moreover, these variants likely down-regulate the RAS/MAPK pathway or are in genes that interact with IDH1 or 2. Subsequent hits in the same or different genes such as IDH1 and IDH2 or other as yet identified genes are involved in the formation of enchondromas and chondrosarcomas. PUBLIC HEALTH RELEVANCE: : Ollier disease and Maffucci syndrome are characterized by multiple enchondromas that can cause multiple swellings on the extremity, deformity around the joints, Madelung deformity, angular deformity such as genu valgus, gene varum, cubitus valgus, coxa vara and coxa valga, limitations in joint mobility, scoliosis, bone shortening, leg-length discrepancy, gait disturbances, pain and loss of function, pathological fractures, facial asymmetry and cranial nerve palsies and the risk of developing a chondrosarcoma in patients with Ollier disease is up to 45.8% and up to 57.1% in patients with Maffucci syndrome. In addition, gliomas, acute myeloid leukemia, and juvenile granulosa cell tumors have been found in patients with OD and pancreatic and hepatic adenocarcinoma, mesenchymal ovarian tumors, brain tumors such as glioma and astrocytoma, and various kinds of sarcomas are observed in patients with MS (Verdegaal et al., 2011). The molecular basis of this two disorders is not completely understood and currently, there is no effective drug therapy for these disorders. | |||
2016 X01 Projects
| Project Number: | 1 X01 HL136998-01 | Contact PI / Project Leader: | Wendy K. Chung |
| Title: | Genomic Analysis of Congenital Diaphragmatic Hernia and Associated Congenital Anomalies | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Congenital diaphragmatic hernia (CDH) is defined as a defect in the muscular or tendinous portion of diaphragm that results in antenatal herniation of the abdominal contents into the thoracic cavity and pulmonary hypoplasia due to compression of the lungs. The incidence of CDH is 1 in 3000 live births, accounting for 1- 2% of infant mortality and 8% of all birth defects, making it one of the most common and lethal congenital anomalies. CDH is isolated in 50-60% of cases but is associated with other major anomalies, most commonly congenital heart disease or central nervous system malformations, in the remaining 40-50%. Historically CDH carried a grave prognosis with mortality of greater than 50%. However, with recent advances in the post-natal care of children with CDH, survival has improved significantly. However, with improved survival, many of the long term morbidities of CDH have been exposed including pulmonary hypertension, the leading cause of CDH morbidity and mortality. In addition, a subset of children with CDH demonstrate significant developmental delay and intellectual disabilities. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. The etiology of CDH is largely unknown. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of CDH and define new genes and conditions associated with CDH by performing whole genome sequencing on parent child trios and RNA sequencing of diaphragm tissue in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. Our long-term goal is to define a set of genes important in the etiology of CDH and characterize new clinical syndromes associated with CDH. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions. PUBLIC HEALTH RELEVANCE: Congenital diaphragmatic hernia (CDH) is a serious birth defect accounting for 1-2% of infant mortality and 8% of all birth defects. We propose to elucidate the underlying genomic architecture of CDH by performing whole genome sequencing and RNA sequencing on diaphragm tissue to characterize new clinical syndromes associated with CDH to provide more accurate clinical prognostic information. | |||
| Project Number: | 1 X01 HL136465-01 | Contact PI / Project Leader: | Mary L. Marazita |
| Title: | Kids First: Genomics of Orofacial Cleft Birth Defects in Latin American Families | Awardee Organization: | University of Pittsburgh |
| Abstract: DESCRIPTION (provided by applicant): Nonsyndromic orofacial cleft birth defects (OFCs) are genetically complex structural birth defects caused by genetic factors, environmental exposures, and their interactions. Before the advent of genomic approaches, evaluation of candidate genes revealed at best modest associations with a number of genes. By contrast, genome-wide linkage and association studies by our group and others have identified approximately 18 genomic regions likely to contribute to the risk for nonsyndromic OFCs, which together account for about 55- 60% of the heritability for this disorder. Despite this substantial progress, the functional/pathogenic variants at OFC-associated regions are mostly still unknown. Because previous OFC genomic studies (genome-wide linkage, genome-wide association studies (GWAS), targeted sequencing) are based on relatively sparse genotyping data, they cannot distinguish between causal variants and variants in linkage disequilibrium with unobserved causal variants. Moreover, it is unknown whether the association or linkage signals are due to single common variants, haplotypes of multiple common variants, clusters of multiple rare variants, or some combination. Part of the “missing heritability” for OFC may be accounted for by rare variants within regions of the genome associated with risk to OFC. Finally, we cannot yet attribute specific genetic risk to individual cases and case families. Therefore, the goal of the current study is identify specific OFC risk variants by performing whole genome sequencing (WGS) of Latin American OFC parent-case trios. Notably, Latin American families are at high risk of OFC. Statistical analyses of the WGS results will identify common and rare variants likely to be involved in OFC risk. The resulting data (genetic and phenotypic), analyses and other resources will be made available through dbGaP, the proposed Pediatric Data Resource of the Kids First Program (and/or other NIH-designated repositories). Additional goals of this project are beyond the scope of the Kids First Initiative, but include replicating risk variants identified by WGS in our large resource of OFC case families and controls, and validating expression and functional significance of replicated variants through our other existing collaborators who focus on animal models of OFC. Successful completion of the proposed specific aims will more fully illuminate the genetic architecture of OFC and will provide insight about the biological mechanisms underlying craniofacial development. Ultimately, this project will translate to improved risk prediction, treatment, and prognosis for individuals affected by OFCs. The specific aims are: (1) to identify risk variants for OFC by WGS of Latin American OFC case trios; (2) to make the WGS results available through the proposed Pediatric Data Commons and/or other NIH-designated repositories; (3) to do combined analyses with the WGW in White Trios (from our previous Kids First project); (4) replicate variants identified in the WGS of proband trios; and (5) to explore functional significance and expression of replicated results in cell lines and animal models. PUBLIC HEALTH RELEVANCE: Nonsyndromic orofacial cleft birth defects (OFCs) are very common structural birth defects caused by genetic factors, environmental exposures, and their interactions. The goal of the current study is to identify specific OFC risk variants by performing whole genome sequencing of Latin American OFC families. Successful completion of the project will more fully illuminate the genetic architecture of OFC, and will ultimately translate to improved risk prediction, treatment, and prognosis for individuals affected by OFCs. Sequence and clinical data released in dbGap: Accession Number: phs001420 | |||
| Project Number: | 1 X01 HL136997-01 | Contact PI / Project Leader: | John M. Maris |
| Title: | Genetic basis of neuroblastoma initiation and progression | Awardee Organization: | Children's Hospital of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Children with disseminated neuroblastoma have a very high risk of treatment failure and death despite receiving intensified chemotherapy, radiation therapy and immunotherapy. The long-term goal of our research program is to ultimately improve neuroblastoma cure rates by first comprehensively defining the genetic basis of the disease. The central hypothesis to be tested here is that neuroblastoma arises largely due to the epistatic interaction of common and rare heritable DNA variation. Here we will perform a comprehensive whole genome sequencing of 563 quartets of neuroblastoma patient germline and diagnostic tumor DNAs and germline DNAs from both parents. The case series was recently collected through a Children's Oncology Group epidemiology clinical trial and is robustly annotated with complete demographic (age, sex, race, ethnicity), clinical (e.g. age at diagnosis, stage, risk group), epidemiologic (parental dietary and exposure questionnaire) and biological (e.g. tumor MYCN status and multiple other tumor genomic measures) co- variates. Subjects were consented for genetic research and DNA is immediately available for shipment for sequencing. We propose Illumina-based whole genome sequencing in the 563 trio germline samples (Aim 1; due to missing parent: 465 neuroblastoma triads, 94 child-mother dyads and 4 father-child dyads = 1591 whole genome sequences) and matched diagnostic tumor DNA (Aim 2; N=484). We propose at least 100x average sequencing depth for these 2075 DNA samples in order to have sufficient sequencing coverage to reliably identify and quantify germline mosaicism and somatic subclonal heterogeneity. We will use our established analytic pipeline that is currently being used to study the germline genomes of all cases sequenced through the NCI supported Therapeutically Applicable Research to Generate Effective Treatments program. We plan a three stage analytic approach, first focusing on classic de novo and inherited Mendelian damaging alterations. We will next integrate our extensive epigenomic data from human neuroblastoma cell lines and genome-wide association study data (N=5,703 neuroblastoma cases to date) to guide a comprehensive assessment of noncoding variants that influence tumor initiation with a recently established analytic pipeline. Finally, we will utilize the tumor DNA analyses to inform relevance via somatic gain or loss of function effects at the sequence and/or copy number levels. All data generated in this project will be immediately placed into the Genomic Data Commons (GDC) and we will compute within this environment by importing our analytic pipelines into the GDC. These data will be fully integrated into the Kids First Data Resource and freely shared with all academically qualified petitioners. This comprehensive data set derived from a large and richly phenotyped series of neuroblastoma DNA quartets will be integrated with existing germline and/or tumor genomic data from over 6,000 neuroblastoma subjects (but none with matched patient-parent germline sequencing data) to provide an unparalleled opportunity to comprehensively discover the genetic basis of neuroblastoma. PUBLIC HEALTH RELEVANCE: The proposed research Program is relevant to public health because we are addressing a major gap in our understanding of the genetic basis of cancer, here focusing on neuroblastoma, a perplexing and often fatal pediatric malignancy. The proposed research Program is highly relevant to the NIH mission of improving health outcomes as we expect that discoveries of the basic genetic mechanisms of tumor initiation will lead to rational new clinical interventions. | |||
| Project Number: | 1 X01 HL136999-01 | Contact PI / Project Leader: | Charles G. Mullighan |
| Title: | Genomic analysis of familial leukemia | Awardee Organization: | St. Jude Children's Research Hospital |
