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- Study Description
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- Talking Glossary of Genetic Terms
This study is part of the NHLBI Trans-Omics for Precision Medicine (TOPMed) Whole Genome Sequencing Program. TOPMed is part of a broader Precision Medicine Initiative, which aims to provide disease treatments that are tailored to an individual's unique genes and environment. TOPMed will contribute to this initiative through the integration of whole-genome sequencing (WGS) and other -omics (e.g., metabolic profiles, protein and RNA expression patterns) data with molecular, behavioral, imaging, environmental, and clinical data. In doing so, this program aims to uncover factors that increase or decrease the risk of disease, to identify subtypes of disease, and to develop more targeted and personalized treatments. Two genotype call sets derived from WGS are now available, Freeze 8 (GRCh38) and Freeze 9b (GRCh38), with largely overlapping sample sets. Information about how to identify other TOPMed WGS accessions for cross-study analysis, as well as descriptions of TOPMed methods of data acquisition, data processing and quality control, are provided in the accompanying documents, "TOPMed Whole Genome Sequencing Project - Freeze 8, Phases 1-4" and "TOPMed Whole Genome Sequencing Project - Freeze 9b, Phases 1-4". Please check the study list at the top of each of these methods documents to determine whether it applies to this study accession.
The Pediatric Cardiovascular Genetics Consortium (PCGC) proposes to define genetic causes for congenital heart defects (CHD) as part of the TOPMed Program are the most common form of heart disease in childhood and are also the most prevalent form of birth defects, occurring in 2-3% of live births. The PCGC has recruited and clinically characterized = 10,000 CHD probands and parents (CHD trios). From whole exome sequencing (WES) of >2800 CHD trios, we identified a substantial enrichment of damaging de novo mutations in genes important for cardiogenesis, particularly implicating histone modifier enzyme gene defects. Analysis of whole genome sequencing (WGS) of 350 probands with CHD unexplained by WES and their parents preliminarily implicated de novo mutations in enhancers of genes previously shown to cause CHD in mouse knock out models. Sequencing of RNA (RNAseq) from discarded cardiac tissues from CHD probands has revealed likely causal allele-specific expression (ASE) as well as biallelic loss of expression (LOE). We have also discovered de novo epimutations, differentially methylated regions (DMRs), some with underlying de novo DNA variation, that are detectable in peripheral blood leukocytes and appear to underlie 10% of CHD. Of note, these assorted 'omic' approaches have enabled one another, both for attributing causality and assessing functional impact. Based on these extensive preliminary data, we hypothesize that PCGC probands with uninformative exomic analyses (WES-negative) harbor de novo genetic and/or epigenetic mutations in critical regulatory elements that participate in developmental expression of cardiac genes. To identify these etiologies, we propose analyses of WGS in 1000 WES-negative CHD trios, prioritizing those with probands with banked CHD tissues (n=78), one damaging variant in a recessive CHD gene, and older fathers (age>45). We also request WGS for 230 probands, for whom we have cardiac tissues but not parental DNAs. We request RNAseq for 308 cardiac tissues. For DNA methylation, which TOPMed will offer through the Illumina 850k array platform, we are requesting analysis of DNAs from peripheral blood leukocytes for all probands for whom WGS will be performed (1000 from trios, 230 singletons) as well as DNAs from cardiac tissues (n=308) to pair with the WGS, RNAseq and blood DNA methylation data. We will use existing resources and capabilities of the PCGC to confirm relevant mutations and those of its companion consortium in the Bench to Bassinet Program, the Cardiovascular Development Consortium, to inform analyses of non-coding mutations as well as to perform confirmatory functional genomics studies using cell and animal models. We expect that the studies resulting from data generated through TOPMed will provide novel insights into the molecular basis for CHD and fundamental knowledge about genes and pathways involved in cardiac development. Aside from being relevant to CHD, we anticipate that our findings will inform the understanding of later-onset cardiovascular diseases, including some arising in adulthood.
- Study Weblinks:
- Study Design:
- Prospective Longitudinal Cohort
- Study Type:
- Case Set
- Parent-Offspring Trios
- dbGaP estimated ancestry using GRAF-pop
- Subject Sample Telemetry Report (SSTR)
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- Authorized Access
- Publicly Available Data (Public ftp)
- Study Inclusion/Exclusion Criteria
- Age 0 - 99 years of age
- Males and females
- No ethnic or race restrictions
- Sporadic and familial cases are included
- Pregnant women who have a fetus with diagnosed CHD
- Isolated patent foramen ovale
- Isolated prematurity-associated patent ductus arteriosus
- Lack of consent
- Selected publications
- Diseases/Traits Related to Study (MeSH terms)
- Primary Phenotype: Heart Defects, Congenital
- Links to Related Resources
- Authorized Data Access Requests
See research articles citing use of the data from this study
- Study Attribution
- Bruce Gelb, MD. Icahn School of Medicine at Mt. Sinai, New York, NY, USA.
- Christine Seidman, MD. Harvard Medical School, Boston, MA, USA.
- X01HL139333. National Institutes of Health, Bethesda, MD, USA.
- UM1HL128711. National Institutes of Health, Bethesda, MD, USA.
- UM1HL098162. National Institutes of Health, Bethesda, MD, USA.
- UM1HL098147. National Institutes of Health, Bethesda, MD, USA.
- UM1HL098123. National Institutes of Health, Bethesda, MD, USA.
- UM1HL128761. National Institutes of Health, Bethesda, MD, USA.
- U01HL131003. National Institutes of Health, Bethesda, MD, USA.
- Principal Investigators