Congenital heart disease (CHD) is the most common birth defect and affects 1% of all live born infants, and genetics likely contribute to 90%. While ~90% of patients with CHD survive into adulthood, there are many comorbidities that make CHD an increasingly significant public health problem. During the first two project periods the PCGC has made significant progress in understanding the genetic architecture of CHD. The highlights of the genomics work are the identification of de-novo variants contributing to ~10% of CHD, the identification of chromatin remodeling genes contributing to 2.3% of all CHD and to a striking 28% of CHD that is associated with extracardiac and neurodevelopmental abnormalities, the identification of novel CHD genes underlying inherited CHD, and the contribution of genes involved in cilia structure and function to CHD. The other most significant finding from the PCGC genomic studies is the tremendous heterogeneity of CHD: over 440 genes contribute to CHD by a dominant inheritance mechanism alone. Combining these findings with previous data on the contribution of copy-number variants and aneuploidy identifies a likely genetic cause for ~40% of CHD. Our hypotheses are that many yet unidentified mutations affecting the genic region contribute to a significant portion of CHD, and that the specific mutations contributing to CHD impact outcomes. The two major questions addressed in this proposal are what is the genetic contribution to the ?missing 55%?, and how do specific mutations impact the cardiac and non-cardiac outcomes and clinical care of patients with CHD? In the setting of large genetic heterogeneity and variable phenotypic expressivity that characterizes CHD, answers to these questions will require very large patient cohorts with genotype and phenotype data.
Aim 1 will define the genetic architecture of CHD through analysis of 30,000 enrolled patients with genomic data in the combined PCGC cohort. Patients are recruited by outreach to the entire Pediatric Cardiology community along with internet-based direct patient recruiting. This will be coupled with a cost-effective tiered sequencing strategy that starts with MIPs-based targeted sequencing on all probands and progresses to whole-exome and whole- genome sequencing in MIPs-negative patients. Since the eventual goal of the PCGC program is to use genomic data to improve clinical care of CHD patients, we will need to link genomic and outcome data efficiently.
Aim 2 will establish a central PCGC data mining center to directly link phenotypic data from the EMR and STS database with genomic data. We will initially focus on two outcomes that are readily available in the EMR and are associated with significant morbidity in CHD patients: the potential role of cilia mutations in progressive valve dysfunction in single-ventricle patients and the potential role of chromatin modifier gene mutations to cancer risk in adult CHD survivors. The informatics paradigms developed for this project can then be applied to investigate potential genetic contribution to a wide range of other CHD outcomes.

Public Health Relevance

A genetic abnormality is thought to underlie a substantial portion of CHD, but the identity of the abnormalities has not been identified in 50% of affected patients. This proposal seeks to apply state-of-the-art genomic technology to a large cohort of CHD patients recruited to the PCGC program and identify the genetic cause of CHD, and then to link the genetic findings to actionable outcomes to improve care of patients with CHD.

Agency
National Institute of Health (NIH)
Institute
National Heart, Lung, and Blood Institute (NHLBI)
Type
Research Project--Cooperative Agreements (U01)
Project #
2U01HL098162-12
Application #
10028193
Study Section
Special Emphasis Panel (ZHL1)
Program Officer
Kaltman, Jonathan R
Project Start
2009-09-30
Project End
2025-07-31
Budget Start
2020-08-01
Budget End
2021-07-31
Support Year
12
Fiscal Year
2020
Total Cost
Indirect Cost
Name
Yale University
Department
Pediatrics
Type
Schools of Medicine
DUNS #
043207562
City
New Haven
State
CT
Country
United States
Zip Code
06520
Manheimer, Kathryn B; Patel, Nihir; Richter, Felix et al. (2018) Robust identification of deletions in exome and genome sequence data based on clustering of Mendelian errors. Hum Mutat 39:870-881
Manheimer, Kathryn B; Richter, Felix; Edelmann, Lisa J et al. (2018) Robust identification of mosaic variants in congenital heart disease. Hum Genet 137:183-193
Shaaban, Sherin; MacKinnon, Sarah; Andrews, Caroline et al. (2018) Genome-Wide Association Study Identifies a Susceptibility Locus for Comitant Esotropia and Suggests a Parent-of-Origin Effect. Invest Ophthalmol Vis Sci 59:4054-4064
Agopian, A J; Goldmuntz, Elizabeth; Hakonarson, Hakon et al. (2017) Genome-Wide Association Studies and Meta-Analyses for Congenital Heart Defects. Circ Cardiovasc Genet 10:e001449
Jin, Sheng Chih; Homsy, Jason; Zaidi, Samir et al. (2017) Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands. Nat Genet 49:1593-1601
McKean, David M; Homsy, Jason; Wakimoto, Hiroko et al. (2016) Loss of RNA expression and allele-specific expression associated with congenital heart disease. Nat Commun 7:12824
Johnson, Douglas B; Balko, Justin M; Compton, Margaret L et al. (2016) Fulminant Myocarditis with Combination Immune Checkpoint Blockade. N Engl J Med 375:1749-1755
Backenroth, Daniel; Homsy, Jason; Murillo, Laura R et al. (2014) CANOES: detecting rare copy number variants from whole exome sequencing data. Nucleic Acids Res 42:e97
Glessner, Joseph T; Bick, Alexander G; Ito, Kaoru et al. (2014) Increased frequency of de novo copy number variants in congenital heart disease by integrative analysis of single nucleotide polymorphism array and exome sequence data. Circ Res 115:884-896
Pediatric Cardiac Genomics Consortium; Gelb, Bruce; Brueckner, Martina et al. (2013) The Congenital Heart Disease Genetic Network Study: rationale, design, and early results. Circ Res 112:698-706

Showing the most recent 10 out of 13 publications