| Abstract: DESCRIPTION (provided by applicant): Acute lymphoblastic leukemia (ALL) is a precursor cell neoplasm and the commonest childhood cancer, and Hodgkin and non-Hodgkin lymphoma (HL) are forms of lymphoma that arise in both children and adults. Both are multi-genic diseases characterized by multiple subtypes and distinct constellations of somatic genetic changes. There is growing evidence for a genetic predisposition to both diseases, demonstrated by genome- wide association studies that have identified associations between common variants in transcription factors and tumor suppressors and ALL risk, subtype and outcome, and the identification of highly penetrant mutations in transcription factor and tumor suppressor genes in familial ALL. However, the landscape of germline predisposition variants that drive familial and sporadic hematological malignancies (HM) are unknown. In this study we will address this knowledge gap by performing whole genome sequencing of kindreds with familial, coupled with recurrence screening of extended cohorts of ALL and HL and integration of germline and somatic data. We have collected over 60 familial HM kindreds that will be subjected to tumor and germline whole genome sequencing (WGS) supported by this grant mechanism (Specific Aim 1). We will examine the frequency of novel variants, and mutations in newly identified genes, in large cohorts of sporadic ALL/HL (Specific Aim 2, funded separately) and examine associations between germline mutations in familial and sporadic ALL and clinical, pathologic and somatic genomic features (Specific Aim 3, funded separately). The project will be conducted by a group of co-investigators at St Jude Children’s Research Hospital with complementary expertise in clinical genetics (Nichols, Kesserwan), germline predisposition (Yang, Mullighan), clinical aspects of ALL and HL (Sandlund, Metzger) and computational approaches (Rampersaud). We have established collaborations with the COG and assembled the recurrence testing cohorts. Many of the familial tumor and germline samples are in hand, with acquisition of relative material ongoing to submit samples for sequencing by study activation. Together, this represents a logical framework to comprehensively dissect the interaction of germline and somatic genetic alterations in HM, and will provide important mechanistic insights, opportunity for clinical translation, and an invaluable public resource of genomic data. PUBLIC HEALTH RELEVANCE: (RELEVANCE STATEMENT) Acute lymphoblastic leukemia (ALL) is the commonest childhood tumor and a leading cause of cancer death in children, adolescents and young adults. Hodgkin and non-Hodgkin lymphoma are also important hematologic malignancies (HM) that occur in children. Each are genetic diseases with growing evidence for a germline predisposition of both familial and sporadic cases, however the inherited genetic basis of ALL/lymphoma are poorly understood. Such knowledge is essential to gain mechanistic insight into the basis of tumor formation, and to guide genetic counseling and genetic management. Here we have assembled an unmatched group of basic genomic, computational and clinical investigators with an interest in the genetics of HM, a large collection of familial HM kindreds, and extended recurrence cohorts of ALL and HL which will be used to identify the genetic basis of familial HM, examine the frequency of germline variants in sporadic ALL and HL, and to integrate inherited and somatic genomic data. These studies have high potential to provide fundamental new insights into the inherited genetic basis of HM, to provide important information to guide clinical management, and to provide an invaluable public resource of genomic data. | |||
| Project Number: | 1 X01 HL136994-01 | Contact PI / Project Leader: | Sharon E. Plon |
| Title: | Identifying novel cancer susceptibility mutations from unselected childhood cancer patient and parent trios | Awardee Organization: | Baylor College of Medicine |
| Abstract: DESCRIPTION (provided by applicant): Genome-scale sequencing methods have allowed studies that demonstrate that approximately 10% of patients carry germline pathogenic variants in a wide spectrum of known cancer susceptibility genes. These results also highlight that our very limited ability to predict which patients are likely to carry a cancer susceptibility mutation based on tumor type and family history. In addition, prior projects have (1) focused on findings in known germline cancer genes, limiting new discovery, and (2) performed the sequencing on the cancer patient without parental samples obviating our ability to systematically determine the underlying genetic mechanisms such as de novo mutations. In this proposal, we describe whole genome sequencing (WGS) of patient germline and parental samples including the tumor sample when available from an unselected racially and ethnically diverse cohort of well phenotyped pediatric cancer patients enrolled in the NIH supported Baylor Advancing Sequencing in Childhood Cancer Care (BASIC3) trial. Based on the detailed medical record extraction we have identified that approximately 20% of this cohort also includes patients with a neurodevelopmental or structural anomaly. Data derived from this project should fill current gaps in our knowledge (1) the proportion and nature of pathogenic or likely pathogenic germline mutations in known cancer genes that are missed by more standard proband only whole exome sequencing methods and (2) identification of new cancer susceptibility genes to better define the underlying structure of pediatric cancer susceptibility, particularly, when data generated by this project is combined with other Gabriela Miller Kids First and TARGET sequencing in the NCI Data Commons. PUBLIC HEALTH RELEVANCE: We describe whole genome sequencing of pediatric cancer patient (n=120) germline and parental samples including the tumor sample when available from an unselected racially and ethnically diverse cohort of well phenotyped solid tumor (CNS and non-CNS) cancer patients. Data derived from the WGS described here should provide substantial new data to define the underlying genetic structure of cancer susceptibility to pediatric cancer. | |||
| Project Number: | 1 X01 HL132375-01A1 | Contact PI / Project Leader: | Jonathan Rios |
| Title: | Genomics of Orthopaedic Disease Program | Awardee Organization: | UT Southwestern Medical Center |
| Abstract: DESCRIPTION (provided by applicant): Pediatric birth defects are a leading cause of pediatric hospitalizations and deaths. The Gabriella Miller Kids First initiative seeks to understand the genetic causes of pediatric birth defects by synergizing state-of-the-art genetic research techniques with detailed clinical assessments in children. In addition, the Kids First initiative will build a collaborative environment by making available genetic and clinical information that will foster collaborative research and ultimately improve our understanding of pediatric birth defects. At Texas Scottish Rite Hospital for Children, the Genomics Of Orthopaedic Disease (GOOD for Kids) program similarly seeks to understand pediatric birth defects, such as adolescent idiopathic scoliosis (AIS), through close interaction and collaboration with orthopaedic surgeons and treating physicians. AIS is a debilitating curvature and rotational deformity of the spine and is the most common pediatric musculoskeletal deformity in the world. Our long- term goal is to improve management and prevention of AIS by discovering genetic and developmental risk factors leading to spine deformity. Our collaborative research team has extensive experience and expertise with gene discovery using next-generation sequence analysis, and we have led the field in identifying genetic risk factors for AIS. To expand on our previous successes, we propose to perform whole-genome sequencing (WGS), the most comprehensive approach to identify genetic causes of pediatric disease, using a tiered approach. In our first tier we propose sequencing families with multiple generations of relatives with AIS. These families provide the greatest power to identify new genes when faced with the vast amounts of data generated by WGS. This approach is supported by detailed clinical characterization and rich histories for families that, in some cases, were treated for multiple generations at our Institutions. Our unique ability to perform WGS analysis in multiple affected family members segregating AIS through multiple generations allows us to identify new genetic causes of AIS despite reduced penetrance of the disease. We also propose Tier 2 families, which include those with affected siblings with AIS but without affected parents and no evidence for dominant inheritance. Recognizing reduced penetrance in AIS, our multi-faceted approach to WGS analysis will include analyses for recessive disease as well as dominant disease with non-penetrant parents for Tier 2 families. Candidate genes identified in each Tier will be validated by re-sequencing, evidence of association from our current GWAS meta-analysis, and individual variant association testing in our singleton collection of >2500 cases with AIS. Our approach is supported by our access to extensive clinical characterization and documentation for each study subject, our close collaboration with referring physicians, and our considerable experience and commitment to genetic analysis of AIS. Together, the power of our clinical and genomic analyses will meet the goals of the Kids First initiative, will expand our understanding of pediatric musculoskeletal disease, and may lead to better diagnosis and treatments for children with AIS. PUBLIC HEALTH RELEVANCE: The Kids First initiative seeks to perform whole-genome sequencing in pediatric patients with birth defects and to merge this genetic information with detailed clinical evaluations, all with the goal of improving our understanding of pediatric birth defects and improving treatment in children. We propose the Genomics Of Orthopaedic Disease (GOOD For Kids) program that will expand our current efforts to understand the genetic etiology of adolescent idiopathic scoliosis (AIS), the most common pediatric musculoskeletal deformity in the world. Our collaborative group has led the field in identifying genetic risk factors for AIS, and, with the Kids First initiative, promises to continue making strides to understand the genetic mechanisms causing disease and hopefully improve diagnosis and care of these children. Sequence and clinical data released in dbGap: Accession Number: phs001410.v1.p1 | |||
| Project Number: | 1 X01 HL136976-01 | Contact PI / Project Leader: | Christine E. Seidman |
| Title: | Discovery of De Novo and Inherited Mutations that Cause Prevalent Birth Defects | Awardee Organization: | Harvard Medical School |
| Abstract: DESCRIPTION (provided by applicant): The Pediatric Cardiovascular Genetics Consortium (PCGC) proposes to define genetic causes for congenital heart defects (CHD) as part of the Gariella Miller Kids First Pediatric Research Program. CHD is the most common birth defect and is often accompanied by another congenital anomaly (CA). The PCGC has recruited and clinically characterized ≥ 10,000 CHD probands and parents (CHC trios), including 30% probands with CHD + CA. From extensive exome sequence (WES) analyses in over 2000 CHD trios, genome sequence (WGS) analyses of 50 CHD trios, and other genetic studies, we identified a substantial enrichment of damaging de novo mutations in developmental genes that modulate embryonic transcription. Based on these discoveries, we hypothesize that PCGC probands with uninformative genomic analyses (WES-negative) carry mutations in critical regulatory elements that participate in developmental expression of cardiac genes. To identify these etiologies, we propose analyses of WGS in 500 prioritized WES-negative CHD trios that include probands with banked CHD tissues (n=278), one damaging variant in a recessive CHD gene (n=186), and older fathers (n=60; age>45). We will capitalize on existing RNAseq data from CHD tissues, DNA methylation studies and the extensive computational and functional data on cardiac enhancers provided by our collaborating investigators, to analyze coding and non-coding, SNVs and SVs. We will use existing resources and capabilities of the PCGC and its companion consortium in the Bench to Bassinet Program, the Cardiovascular Development Consortium, to perform confirmatory functional genomics studies using cell and animal models outside of the GMKF program. We expect that these studies will provide novel insights into the molecular basis for birth defects and fundamental knowledge about genes and pathways involved in the development of the heart and other organs. Our aims are to: 1. Define de novo and transmitted variants, both SNVs and SVs, that cause dominant, recessive, and sporadic CHD ± CA. 2. Identify pathogenic de novo and transmitted variants in coding and regulatory regions both by case- control analyses and orthogonal data sets (ENCODE, cardiac enhancers, promoters, and regulatory ncRNAs, genes with unexplained loss of expression or allelic-specific expression in CHD tissues, and genome-wide DNA methylation data). PUBLIC HEALTH RELEVANCE: Through the use of whole genome sequencing of individuals with congenital heart disease (CHD) and other congenital malformations, and their unaffected parents, this project will drive discovery of the genetic causes for common birth defects. The new insights gained from this project will improve care by enabling DNA diagnostics for birth defects and by providing novel mechanistic insights, with which new therapies can be developed. Sequence and clinical data released in dbGap: Accession Number: : phs001138 | |||
| Project Number: | X01 HL132380-01A1 | Contact PI / Project Leader: | Jun Shen |
| Title: | Hear-n-Seq: Sequencing Kids First for Hearing | Awardee Organization: | Brigham and Women's Hospital |
