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2019 X01 Projects Abstracts

Project Number:N/AContact PI / Project Leader:Chung, Wendy K (Contact); Shen, Yufeng
Title:Genomic Analysis of Esophageal Atresia and Tracheoesophageal Fistulas and Associated Congenital AnomaliesAwardee 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/AContact 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/AContact PI / Project Leader:Gleeson, Joseph G
Title:Whole Exome and Genome Sequencing in Structural Defects of The Neural TubeAwardee 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/AContact PI / Project Leader:Gleeson, Joseph G 
Title:Whole Exome, Genome, and RNA Sequencing in Recessive Structural Brain Defects in ChildrenAwardee 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/AContact PI / Project Leader:Leslie, Elizabeth Jane (Contact); Marazita, Mary L.; Murray, Jeffrey C
Title:>Genomics of Orofacial Clefts in the PhilippinesAwardee 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/AContact PI / Project Leader:upo, Philip J (contact); Plon, Sharon E.
Title:Genomic Analysis of Pediatric RhabdomyosarcomaAwardee 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/AContact PI / Project Leader:Martin, Donna M. 
Title:Genomic Etiologies of CHARGE Syndrome, Related Conditions and Structural AnomaliesAwardee 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/AContact PI / Project Leader:Poynter, Jenny N.
Title:Genetic susceptibility of extracranial germ cell tumorsAwardee 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/AContact 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 LeukemiaAwardee 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/AContact PI / Project Leader:Ware, Stephanie 
Title:Genomic Analysis of Laterality Birth DefectsAwardee 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.

 

This page last reviewed on January 23, 2024