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.

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.

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. In fact, there is evidence that gene duplication of TBC1D3, a hominoid specific gene, contributes to the expansion of the human brain. In chimpanzees (one of humans' closest ancestral lineages), only one copy of TBC1D3 has been observed whereas several copies have been reported in humans. Gene amplification and overexpression of TBC1D3 has been reported in prostate and breast cancers, suggesting increasing copies of this gene may also contribute to oncogenesis. TBC1D3 resides in chromosome 17q12. Gains of chromosome 17q have been observed in 62% of group 3 and 73% of group 4 medulloblastomas. Together, there is strong evidence to suggest that TBC1D3 may contribute to the etiology of medulloblastoma, an area of research that has yet to be examined. Because of the highly repetitive sequence of TBC1D3 and variability of copies across humans, accurately genotyping this region 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 genomic variation of TBC1D3 in tumor and germline may contribute to the development of medulloblastoma. We hypothesize that a higher copy number of TBC1D3 will correlate to the risk of developing group 3 and group 4 medulloblastoma. We additionally hypothesize that other structural variation 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. PUBLIC HEALTH RELEVANCE: Medulloblastoma is the most common, malignant brain tumor in children and adolescents, is molecularly heterogeneous, and its risk factors are not well understood. Forming a team of molecular epidemiologists, neurosurgeon, biologist with expertise in the molecular biology of medulloblastoma, and a computational biologist, the proposed research leverages existing resources to better characterize the structural variation landscape of medulloblastoma in tumor and germline tissue. This study will address a novel research question related to structural variation and identify novel medulloblastoma predisposition genes.

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.

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.

HD117362

University of Illinois at Chicago

Whole genome analysis in patients with vertebral malformations and congenital scoliosis

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.

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.

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.