| Abstract: DESCRIPTION (provided by applicant): With hearing loss of 40 decibels or more and 1 in 100 children will lose significant hearing by school age, making it one of the single most common structural defects affecting the pediatric population. Hearing loss can affect a child's ability to develop speech, language, cognitive and social skills. The earlier a child with hearing loss starts receiving appropriate medical and educational services, the more likely they are to reach their full potential. More than half of early hearing loss is due to genetic factors. Approximately 1 in 500 babies is born While the majority of prelingual hearing loss is nonsyndromic, over 400 syndromes have been described that have hearing impairment as a component. It is critically important to identify the etiology of hearing loss for many reasons, as there may be important health surveillance implications particularly with syndromic causes. Genetic testing is available for congenital hearing loss, but the current standard of care is by no means comprehensive because: 1) many types of genetic variants in known hearing loss genes are not detectable by clinical testing, and 2) it is estimated that more than 100 hearing loss genes are as yet unknown. With this proposal called Hear-'n-SEQ, we will leverage the resources of the NIH Common Fund's Gabriella Miller Kids First Pediatric Research program to"seek-out" the genetic etiology of childhood hearing loss through comprehensive phenotypic and genomic analyses in an international cohort of hearing impaired patients. By sharing both the clinical and sequence data with the pediatric research community we will be empowered to identify genetic pathways that underlie hearing loss as well as pathways shared with other pediatric conditions. This project will be coordinated through the Harvard Medical School Center for Hereditary Deafness (HMSCHD). The Specific Aims of the project are to: (1) build an international consortium to identify and collect well-curated patient clinical information and DNA samples from children with hearing loss and their parents (trios) or carefully selected multiple affected individuals based on the pedigree structure, (2) submit appropriate DNA samples for whole genome sequencing at an NIH-supported sequencing center, and, (3) identify the genetic etiology of hearing impairment in individuals where possible, and integrate the data collectively into a shared data resource. Because of the tremendous genetic heterogeneity inherent in hearing loss, the proposed international collaboration will produce a maximum yield of diverse genetic causes, as it has been well established that different populations segregate distinct concentrations of hearing loss alleles. Therefore we will sample the hearing impaired pediatric populations of parts of Asia (Hong Kong), the Middle East (Turkey), and the US (individuals of European, African American, Central American and Caribbean descent). In addition to identifying novel etiologies for hearing loss, ultimately this work is designed to help create a pipeline for routinely integrating genomic sequencing into clinical diagnostics, generating more refined diagnostic capabilities, and ultimately more targeted therapies or interventions for children with hearing loss. PUBLIC HEALTH RELEVANCE: Hearing loss is the most common structural birth defect detected through newborn screening. Genetic factors contribute to the majority of childhood hearing loss, but currently available genetic testing can only identify the cause in 1/3 of patients. This Hear-'n-SEQ project proposes to use the latest DNA sequencing and comprehensive genetic analysis technologies to identify the genetic causes of previously unsolved hearing loss cases, with an overarching goal of offering better and timelier treatment options for children with hearing loss. | |||
2016 X01 Projects
| Project Number: | 1 X01 HL136998-01 | Contact PI / Project Leader: | Wendy K. Chung |
| Title: | Genomic Analysis of Congenital Diaphragmatic Hernia and Associated Congenital Anomalies | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Congenital diaphragmatic hernia (CDH) is defined as a defect in the muscular or tendinous portion of diaphragm that results in antenatal herniation of the abdominal contents into the thoracic cavity and pulmonary hypoplasia due to compression of the lungs. The incidence of CDH is 1 in 3000 live births, accounting for 1- 2% of infant mortality and 8% of all birth defects, making it one of the most common and lethal congenital anomalies. CDH is isolated in 50-60% of cases but is associated with other major anomalies, most commonly congenital heart disease or central nervous system malformations, in the remaining 40-50%. Historically CDH carried a grave prognosis with mortality of greater than 50%. However, with recent advances in the post-natal care of children with CDH, survival has improved significantly. However, with improved survival, many of the long term morbidities of CDH have been exposed including pulmonary hypertension, the leading cause of CDH morbidity and mortality. In addition, a subset of children with CDH demonstrate significant developmental delay and intellectual disabilities. Many families and health care providers seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. The etiology of CDH is largely unknown. Evidence is accumulating that many congenital anomalies can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of CDH and define new genes and conditions associated with CDH by performing whole genome sequencing on parent child trios and RNA sequencing of diaphragm tissue in a clinically well characterized cohort to identify rare de novo mutations and inherited variants. Our long-term goal is to define a set of genes important in the etiology of CDH and characterize new clinical syndromes associated with CDH. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information to guide clinic decisions. PUBLIC HEALTH RELEVANCE: Congenital diaphragmatic hernia (CDH) is a serious birth defect accounting for 1-2% of infant mortality and 8% of all birth defects. We propose to elucidate the underlying genomic architecture of CDH by performing whole genome sequencing and RNA sequencing on diaphragm tissue to characterize new clinical syndromes associated with CDH to provide more accurate clinical prognostic information. | |||
| Project Number: | 1 X01 HL136465-01 | Contact PI / Project Leader: | Mary L. Marazita |
| Title: | Kids First: Genomics of Orofacial Cleft Birth Defects in Latin American Families | Awardee Organization: | University of Pittsburgh |
| Abstract: DESCRIPTION (provided by applicant): Nonsyndromic orofacial cleft birth defects (OFCs) are genetically complex structural birth defects caused by genetic factors, environmental exposures, and their interactions. Before the advent of genomic approaches, evaluation of candidate genes revealed at best modest associations with a number of genes. By contrast, genome-wide linkage and association studies by our group and others have identified approximately 18 genomic regions likely to contribute to the risk for nonsyndromic OFCs, which together account for about 55- 60% of the heritability for this disorder. Despite this substantial progress, the functional/pathogenic variants at OFC-associated regions are mostly still unknown. Because previous OFC genomic studies (genome-wide linkage, genome-wide association studies (GWAS), targeted sequencing) are based on relatively sparse genotyping data, they cannot distinguish between causal variants and variants in linkage disequilibrium with unobserved causal variants. Moreover, it is unknown whether the association or linkage signals are due to single common variants, haplotypes of multiple common variants, clusters of multiple rare variants, or some combination. Part of the “missing heritability” for OFC may be accounted for by rare variants within regions of the genome associated with risk to OFC. Finally, we cannot yet attribute specific genetic risk to individual cases and case families. Therefore, the goal of the current study is identify specific OFC risk variants by performing whole genome sequencing (WGS) of Latin American OFC parent-case trios. Notably, Latin American families are at high risk of OFC. Statistical analyses of the WGS results will identify common and rare variants likely to be involved in OFC risk. The resulting data (genetic and phenotypic), analyses and other resources will be made available through dbGaP, the proposed Pediatric Data Resource of the Kids First Program (and/or other NIH-designated repositories). Additional goals of this project are beyond the scope of the Kids First Initiative, but include replicating risk variants identified by WGS in our large resource of OFC case families and controls, and validating expression and functional significance of replicated variants through our other existing collaborators who focus on animal models of OFC. Successful completion of the proposed specific aims will more fully illuminate the genetic architecture of OFC and will provide insight about the biological mechanisms underlying craniofacial development. Ultimately, this project will translate to improved risk prediction, treatment, and prognosis for individuals affected by OFCs. The specific aims are: (1) to identify risk variants for OFC by WGS of Latin American OFC case trios; (2) to make the WGS results available through the proposed Pediatric Data Commons and/or other NIH-designated repositories; (3) to do combined analyses with the WGW in White Trios (from our previous Kids First project); (4) replicate variants identified in the WGS of proband trios; and (5) to explore functional significance and expression of replicated results in cell lines and animal models. PUBLIC HEALTH RELEVANCE: Nonsyndromic orofacial cleft birth defects (OFCs) are very common structural birth defects caused by genetic factors, environmental exposures, and their interactions. The goal of the current study is to identify specific OFC risk variants by performing whole genome sequencing of Latin American OFC families. Successful completion of the project will more fully illuminate the genetic architecture of OFC, and will ultimately translate to improved risk prediction, treatment, and prognosis for individuals affected by OFCs. Sequence and clinical data released in dbGap: Accession Number: phs001420 | |||
| Project Number: | 1 X01 HL136997-01 | Contact PI / Project Leader: | John M. Maris |
| Title: | Genetic basis of neuroblastoma initiation and progression | Awardee Organization: | Children's Hospital of Philadelphia |
| Abstract: DESCRIPTION (provided by applicant): Children with disseminated neuroblastoma have a very high risk of treatment failure and death despite receiving intensified chemotherapy, radiation therapy and immunotherapy. The long-term goal of our research program is to ultimately improve neuroblastoma cure rates by first comprehensively defining the genetic basis of the disease. The central hypothesis to be tested here is that neuroblastoma arises largely due to the epistatic interaction of common and rare heritable DNA variation. Here we will perform a comprehensive whole genome sequencing of 563 quartets of neuroblastoma patient germline and diagnostic tumor DNAs and germline DNAs from both parents. The case series was recently collected through a Children's Oncology Group epidemiology clinical trial and is robustly annotated with complete demographic (age, sex, race, ethnicity), clinical (e.g. age at diagnosis, stage, risk group), epidemiologic (parental dietary and exposure questionnaire) and biological (e.g. tumor MYCN status and multiple other tumor genomic measures) co- variates. Subjects were consented for genetic research and DNA is immediately available for shipment for sequencing. We propose Illumina-based whole genome sequencing in the 563 trio germline samples (Aim 1; due to missing parent: 465 neuroblastoma triads, 94 child-mother dyads and 4 father-child dyads = 1591 whole genome sequences) and matched diagnostic tumor DNA (Aim 2; N=484). We propose at least 100x average sequencing depth for these 2075 DNA samples in order to have sufficient sequencing coverage to reliably identify and quantify germline mosaicism and somatic subclonal heterogeneity. We will use our established analytic pipeline that is currently being used to study the germline genomes of all cases sequenced through the NCI supported Therapeutically Applicable Research to Generate Effective Treatments program. We plan a three stage analytic approach, first focusing on classic de novo and inherited Mendelian damaging alterations. We will next integrate our extensive epigenomic data from human neuroblastoma cell lines and genome-wide association study data (N=5,703 neuroblastoma cases to date) to guide a comprehensive assessment of noncoding variants that influence tumor initiation with a recently established analytic pipeline. Finally, we will utilize the tumor DNA analyses to inform relevance via somatic gain or loss of function effects at the sequence and/or copy number levels. All data generated in this project will be immediately placed into the Genomic Data Commons (GDC) and we will compute within this environment by importing our analytic pipelines into the GDC. These data will be fully integrated into the Kids First Data Resource and freely shared with all academically qualified petitioners. This comprehensive data set derived from a large and richly phenotyped series of neuroblastoma DNA quartets will be integrated with existing germline and/or tumor genomic data from over 6,000 neuroblastoma subjects (but none with matched patient-parent germline sequencing data) to provide an unparalleled opportunity to comprehensively discover the genetic basis of neuroblastoma. PUBLIC HEALTH RELEVANCE: The proposed research Program is relevant to public health because we are addressing a major gap in our understanding of the genetic basis of cancer, here focusing on neuroblastoma, a perplexing and often fatal pediatric malignancy. The proposed research Program is highly relevant to the NIH mission of improving health outcomes as we expect that discoveries of the basic genetic mechanisms of tumor initiation will lead to rational new clinical interventions. | |||
