De novo mutations in histone modifying genes in congenital heart disease The Harvard community has made this article openly available. Please share how this access benefits you. Your story matters Citation Zaidi, S., M. Choi, H. Wakimoto, L. Ma, J. Jiang, J. D. Overton, A. Romano-Adesman, et al. 2013. “De novo mutations in histone modifying genes in congenital heart disease.” Nature 498 (7453): 220-223. doi:10.1038/nature12141. http://dx.doi.org/10.1038/ nature12141. Published Version doi:10.1038/nature12141 Citable link http://nrs.harvard.edu/urn-3:HUL.InstRepos:11879354 Terms of Use This article was downloaded from Harvard University’s DASH repository, and is made available under the terms and conditions applicable to Other Posted Material, as set forth at http:// nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of- use#LAA NIH Public Access Author Manuscript Nature. Author manuscript; available in PMC 2013 December 13. NIH-PA Author ManuscriptPublished NIH-PA Author Manuscript in final edited NIH-PA Author Manuscript form as: Nature. 2013 June 13; 498(7453): 220–223. doi:10.1038/nature12141. De novo mutations in histone modifying genes in congenital heart disease Samir Zaidi1,2,*, Murim Choi1,2,*, Hiroko Wakimoto3, Lijiang Ma4, Jianming Jiang3,5, John D. Overton1,6,7, Angela Romano-Adesman8, Robert D. Bjornson7,9, Roger E. Breitbart10, Kerry K. Brown3, Nicholas J. Carriero7,9, Yee Him Cheung11, John Deanfield12, Steve DePalma3, Khalid A. Fakhro1,2, Joseph Glessner13, Hakon Hakonarson13,14, Michael Italia15, Jonathan R. Kaltman16, Juan Kaski12, Richard Kim17, Jennie K. Kline18, Teresa Lee4, Jeremy Leipzig15, Alexander Lopez1,6,7, Shrikant M. