Increased Frequency of De novo Copy Number Variations in Congenital Heart Disease by Integrative Analysis of SNP Array and Exome Sequence Data. J. T. Glessner1,2, A. G. Bick3, K. Ito3, J. Homsy3, L. Rodriguez-Murillo4,5, M. Fromer5,6,7, E. Mazaika3, B. Vardarajan8, M. Italia9, J. Leipzig9, S. R. DePalma3, R. Golhar1, S. J. Sanders10,11, B. Yamrom12, M. Ronemus12, I. Iossifov12, A. J. Willsey10,11, M. W. State10,11, J. R. Kaltman13, P. S. White9, Y. Shen8, D. Warburton14, M. Brueckner15, C. Seidman3, E. Goldmuntz16, B. D. Gelb4,5, R. Lifton10,17, J. Seidman3, W. K. Chung18, H. Hakonarson1,2 1) Ctr Applied Genomics, Children's Hosp Philadelphia, Philadelphia, PA; 2) Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; 3) Department of Genetics, Harvard Medical School, Boston, MA; 4) Mindich Child Health and Development Institute, Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY; 5) Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY; 6) Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY; 7) Division of Psychiatric Genomics in the Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, NY; 8) Department of Systems Biology, Columbia University Medical Center, New York, NY; 9) Center for Biomedical Informatics, Childrens Hospital of Philadelphia, Philadelphia, PA; 10) Department of Genetics, Yale University, New Haven, CT; 11) Department of Psychiatry, University of California, San Francisco, San Francisco, CA; 12) Cold Spring Harbor Laboratory, Cold Spring Harbor, NY; 13) Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD; 14) Department of Genetics and Development (in Medicine), Columbia University Medical Center, New York, NY; 15) Department of Pediatrics, Yale University, New Haven, CT; 16) Division of Cardiology, Childrens Hospital of Philadelphia; and Department of Pediatrics, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA; 17) Department of Medicine, Yale University, New Haven, CT; 18) Departments of Pediatrics and Medicine, Columbia University Medical Center, New York, NY.
Congenital heart disease (CHD) is among the most common birth defects. Most cases are of unknown etiology. To determine the contribution of de novo copy number variants (CNVs) in the etiology of sporadic congenital heart disease (CHD), we studied 538 CHD trios using genome-wide dense single nucleotide polymorphism (SNP) arrays and/or whole exome sequencing (WES). Results were experimentally validated using digital droplet PCR. SNP and WES methods identified overlapping and unique CNVs; WES data enabled consistent detection of 1-10 kb CNVs, an order of magnitude smaller than previous reports. We compared validated CNVs in CHD cases to CNVs in 1,301 healthy control trios. The two complementary high-resolution technologies identified 65 validated de novo CNVs in 53 CHD cases, with median size of 110 kb. CNVs were identified as small as 2 kb (arrays) and 0.1 kb (WES). Two-thirds of CNVs contained five or fewer genes. A significant increase in CNV burden was observed when comparing CHD trios with healthy trios, using either SNP array (p=7x10-5, Odds Ratio (OR)=4.6) or WES data (p=6x10-4, OR=3.5). A significant increase in CNV burden remained, even after removing from these analyses the 16% of de novo CNV loci that were previously reported as pathogenic (p=0.02, OR=2.7). Among CHD cases, we observed recurrent de novo CNVs on 15q11.2 encompassing CYFIP1, NIPA1, and NIPA2 and single de novo CNVs encompassing DUSP1, JUN, JUP, MED15, MED9, PTPRE SREBF1, TOP2A, and ZEB2, genes that interact with established CHD proteins such as NKX2-5 and GATA4. Integrating de novo variants in WES and CNV data suggests that ETS1 is the pathogenic gene altered by 11q24.2-q25 deletions in Jacobsen syndrome and that CTBP2 is the pathogenic gene in 10q sub-telomeric deletions. Collectively, these results demonstrate a significantly increased frequency of rare de novo CNVs in CHD patients compared with healthy controls and suggest several novel genetic loci for CHD.