| Project Number: | 1 X01 HL136999-01 | Contact PI / Project Leader: | Charles G. Mullighan |
| Title: | Genomic analysis of familial leukemia | Awardee Organization: | St. Jude Children's Research Hospital |
| Abstract: DESCRIPTION (provided by applicant): Acute lymphoblastic leukemia (ALL) is a precursor cell neoplasm and the commonest childhood cancer, and Hodgkin and non-Hodgkin lymphoma (HL) are forms of lymphoma that arise in both children and adults. Both are multi-genic diseases characterized by multiple subtypes and distinct constellations of somatic genetic changes. There is growing evidence for a genetic predisposition to both diseases, demonstrated by genome- wide association studies that have identified associations between common variants in transcription factors and tumor suppressors and ALL risk, subtype and outcome, and the identification of highly penetrant mutations in transcription factor and tumor suppressor genes in familial ALL. However, the landscape of germline predisposition variants that drive familial and sporadic hematological malignancies (HM) are unknown. In this study we will address this knowledge gap by performing whole genome sequencing of kindreds with familial, coupled with recurrence screening of extended cohorts of ALL and HL and integration of germline and somatic data. We have collected over 60 familial HM kindreds that will be subjected to tumor and germline whole genome sequencing (WGS) supported by this grant mechanism (Specific Aim 1). We will examine the frequency of novel variants, and mutations in newly identified genes, in large cohorts of sporadic ALL/HL (Specific Aim 2, funded separately) and examine associations between germline mutations in familial and sporadic ALL and clinical, pathologic and somatic genomic features (Specific Aim 3, funded separately). The project will be conducted by a group of co-investigators at St Jude Children’s Research Hospital with complementary expertise in clinical genetics (Nichols, Kesserwan), germline predisposition (Yang, Mullighan), clinical aspects of ALL and HL (Sandlund, Metzger) and computational approaches (Rampersaud). We have established collaborations with the COG and assembled the recurrence testing cohorts. Many of the familial tumor and germline samples are in hand, with acquisition of relative material ongoing to submit samples for sequencing by study activation. Together, this represents a logical framework to comprehensively dissect the interaction of germline and somatic genetic alterations in HM, and will provide important mechanistic insights, opportunity for clinical translation, and an invaluable public resource of genomic data. PUBLIC HEALTH RELEVANCE: (RELEVANCE STATEMENT) Acute lymphoblastic leukemia (ALL) is the commonest childhood tumor and a leading cause of cancer death in children, adolescents and young adults. Hodgkin and non-Hodgkin lymphoma are also important hematologic malignancies (HM) that occur in children. Each are genetic diseases with growing evidence for a germline predisposition of both familial and sporadic cases, however the inherited genetic basis of ALL/lymphoma are poorly understood. Such knowledge is essential to gain mechanistic insight into the basis of tumor formation, and to guide genetic counseling and genetic management. Here we have assembled an unmatched group of basic genomic, computational and clinical investigators with an interest in the genetics of HM, a large collection of familial HM kindreds, and extended recurrence cohorts of ALL and HL which will be used to identify the genetic basis of familial HM, examine the frequency of germline variants in sporadic ALL and HL, and to integrate inherited and somatic genomic data. These studies have high potential to provide fundamental new insights into the inherited genetic basis of HM, to provide important information to guide clinical management, and to provide an invaluable public resource of genomic data. | |||
| Project Number: | 1 X01 HL136994-01 | Contact PI / Project Leader: | Sharon E. Plon |
| Title: | Identifying novel cancer susceptibility mutations from unselected childhood cancer patient and parent trios | Awardee Organization: | Baylor College of Medicine |
| Abstract: DESCRIPTION (provided by applicant): Genome-scale sequencing methods have allowed studies that demonstrate that approximately 10% of patients carry germline pathogenic variants in a wide spectrum of known cancer susceptibility genes. These results also highlight that our very limited ability to predict which patients are likely to carry a cancer susceptibility mutation based on tumor type and family history. In addition, prior projects have (1) focused on findings in known germline cancer genes, limiting new discovery, and (2) performed the sequencing on the cancer patient without parental samples obviating our ability to systematically determine the underlying genetic mechanisms such as de novo mutations. In this proposal, we describe whole genome sequencing (WGS) of patient germline and parental samples including the tumor sample when available from an unselected racially and ethnically diverse cohort of well phenotyped pediatric cancer patients enrolled in the NIH supported Baylor Advancing Sequencing in Childhood Cancer Care (BASIC3) trial. Based on the detailed medical record extraction we have identified that approximately 20% of this cohort also includes patients with a neurodevelopmental or structural anomaly. Data derived from this project should fill current gaps in our knowledge (1) the proportion and nature of pathogenic or likely pathogenic germline mutations in known cancer genes that are missed by more standard proband only whole exome sequencing methods and (2) identification of new cancer susceptibility genes to better define the underlying structure of pediatric cancer susceptibility, particularly, when data generated by this project is combined with other Gabriela Miller Kids First and TARGET sequencing in the NCI Data Commons. PUBLIC HEALTH RELEVANCE: We describe whole genome sequencing of pediatric cancer patient (n=120) germline and parental samples including the tumor sample when available from an unselected racially and ethnically diverse cohort of well phenotyped solid tumor (CNS and non-CNS) cancer patients. Data derived from the WGS described here should provide substantial new data to define the underlying genetic structure of cancer susceptibility to pediatric cancer. | |||
| Project Number: | 1 X01 HL132375-01A1 | Contact PI / Project Leader: | Jonathan Rios |
| Title: | Genomics of Orthopaedic Disease Program | Awardee Organization: | UT Southwestern Medical Center |
| Abstract: DESCRIPTION (provided by applicant): Pediatric birth defects are a leading cause of pediatric hospitalizations and deaths. The Gabriella Miller Kids First initiative seeks to understand the genetic causes of pediatric birth defects by synergizing state-of-the-art genetic research techniques with detailed clinical assessments in children. In addition, the Kids First initiative will build a collaborative environment by making available genetic and clinical information that will foster collaborative research and ultimately improve our understanding of pediatric birth defects. At Texas Scottish Rite Hospital for Children, the Genomics Of Orthopaedic Disease (GOOD for Kids) program similarly seeks to understand pediatric birth defects, such as adolescent idiopathic scoliosis (AIS), through close interaction and collaboration with orthopaedic surgeons and treating physicians. AIS is a debilitating curvature and rotational deformity of the spine and is the most common pediatric musculoskeletal deformity in the world. Our long- term goal is to improve management and prevention of AIS by discovering genetic and developmental risk factors leading to spine deformity. Our collaborative research team has extensive experience and expertise with gene discovery using next-generation sequence analysis, and we have led the field in identifying genetic risk factors for AIS. To expand on our previous successes, we propose to perform whole-genome sequencing (WGS), the most comprehensive approach to identify genetic causes of pediatric disease, using a tiered approach. In our first tier we propose sequencing families with multiple generations of relatives with AIS. These families provide the greatest power to identify new genes when faced with the vast amounts of data generated by WGS. This approach is supported by detailed clinical characterization and rich histories for families that, in some cases, were treated for multiple generations at our Institutions. Our unique ability to perform WGS analysis in multiple affected family members segregating AIS through multiple generations allows us to identify new genetic causes of AIS despite reduced penetrance of the disease. We also propose Tier 2 families, which include those with affected siblings with AIS but without affected parents and no evidence for dominant inheritance. Recognizing reduced penetrance in AIS, our multi-faceted approach to WGS analysis will include analyses for recessive disease as well as dominant disease with non-penetrant parents for Tier 2 families. Candidate genes identified in each Tier will be validated by re-sequencing, evidence of association from our current GWAS meta-analysis, and individual variant association testing in our singleton collection of >2500 cases with AIS. Our approach is supported by our access to extensive clinical characterization and documentation for each study subject, our close collaboration with referring physicians, and our considerable experience and commitment to genetic analysis of AIS. Together, the power of our clinical and genomic analyses will meet the goals of the Kids First initiative, will expand our understanding of pediatric musculoskeletal disease, and may lead to better diagnosis and treatments for children with AIS. PUBLIC HEALTH RELEVANCE: The Kids First initiative seeks to perform whole-genome sequencing in pediatric patients with birth defects and to merge this genetic information with detailed clinical evaluations, all with the goal of improving our understanding of pediatric birth defects and improving treatment in children. We propose the Genomics Of Orthopaedic Disease (GOOD For Kids) program that will expand our current efforts to understand the genetic etiology of adolescent idiopathic scoliosis (AIS), the most common pediatric musculoskeletal deformity in the world. Our collaborative group has led the field in identifying genetic risk factors for AIS, and, with the Kids First initiative, promises to continue making strides to understand the genetic mechanisms causing disease and hopefully improve diagnosis and care of these children. Sequence and clinical data released in dbGap: Accession Number: phs001410.v1.p1 | |||
| Project Number: | 1 X01 HL136976-01 | Contact PI / Project Leader: | Christine E. Seidman |
| Title: | Discovery of De Novo and Inherited Mutations that Cause Prevalent Birth Defects | Awardee Organization: | Harvard Medical School |
| Abstract: DESCRIPTION (provided by applicant): The Pediatric Cardiovascular Genetics Consortium (PCGC) proposes to define genetic causes for congenital heart defects (CHD) as part of the Gariella Miller Kids First Pediatric Research Program. CHD is the most common birth defect and is often accompanied by another congenital anomaly (CA). The PCGC has recruited and clinically characterized ≥ 10,000 CHD probands and parents (CHC trios), including 30% probands with CHD + CA. From extensive exome sequence (WES) analyses in over 2000 CHD trios, genome sequence (WGS) analyses of 50 CHD trios, and other genetic studies, we identified a substantial enrichment of damaging de novo mutations in developmental genes that modulate embryonic transcription. Based on these discoveries, we hypothesize that PCGC probands with uninformative genomic analyses (WES-negative) carry mutations in critical regulatory elements that participate in developmental expression of cardiac genes. To identify these etiologies, we propose analyses of WGS in 500 prioritized WES-negative CHD trios that include probands with banked CHD tissues (n=278), one damaging variant in a recessive CHD gene (n=186), and older fathers (n=60; age>45). We will capitalize on existing RNAseq data from CHD tissues, DNA methylation studies and the extensive computational and functional data on cardiac enhancers provided by our collaborating investigators, to analyze coding and non-coding, SNVs and SVs. We will use existing resources and capabilities of the PCGC and its companion consortium in the Bench to Bassinet Program, the Cardiovascular Development Consortium, to perform confirmatory functional genomics studies using cell and animal models outside of the GMKF program. We expect that these studies will provide novel insights into the molecular basis for birth defects and fundamental knowledge about genes and pathways involved in the development of the heart and other organs. Our aims are to: 1. Define de novo and transmitted variants, both SNVs and SVs, that cause dominant, recessive, and sporadic CHD ± CA. 2. Identify pathogenic de novo and transmitted variants in coding and regulatory regions both by case- control analyses and orthogonal data sets (ENCODE, cardiac enhancers, promoters, and regulatory ncRNAs, genes with unexplained loss of expression or allelic-specific expression in CHD tissues, and genome-wide DNA methylation data). PUBLIC HEALTH RELEVANCE: Through the use of whole genome sequencing of individuals with congenital heart disease (CHD) and other congenital malformations, and their unaffected parents, this project will drive discovery of the genetic causes for common birth defects. The new insights gained from this project will improve care by enabling DNA diagnostics for birth defects and by providing novel mechanistic insights, with which new therapies can be developed. Sequence and clinical data released in dbGap: Accession Number: : phs001138 | |||
| Project Number: | X01 HL132380-01A1 | Contact PI / Project Leader: | Jun Shen |
| Title: | Hear-n-Seq: Sequencing Kids First for Hearing | Awardee Organization: | Brigham and Women's Hospital |
| Abstract: DESCRIPTION (provided by applicant): With hearing loss of 40 decibels or more and 1 in 100 children will lose significant hearing by school age, making it one of the single most common structural defects affecting the pediatric population. Hearing loss can affect a child's ability to develop speech, language, cognitive and social skills. The earlier a child with hearing loss starts receiving appropriate medical and educational services, the more likely they are to reach their full potential. More than half of early hearing loss is due to genetic factors. Approximately 1 in 500 babies is born While the majority of prelingual hearing loss is nonsyndromic, over 400 syndromes have been described that have hearing impairment as a component. It is critically important to identify the etiology of hearing loss for many reasons, as there may be important health surveillance implications particularly with syndromic causes. Genetic testing is available for congenital hearing loss, but the current standard of care is by no means comprehensive because: 1) many types of genetic variants in known hearing loss genes are not detectable by clinical testing, and 2) it is estimated that more than 100 hearing loss genes are as yet unknown. With this proposal called Hear-'n-SEQ, we will leverage the resources of the NIH Common Fund's Gabriella Miller Kids First Pediatric Research program to"seek-out" the genetic etiology of childhood hearing loss through comprehensive phenotypic and genomic analyses in an international cohort of hearing impaired patients. By sharing both the clinical and sequence data with the pediatric research community we will be empowered to identify genetic pathways that underlie hearing loss as well as pathways shared with other pediatric conditions. This project will be coordinated through the Harvard Medical School Center for Hereditary Deafness (HMSCHD). The Specific Aims of the project are to: (1) build an international consortium to identify and collect well-curated patient clinical information and DNA samples from children with hearing loss and their parents (trios) or carefully selected multiple affected individuals based on the pedigree structure, (2) submit appropriate DNA samples for whole genome sequencing at an NIH-supported sequencing center, and, (3) identify the genetic etiology of hearing impairment in individuals where possible, and integrate the data collectively into a shared data resource. Because of the tremendous genetic heterogeneity inherent in hearing loss, the proposed international collaboration will produce a maximum yield of diverse genetic causes, as it has been well established that different populations segregate distinct concentrations of hearing loss alleles. Therefore we will sample the hearing impaired pediatric populations of parts of Asia (Hong Kong), the Middle East (Turkey), and the US (individuals of European, African American, Central American and Caribbean descent). In addition to identifying novel etiologies for hearing loss, ultimately this work is designed to help create a pipeline for routinely integrating genomic sequencing into clinical diagnostics, generating more refined diagnostic capabilities, and ultimately more targeted therapies or interventions for children with hearing loss. PUBLIC HEALTH RELEVANCE: Hearing loss is the most common structural birth defect detected through newborn screening. Genetic factors contribute to the majority of childhood hearing loss, but currently available genetic testing can only identify the cause in 1/3 of patients. This Hear-'n-SEQ project proposes to use the latest DNA sequencing and comprehensive genetic analysis technologies to identify the genetic causes of previously unsolved hearing loss cases, with an overarching goal of offering better and timelier treatment options for children with hearing loss. | |||
2015 X01 Projects
| Project Number: | 1 X01 HL 132366-01 | Contact PI / Project Leader: | Wendy K. Chung |
| Title: | Genomic Analysis of Congenital Diaphragmatic Hernia | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Congenital diaphragmatic hernia (CDH) is defined as a defect in the muscular or tendinous portion of diaphragm that results in antenatal herniation of the abdominal contents into the thoracic cavity and pulmonary hypoplasia due to compression of the lungs. The incidence of CDH is 1 in 3000 live births, accounting for 1- 2% of infant mortality and 8% of all birth defects, making it one of the most common and lethal congenital anomalies. CDH is isolated in 50-60% of cases but is associated with other major anomalies, most commonly congenital heart disease or central nervous system malformations, in the remaining 40-50%. Historically CDH carried a grave prognosis with mortality of greater than 50%. However, with recent advances in the post-natal care of children with CDH, survival has improved significantly. However, with improved survival, many of the long term morbidities of CDH have been exposed including pulmonary hypertension, the leading cause of CDH morbidity and mortality. In addition, a subset of children with CDH demonstrate significant developmental delay and intellectual disabilities. Many parents and prospective parents seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. The etiology of CDH is largely unknown. Evidence is accumulating that many birth defects can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of CDH by performing whole genome sequencing on parent child trios and RNA sequencing of diaphragm tissue in a clinically well characterized cohort to identify de novo mutations and inherited rare variants. Our long-term goal is to define a set of genes important in the etiology of CDH and characterize new clinical syndromes associated with CDH. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information. PUBLIC HEALTH RELEVANCE: Congenital diaphragmatic hernia (CDH) is a serious birth defect accounting for 1-2% of infant mortality and 8% of all birth defects. We propose to elucidate the underlying genomic architecture of CDH by performing whole genome sequencing and RNA sequencing on diaphragm tissue to characterize new clinical syndromes associated with CDH to provide more accurate clinical prognostic information. Sequence and clinical data released in dbGap: Accession Number: phs001110 | |||
| Project Number: | 1 X01 HL 132377-01 | Contact PI / Project Leader: | Elizabeth C. Engle |
| Title: | BCH Structural Birth Defects Collaboration: Syndromic cranial dysinnervation disorders | Awardee Organization: | Children’s Hospital Corporation |
| Abstract: DESCRIPTION (provided by applicant): It is estimated that approximately 1 of every 33 infants in the United States is born with a birth defect. Among these, the subset associated with inability to move the eyes and face cause significant disability, are frequently accompanied by additional structural birth defects, and often segregate within families or arise from de novo mutations. The applicant's genetic and developmental studies have led to the definition of these syndromes as a new category of human disease referred to as the `congenital cranial dysinnervation disorders' (CCDDs). The applicant has defined multiple CCDD syndromes, uncovered their genetic etiologies, and determined that these disorders often result from maldevelopment of cranial motor neurons and their axonal processes. Despite the many CCDD genes and pathways identified by the applicant, many families remain genetically undefined. Thus, the goal of this proposal is to generate and interpret whole genome sequence (WGS) data to identify previously undefined genetic causes of CCDDs and related anomalies. WGS will allow the detection of non-coding variants, CNVs, and complex rearrangements, while also providing better coverage of coding regions than exome sequencing, thus filling a gap of information obtained by other genetic approaches. We have chosen DNA samples for WGS from a large and unique cohort of deeply phenotyped research participants, many of whom have associated findings and multiple organ involvement. The DNA samples have been screened for mutations in the known CCDD genes and many have had whole exome sequencing (WES), yet remain genetically unsolved. The participants have consented to sharing of WGS and relevant phenotype data through an NIH-approved controlled-access repository, and almost all have consented to recontact, permitting us to collect additional phenotyping data and samples, reconsent when necessary, and to discuss enrollment in additional studies. Because a barrier to informative discovery from WGS is proper data analysis, these data will be analyzed in collaboration with leaders in genetics and genomics at the Broad Institute of MIT and Harvard and at the Boston Children's Hospital, and in collaboration with CCDD researchers at Mount Sinai Medical Center and NIH. These joint analyses should greatly improve the quality and interpretation of the genome data generated, and significantly increase our likelihood of identifying multiple new genetic etiologies or CCDDs and their associated anomalies. As part of this grant mechanism, the WGS and phenotype data will become part of the integrated NIH Pediatric Research Data Resource and the applicant will also participate in development of the Kids First Data Resource Consortium. This will be followed by functional studies to further uncover CCDDs mechanisms and shared pathways among CCDDs and between CCDDs and other structural birth defects, and should lead to refined diagnostic capabilities and improved therapies. PUBLIC HEALTH RELEVANCE: Congenital paralysis of eye and facial movements arise from structural birth defects, result in impaired vision, perturbed facial and speech communication, profoundly disturbed interpersonal interactions and self-esteem, and are often accompanied by additional anomalies of the nervous system and other organs. To determine their genetic causes, DNA samples from a large cohort of research participants will be submitted for whole genome sequencing, and the data analyzed by a team of researchers at Boston Children's Hospital, the Broad Institute of MIT and Harvard, Mount Sinai Medical Center, and National Institute of Health. As part of this grant mechanism, these data will become part of the integrated NIH Pediatric Research Data Resource and the applicant will participate in the Kids First Data Resource Consortium. Sequence and clinical data accessible through dbGaP: Accession Number: phs001247 | |||
| Project Number: | 1 X01 HL 132363-01 | Contact PI / Project Leader: | Mary L. Marazita |
| Title: | Genomic Studies of Orofacial Cleft Birth Defects | Awardee Organization: | University of Pittsburgh |
| Abstract: DESCRIPTION (provided by applicant): Nonsyndromic orofacial cleft birth defects (OFCs) are genetically complex structural birth defects caused by genetic factors, environmental exposures, and their interactions. Before the advent of genomic approaches, evaluation of candidate genes revealed at best modest associations with a number of genes. By contrast, genome-wide linkage and association studies by our group and others have identified approximately 18 genomic regions likely to contribute to the risk for nonsyndromic OFCs, which together account for about 55- 60% of the heritability for this disorder. Despite this substantial progress, the functional/pathogenic variants at OFC-associated regions are mostly still unknown. Because previous OFC genomic studies (genome-wide linkage, genome-wide association studies (GWAS), targeted sequencing) are based on relatively sparse genotyping data, they cannot distinguish between causal variants and variants in linkage disequilibrium with unobserved causal variants. Moreover, it is unknown whether the association or linkage signals are due to single common variants, haplotypes of multiple common variants, clusters of multiple rare variants, or some combination. Part of the "missing heritability" for OFC may be accounted for by rare variants within regions of the genome associated with risk to OFC. Finally, we cannot yet attribute specific genetic risk to individual cases and case families. Therefore, the goal of the current study is identify specific OFC risk variants by performing whole genome sequencing (WGS) of OFC parent-case trios. Statistical analyses of the WGS results will identify common and rare variants likely to be involved in OFC risk. The resulting data (genetic and phenotypic), analyses and other resources will be made available through the proposed Pediatric Data Commons of the Kids First Program (and/or other NIH-designated repositories). Additional goals of this project are beyond the scope of the Kids First Initiative, but include replicating risk variants identified by WGS in our large resource of OFC case families and controls, and validating expression and functional significance of replicated variants through our other existing collaborators who focus on animal models of OFC. Successful completion of the proposed specific aims will more fully illuminate the genetic architecture of OFC and will provide insight about the biological mechanisms underlying craniofacial development. Ultimately, this project will translate to improved risk prediction, treatment, and prognosis for individuals affected by OFCs. The specific aims are: (1) to identify risk variants for OFC by WGS of OFC case trios; (2) to make the WGS results available through the proposed Pediatric Data Commons and/or other NIH-designated repositories; (3) to replicate variants identified in the WGS of proband trios; and (4) to explore functional significance and expression of replicated results in cell lines and animal models. PUBLIC HEALTH RELEVANCE: Nonsyndromic orofacial cleft birth defects (OFCs) are very common structural birth defects caused by genetic factors, environmental exposures, and their interactions. The goal of the current study is to identify specific OFC risk variants by performing whole genome sequencing of OFC families. Successful completion of the project will more fully illuminate the genetic architecture of OFC, and will ultimately translate to improved risk prediction, treatment, and prognosis for individuals affected by OFCs. Sequence and clinical data accessible through dbGaP: Accession Number: phs001168 | |||
| Project Number: | 1 X01 HL 132378-01 | Contact PI / Project Leader: | Kenan Onel |
| Title: | An Integrated Clinical and Genomic Analysis of Treatment Failure in Pediatric Osteosarcoma | Awardee Organization: | The University of Chicago |
| Abstract: DESCRIPTION (provided by applicant): For children with osteosarcoma, it has long been known that response to chemotherapy as measured by percent necrosis at the time of definitive surgery is a powerful prognostic biomarker. Patients with 90 percent or more tumor necrosis are likely to be cured of their disease, whereas those with less than 90 percent tumor necrosis are at high risk for treatment failure. Despite its clinical importance, however, virtually nothing is known about the genetic and molecular basis of this phenomenon. Consequently, there have been few advances in the treatment of osteosarcoma in decades. In this proposal, we will perform whole genome sequencing on serial samples obtained over time from a set of 198 patients with osteosarcoma, all treated similarly, and for whom we have complete clinical information. Of these patients, 52 have suffered a relapse of their disease. Our primary objective is to determine whether there are recurrent mutations in these relapse samples that may point towards common mechanisms of treatment failure, and may, therefore, suggest novel therapies for relapsed osteosarcoma. Our secondary objective is to determine the genetic drivers of treatment failure in osteosarcoma by analyzing within each patient the evolving spectrum of mutations selected by chemotherapy exposure over time. To our knowledge, this is the largest set of matched pre-therapy, post- therapy, and relapse samples ever assembled for any cancer. If successful, this project sets the stage for future functional studies exploiting our genetic findings to investigate the mechanisms of drug resistance in osteosarcoma. Perhaps more importantly, it also holds forth the promise of changing the paradigm for therapy in osteosarcoma, a disease that has thus far proven refractory to innovative therapies to improve the dismal survival of children with tumors that respond poorly to current chemotherapy protocols. PUBLIC HEALTH RELEVANCE: Although the survival of children with relapsed osteosarcoma is very poor, little is known about the etiology of treatment failure in this disease. The purpose of this project is to perform whole genome sequencing on serial samples from patients with osteosarcoma obtained before treatment, after treatment, and at relapse in order to identify the mutations and pathways that are drivers of drug resistance. If successful, our results may help identify patients at high risk for treatment failure and may yield new treatments for children who cannot currently be cured. | |||
| Project Number: | 1 X01 HL 132385-01 | Contact PI / Project Leader: | Joshua D. Schiffman |
| Title: | Genetic Contribution to Ewing Sarcoma in 330 parent-Offspring Trios | Awardee Organization: | University of Utah |
| Abstract: DESCRIPTION (provided by applicant): Ewing sarcoma (ES) is a deadly bone cancer that occurs in children and adolescents. Mounting evidence suggests that a genetic predisposition exists for this pediatric cancer, although the specific genetic contribution has yet to be identified. ES has never been linked to a specific cancer predisposition syndrome, although several case reports have been published that describe siblings and cousins with ES. Furthermore, neuroectodermal tumors appear to occur more commonly in families with ES. The two consistent epidemiology findings in ES include a very strong Caucasian predilection and increased rates of hernia in ES patients and their family members. Finally, the role of genetic microsatellite repeats in ES tumorigenesis has been recently described, and these GGAA microsatellites are polymorphic in repeat size and location across the genome. The Children's Oncology Group (COG) Study AEPI10N5 ("Genetic Epidemiology of Ewing Sarcoma") was begun to collect germline DNA from ES parent-offspring trios to explore the genetic risk for disease development. Each trio contains germline DNA and has been well characterized through a complete medical and family history evaluation. As part of the Gabriella Miller Kids First Pediatric Research Program, we will submit 330 ES trios from AEPI10N5 for whole genome sequencing (WGS). The study goals of this Kids First proposal include (1) To identify cancer predisposition genes in ES trios increasing disease risk, (2) To identify genome-wide GGAA microsatellite repeats in ES trios increasing disease risk, and (3) To identity de novo mutation and structural variant rates in ES trios reflecting underlying DNA repair defects that increase disease risk. As part of the Kids First Common Fund initiative, this study proposal will further elucidate the genetic contribution to pediatric cancer development. All of the WGS and phenotype data from this study will be deposited into the designated data repository for the Kids First Common Fund and will be accessible to other researchers. The WGS of these 330 ES trios will help us to understand the genetic origins of a deadly childhood cancer and may lead to novel strategies for prevention and treatment. PUBLIC HEALTH RELEVANCE: Ewing sarcoma (ES) is a deadly pediatric bone cancer striking children and adolescents. We will submit 330 ES trios for whole genome sequencing (WGS) as part of the Gabriella Miller Kids First Pediatric Research Program. The ES trios have been collected as part of the Children's Oncology Group's AEPI10N5 Study ("Genetic Epidemiology of Ewing Sarcoma"), and each trio has associated phenotypic data including a detailed family history. We will interrogate the sequence data using our genomic analysis pipeline at the University of Utah and the Utah Science Technology and Research initiative's (USTAR) Center for Genetic Discovery. We will look for the genetic contribution to ES and the sequence data with be shared in a repository designated by the Kids First Common Fund. Sequence and clinical data accessible through dbGaP: Accession Number: phs001228 | |||
| Project Number: | 1 X01 HL 132370-01 | Contact PI / Project Leader: | Christine E. Seidman |
| Title: | Discovery of the Genetic Basis of Structural Heart and Other Birth Defects | Awardee Organization: | Harvard Medical School |
| Abstract: DESCRIPTION (provided by applicant): The Pediatric Cardiovascular Genetics Consortium (PCGC) proposes to define genetic causes for congenital heart defects (CHD) as part of the Gabriella Miller Kids First Pediatric Research Program. CHD is the most common birth defect and is often accompanied by another congenital anomaly (CA). The PCGC has recruited and clinically phenotyped ≥ 20,000 probands and parents (trios) with CHD, including 30% with CHD + CA. From exome sequencing and other genetic analyses, we discovered that CHD probands are enriched for damaging de novo mutations in developmental genes that modulate embryonic transcription. Based on these discoveries, we hypothesize that PCGC probands with uninformative prior genomic analyses will carry mutations in critical regulatory elements that participate in developmental gene expression. To identify these etiologies, we propose analyses of whole genome sequencing (WGS) of probands/unaffected parents trios, capitalizing on existing RNAseq data from CHD tissues, DNA methylation studies and the extensive expertise with cardiac enhancers of our collaborating investigators to inform prioritization of de novo non-coding, regulatory sequence variants. We will use resources and capabilities of the PCGC and its companion consortium in the Bench to Bassinet Program, the Cardiovascular Development Consortium, to perform confirmatory functional genomics studies using cell and animal models. Our studies will provide novel insights into the genes and pathways involved in the development of the heart and other organs as well as into the clinical spectrum of birth defects. Our specific aims are: Aim 1. Select cohorts of CHD ± CA trios for WGS and rapidly provide high-quality DNA to the NIH- designated sequencing site. Aim 2. Identify de novo structural variants and variants that alter exome and splice sites. Aim 3. Identify de novo variants in CHD ± CA probands in non-coding regulatory elements. PUBLIC HEALTH RELEVANCE: Through the use of whole genome sequencing of individuals with congenital heart disease (CHD) and their unaffected parents, this project will drive discovery of the genetic causes of this class of birth defects, which will also have relevance for other types of congenital anomalies. The new insights gained from this project will improve care by enabling DNA diagnostics for birth defects and by providing novel mechanistic insights, with which new therapies can be developed. Sequence and clinical data accessible through dbGaP: Accession Number: phs001138 | |||
| Project Number: | 1 X01 HL 132384-01 | Contact PI / Project Leader: | Eric J. Vilain |
| Title: | Genetic Basis of Disorders/Differences of Sex Development (DSD) | Awardee Organization: | University of California Los Angeles |
| Abstract: DESCRIPTION (provided by applicant): Disorders of Sex Development (DSD) are phenotypically heterogeneous, ranging from minor genital malformations (hypospadias, cryptorchidism, hypertrophy of the clitoris) to genital ambiguity. In the aggregate, DSD have an estimated incidence of about 1%. DSD can result in severe consequences for behavioral health, fertility, cancer risk and quality of life. For families, the birth of a child with a DSD, and the accompanying uncertainty about future psychological and sexual development, is believed to be extraordinarily stressful. Recently, the debate over clinical management of DSD, in particular gender assignment and genital surgery, has intensified; yet the scientific data on patient outcomes have remained very incomplete. Major obstacles to optimal clinical management of DSD include lack of outcome studies, but also a low genetic diagnostic yield, leading to gaps in the understanding of pathophysiology, and increasing the uncertainty around the clinical management of DSD. Here we propose to use the existing resource of the DSD Translational Research Network (DSD-TRN, PIs Vilain and Sandberg), a network of 10 clinical sites collecting standardized phenotypic information, banking DNA of patients with a DSD, and populating a Registry located at UCLA. We propose to perform Whole-Genome Sequencing (WGS) on 150 patients with DSD and their parents, as well as an additional 26 historical cases for which Whole-Exome Sequencing did not yield a causative variant, in order to investigate the following aims: Aim 1: To identify new exomic causes of DSD. Analysis of exomic variants is expected to yield causative variants in 35% of cases; Aim 2: To identify non exomic causes of DSD, with a three-prong approach: 2a- Specific search for variants within promoters and introns of known DSD genes, and in the promoters of genes for which WGS identified a variant in one exonic allele or a heterozygous structural variant; 2b- Search for de novo variants; and 2c- Search for large rearrangements (translocations, duplications, inversions); Aim 3: To identify the influence of environmental exposure on phenotypic variability of DSD. We will perform a systematic collection of environmental exposure by a comprehensive environmental questionnaire (NHANES) as well as NHGRI's PhenX tool kit and by modeling patient's environmental exposure using the family's geographical information. The environmental analysis will be focused on whether there are significant environmental differences between patients with a variant in the same gene and different degrees of phenotypic severity. The accessibility of a large sample of well characterized patients with DSD, and the collective expertise of our multidisciplinary team (medical genetics, statistics, computer science) increases the likelihood of a successful deciphering of causes of DSD and of improvement of outcomes for DSD. PUBLIC HEALTH RELEVANCE: A defining moment of our lives begins when we embark on a male or female path in the womb; disruption of typical male or female development results in Disorders/Differences of Sex Development (DSD), which occur frequently -- in about 1% of the human population. The quality of life of people affected by DSD and their families is often threatened by uncertainty about what caused the condition, leading to uncertainty about choices in care, and the chronic stress associated with experienced stigma and lifelong clinical care. To improve clinical care for patients with DSD and their families, we propose a study that uncovers the genetic causes of DSD by sequencing their entire genome. Sequence and clinical data accessible through dbGaP: Accession Number: phs001178 | |||
2015 X01 Projects
| Project Number: | 1 X01 HL 132366-01 | Contact PI / Project Leader: | Wendy K. Chung |
| Title: | Genomic Analysis of Congenital Diaphragmatic Hernia | Awardee Organization: | Columbia University Health Sciences |
| Abstract: DESCRIPTION (provided by applicant): Congenital diaphragmatic hernia (CDH) is defined as a defect in the muscular or tendinous portion of diaphragm that results in antenatal herniation of the abdominal contents into the thoracic cavity and pulmonary hypoplasia due to compression of the lungs. The incidence of CDH is 1 in 3000 live births, accounting for 1- 2% of infant mortality and 8% of all birth defects, making it one of the most common and lethal congenital anomalies. CDH is isolated in 50-60% of cases but is associated with other major anomalies, most commonly congenital heart disease or central nervous system malformations, in the remaining 40-50%. Historically CDH carried a grave prognosis with mortality of greater than 50%. However, with recent advances in the post-natal care of children with CDH, survival has improved significantly. However, with improved survival, many of the long term morbidities of CDH have been exposed including pulmonary hypertension, the leading cause of CDH morbidity and mortality. In addition, a subset of children with CDH demonstrate significant developmental delay and intellectual disabilities. Many parents and prospective parents seek prognostic clinical information about other associated birth defects or genetic syndromes, but prognostic data are extremely limited unless a chromosomal anomaly is identified. The etiology of CDH is largely unknown. Evidence is accumulating that many birth defects can result from copy number variants, de novo mutations, and inherited rare mutations, often unique to the family. We propose to elucidate the underlying genomic architecture of CDH by performing whole genome sequencing on parent child trios and RNA sequencing of diaphragm tissue in a clinically well characterized cohort to identify de novo mutations and inherited rare variants. Our long-term goal is to define a set of genes important in the etiology of CDH and characterize new clinical syndromes associated with CDH. We believe this information will improve genetic diagnostic methods and provide more accurate clinical prognostic information. PUBLIC HEALTH RELEVANCE: Congenital diaphragmatic hernia (CDH) is a serious birth defect accounting for 1-2% of infant mortality and 8% of all birth defects. We propose to elucidate the underlying genomic architecture of CDH by performing whole genome sequencing and RNA sequencing on diaphragm tissue to characterize new clinical syndromes associated with CDH to provide more accurate clinical prognostic information. Sequence and clinical data released in dbGap: Accession Number: phs001110 | |||
| Project Number: | 1 X01 HL 132377-01 | Contact PI / Project Leader: | Elizabeth C. Engle |
| Title: | BCH Structural Birth Defects Collaboration: Syndromic cranial dysinnervation disorders | Awardee Organization: | Children’s Hospital Corporation |
| Abstract: DESCRIPTION (provided by applicant): It is estimated that approximately 1 of every 33 infants in the United States is born with a birth defect. Among these, the subset associated with inability to move the eyes and face cause significant disability, are frequently accompanied by additional structural birth defects, and often segregate within families or arise from de novo mutations. The applicant's genetic and developmental studies have led to the definition of these syndromes as a new category of human disease referred to as the `congenital cranial dysinnervation disorders' (CCDDs). The applicant has defined multiple CCDD syndromes, uncovered their genetic etiologies, and determined that these disorders often result from maldevelopment of cranial motor neurons and their axonal processes. Despite the many CCDD genes and pathways identified by the applicant, many families remain genetically undefined. Thus, the goal of this proposal is to generate and interpret whole genome sequence (WGS) data to identify previously undefined genetic causes of CCDDs and related anomalies. WGS will allow the detection of non-coding variants, CNVs, and complex rearrangements, while also providing better coverage of coding regions than exome sequencing, thus filling a gap of information obtained by other genetic approaches. We have chosen DNA samples for WGS from a large and unique cohort of deeply phenotyped research participants, many of whom have associated findings and multiple organ involvement. The DNA samples have been screened for mutations in the known CCDD genes and many have had whole exome sequencing (WES), yet remain genetically unsolved. The participants have consented to sharing of WGS and relevant phenotype data through an NIH-approved controlled-access repository, and almost all have consented to recontact, permitting us to collect additional phenotyping data and samples, reconsent when necessary, and to discuss enrollment in additional studies. Because a barrier to informative discovery from WGS is proper data analysis, these data will be analyzed in collaboration with leaders in genetics and genomics at the Broad Institute of MIT and Harvard and at the Boston Children's Hospital, and in collaboration with CCDD researchers at Mount Sinai Medical Center and NIH. These joint analyses should greatly improve the quality and interpretation of the genome data generated, and significantly increase our likelihood of identifying multiple new genetic etiologies or CCDDs and their associated anomalies. As part of this grant mechanism, the WGS and phenotype data will become part of the integrated NIH Pediatric Research Data Resource and the applicant will also participate in development of the Kids First Data Resource Consortium. This will be followed by functional studies to further uncover CCDDs mechanisms and shared pathways among CCDDs and between CCDDs and other structural birth defects, and should lead to refined diagnostic capabilities and improved therapies. PUBLIC HEALTH RELEVANCE: Congenital paralysis of eye and facial movements arise from structural birth defects, result in impaired vision, perturbed facial and speech communication, profoundly disturbed interpersonal interactions and self-esteem, and are often accompanied by additional anomalies of the nervous system and other organs. To determine their genetic causes, DNA samples from a large cohort of research participants will be submitted for whole genome sequencing, and the data analyzed by a team of researchers at Boston Children's Hospital, the Broad Institute of MIT and Harvard, Mount Sinai Medical Center, and National Institute of Health. As part of this grant mechanism, these data will become part of the integrated NIH Pediatric Research Data Resource and the applicant will participate in the Kids First Data Resource Consortium. Sequence and clinical data accessible through dbGaP: Accession Number: phs001247 | |||
| Project Number: | 1 X01 HL 132363-01 | Contact PI / Project Leader: | Mary L. Marazita |
| Title: | Genomic Studies of Orofacial Cleft Birth Defects | Awardee Organization: | University of Pittsburgh |
| Abstract: DESCRIPTION (provided by applicant): Nonsyndromic orofacial cleft birth defects (OFCs) are genetically complex structural birth defects caused by genetic factors, environmental exposures, and their interactions. Before the advent of genomic approaches, evaluation of candidate genes revealed at best modest associations with a number of genes. By contrast, genome-wide linkage and association studies by our group and others have identified approximately 18 genomic regions likely to contribute to the risk for nonsyndromic OFCs, which together account for about 55- 60% of the heritability for this disorder. Despite this substantial progress, the functional/pathogenic variants at OFC-associated regions are mostly still unknown. Because previous OFC genomic studies (genome-wide linkage, genome-wide association studies (GWAS), targeted sequencing) are based on relatively sparse genotyping data, they cannot distinguish between causal variants and variants in linkage disequilibrium with unobserved causal variants. Moreover, it is unknown whether the association or linkage signals are due to single common variants, haplotypes of multiple common variants, clusters of multiple rare variants, or some combination. Part of the "missing heritability" for OFC may be accounted for by rare variants within regions of the genome associated with risk to OFC. Finally, we cannot yet attribute specific genetic risk to individual cases and case families. Therefore, the goal of the current study is identify specific OFC risk variants by performing whole genome sequencing (WGS) of OFC parent-case trios. Statistical analyses of the WGS results will identify common and rare variants likely to be involved in OFC risk. The resulting data (genetic and phenotypic), analyses and other resources will be made available through the proposed Pediatric Data Commons of the Kids First Program (and/or other NIH-designated repositories). Additional goals of this project are beyond the scope of the Kids First Initiative, but include replicating risk variants identified by WGS in our large resource of OFC case families and controls, and validating expression and functional significance of replicated variants through our other existing collaborators who focus on animal models of OFC. Successful completion of the proposed specific aims will more fully illuminate the genetic architecture of OFC and will provide insight about the biological mechanisms underlying craniofacial development. Ultimately, this project will translate to improved risk prediction, treatment, and prognosis for individuals affected by OFCs. The specific aims are: (1) to identify risk variants for OFC by WGS of OFC case trios; (2) to make the WGS results available through the proposed Pediatric Data Commons and/or other NIH-designated repositories; (3) to replicate variants identified in the WGS of proband trios; and (4) to explore functional significance and expression of replicated results in cell lines and animal models. PUBLIC HEALTH RELEVANCE: Nonsyndromic orofacial cleft birth defects (OFCs) are very common structural birth defects caused by genetic factors, environmental exposures, and their interactions. The goal of the current study is to identify specific OFC risk variants by performing whole genome sequencing of OFC families. Successful completion of the project will more fully illuminate the genetic architecture of OFC, and will ultimately translate to improved risk prediction, treatment, and prognosis for individuals affected by OFCs. Sequence and clinical data accessible through dbGaP: Accession Number: phs001168 | |||
| Project Number: | 1 X01 HL 132378-01 | Contact PI / Project Leader: | Kenan Onel |
| Title: | An Integrated Clinical and Genomic Analysis of Treatment Failure in Pediatric Osteosarcoma | Awardee Organization: | The University of Chicago |
| Abstract: DESCRIPTION (provided by applicant): For children with osteosarcoma, it has long been known that response to chemotherapy as measured by percent necrosis at the time of definitive surgery is a powerful prognostic biomarker. Patients with 90 percent or more tumor necrosis are likely to be cured of their disease, whereas those with less than 90 percent tumor necrosis are at high risk for treatment failure. Despite its clinical importance, however, virtually nothing is known about the genetic and molecular basis of this phenomenon. Consequently, there have been few advances in the treatment of osteosarcoma in decades. In this proposal, we will perform whole genome sequencing on serial samples obtained over time from a set of 198 patients with osteosarcoma, all treated similarly, and for whom we have complete clinical information. Of these patients, 52 have suffered a relapse of their disease. Our primary objective is to determine whether there are recurrent mutations in these relapse samples that may point towards common mechanisms of treatment failure, and may, therefore, suggest novel therapies for relapsed osteosarcoma. Our secondary objective is to determine the genetic drivers of treatment failure in osteosarcoma by analyzing within each patient the evolving spectrum of mutations selected by chemotherapy exposure over time. To our knowledge, this is the largest set of matched pre-therapy, post- therapy, and relapse samples ever assembled for any cancer. If successful, this project sets the stage for future functional studies exploiting our genetic findings to investigate the mechanisms of drug resistance in osteosarcoma. Perhaps more importantly, it also holds forth the promise of changing the paradigm for therapy in osteosarcoma, a disease that has thus far proven refractory to innovative therapies to improve the dismal survival of children with tumors that respond poorly to current chemotherapy protocols. PUBLIC HEALTH RELEVANCE: Although the survival of children with relapsed osteosarcoma is very poor, little is known about the etiology of treatment failure in this disease. The purpose of this project is to perform whole genome sequencing on serial samples from patients with osteosarcoma obtained before treatment, after treatment, and at relapse in order to identify the mutations and pathways that are drivers of drug resistance. If successful, our results may help identify patients at high risk for treatment failure and may yield new treatments for children who cannot currently be cured. | |||
| Project Number: | 1 X01 HL 132385-01 | Contact PI / Project Leader: | Joshua D. Schiffman |
| Title: | Genetic Contribution to Ewing Sarcoma in 330 parent-Offspring Trios | Awardee Organization: | University of Utah |
| Abstract: DESCRIPTION (provided by applicant): Ewing sarcoma (ES) is a deadly bone cancer that occurs in children and adolescents. Mounting evidence suggests that a genetic predisposition exists for this pediatric cancer, although the specific genetic contribution has yet to be identified. ES has never been linked to a specific cancer predisposition syndrome, although several case reports have been published that describe siblings and cousins with ES. Furthermore, neuroectodermal tumors appear to occur more commonly in families with ES. The two consistent epidemiology findings in ES include a very strong Caucasian predilection and increased rates of hernia in ES patients and their family members. Finally, the role of genetic microsatellite repeats in ES tumorigenesis has been recently described, and these GGAA microsatellites are polymorphic in repeat size and location across the genome. The Children's Oncology Group (COG) Study AEPI10N5 ("Genetic Epidemiology of Ewing Sarcoma") was begun to collect germline DNA from ES parent-offspring trios to explore the genetic risk for disease development. Each trio contains germline DNA and has been well characterized through a complete medical and family history evaluation. As part of the Gabriella Miller Kids First Pediatric Research Program, we will submit 330 ES trios from AEPI10N5 for whole genome sequencing (WGS). The study goals of this Kids First proposal include (1) To identify cancer predisposition genes in ES trios increasing disease risk, (2) To identify genome-wide GGAA microsatellite repeats in ES trios increasing disease risk, and (3) To identity de novo mutation and structural variant rates in ES trios reflecting underlying DNA repair defects that increase disease risk. As part of the Kids First Common Fund initiative, this study proposal will further elucidate the genetic contribution to pediatric cancer development. All of the WGS and phenotype data from this study will be deposited into the designated data repository for the Kids First Common Fund and will be accessible to other researchers. The WGS of these 330 ES trios will help us to understand the genetic origins of a deadly childhood cancer and may lead to novel strategies for prevention and treatment. PUBLIC HEALTH RELEVANCE: Ewing sarcoma (ES) is a deadly pediatric bone cancer striking children and adolescents. We will submit 330 ES trios for whole genome sequencing (WGS) as part of the Gabriella Miller Kids First Pediatric Research Program. The ES trios have been collected as part of the Children's Oncology Group's AEPI10N5 Study ("Genetic Epidemiology of Ewing Sarcoma"), and each trio has associated phenotypic data including a detailed family history. We will interrogate the sequence data using our genomic analysis pipeline at the University of Utah and the Utah Science Technology and Research initiative's (USTAR) Center for Genetic Discovery. We will look for the genetic contribution to ES and the sequence data with be shared in a repository designated by the Kids First Common Fund. Sequence and clinical data accessible through dbGaP: Accession Number: phs001228 | |||
| Project Number: | 1 X01 HL 132370-01 | Contact PI / Project Leader: | Christine E. Seidman |
| Title: | Discovery of the Genetic Basis of Structural Heart and Other Birth Defects | Awardee Organization: | Harvard Medical School |
| Abstract: DESCRIPTION (provided by applicant): The Pediatric Cardiovascular Genetics Consortium (PCGC) proposes to define genetic causes for congenital heart defects (CHD) as part of the Gabriella Miller Kids First Pediatric Research Program. CHD is the most common birth defect and is often accompanied by another congenital anomaly (CA). The PCGC has recruited and clinically phenotyped ≥ 20,000 probands and parents (trios) with CHD, including 30% with CHD + CA. From exome sequencing and other genetic analyses, we discovered that CHD probands are enriched for damaging de novo mutations in developmental genes that modulate embryonic transcription. Based on these discoveries, we hypothesize that PCGC probands with uninformative prior genomic analyses will carry mutations in critical regulatory elements that participate in developmental gene expression. To identify these etiologies, we propose analyses of whole genome sequencing (WGS) of probands/unaffected parents trios, capitalizing on existing RNAseq data from CHD tissues, DNA methylation studies and the extensive expertise with cardiac enhancers of our collaborating investigators to inform prioritization of de novo non-coding, regulatory sequence variants. We will use resources and capabilities of the PCGC and its companion consortium in the Bench to Bassinet Program, the Cardiovascular Development Consortium, to perform confirmatory functional genomics studies using cell and animal models. Our studies will provide novel insights into the genes and pathways involved in the development of the heart and other organs as well as into the clinical spectrum of birth defects. Our specific aims are: Aim 1. Select cohorts of CHD ± CA trios for WGS and rapidly provide high-quality DNA to the NIH- designated sequencing site. Aim 2. Identify de novo structural variants and variants that alter exome and splice sites. Aim 3. Identify de novo variants in CHD ± CA probands in non-coding regulatory elements. PUBLIC HEALTH RELEVANCE: Through the use of whole genome sequencing of individuals with congenital heart disease (CHD) and their unaffected parents, this project will drive discovery of the genetic causes of this class of birth defects, which will also have relevance for other types of congenital anomalies. The new insights gained from this project will improve care by enabling DNA diagnostics for birth defects and by providing novel mechanistic insights, with which new therapies can be developed. Sequence and clinical data accessible through dbGaP: Accession Number: phs001138 | |||
| Project Number: | 1 X01 HL 132384-01 | Contact PI / Project Leader: | Eric J. Vilain |
| Title: | Genetic Basis of Disorders/Differences of Sex Development (DSD) | Awardee Organization: | University of California Los Angeles |
| Abstract: DESCRIPTION (provided by applicant): Disorders of Sex Development (DSD) are phenotypically heterogeneous, ranging from minor genital malformations (hypospadias, cryptorchidism, hypertrophy of the clitoris) to genital ambiguity. In the aggregate, DSD have an estimated incidence of about 1%. DSD can result in severe consequences for behavioral health, fertility, cancer risk and quality of life. For families, the birth of a child with a DSD, and the accompanying uncertainty about future psychological and sexual development, is believed to be extraordinarily stressful. Recently, the debate over clinical management of DSD, in particular gender assignment and genital surgery, has intensified; yet the scientific data on patient outcomes have remained very incomplete. Major obstacles to optimal clinical management of DSD include lack of outcome studies, but also a low genetic diagnostic yield, leading to gaps in the understanding of pathophysiology, and increasing the uncertainty around the clinical management of DSD. Here we propose to use the existing resource of the DSD Translational Research Network (DSD-TRN, PIs Vilain and Sandberg), a network of 10 clinical sites collecting standardized phenotypic information, banking DNA of patients with a DSD, and populating a Registry located at UCLA. We propose to perform Whole-Genome Sequencing (WGS) on 150 patients with DSD and their parents, as well as an additional 26 historical cases for which Whole-Exome Sequencing did not yield a causative variant, in order to investigate the following aims: Aim 1: To identify new exomic causes of DSD. Analysis of exomic variants is expected to yield causative variants in 35% of cases; Aim 2: To identify non exomic causes of DSD, with a three-prong approach: 2a- Specific search for variants within promoters and introns of known DSD genes, and in the promoters of genes for which WGS identified a variant in one exonic allele or a heterozygous structural variant; 2b- Search for de novo variants; and 2c- Search for large rearrangements (translocations, duplications, inversions); Aim 3: To identify the influence of environmental exposure on phenotypic variability of DSD. We will perform a systematic collection of environmental exposure by a comprehensive environmental questionnaire (NHANES) as well as NHGRI's PhenX tool kit and by modeling patient's environmental exposure using the family's geographical information. The environmental analysis will be focused on whether there are significant environmental differences between patients with a variant in the same gene and different degrees of phenotypic severity. The accessibility of a large sample of well characterized patients with DSD, and the collective expertise of our multidisciplinary team (medical genetics, statistics, computer science) increases the likelihood of a successful deciphering of causes of DSD and of improvement of outcomes for DSD. PUBLIC HEALTH RELEVANCE: A defining moment of our lives begins when we embark on a male or female path in the womb; disruption of typical male or female development results in Disorders/Differences of Sex Development (DSD), which occur frequently -- in about 1% of the human population. The quality of life of people affected by DSD and their families is often threatened by uncertainty about what caused the condition, leading to uncertainty about choices in care, and the chronic stress associated with experienced stigma and lifelong clinical care. To improve clinical care for patients with DSD and their families, we propose a study that uncovers the genetic causes of DSD by sequencing their entire genome. Sequence and clinical data accessible through dbGaP: Accession Number: phs001178 | |||
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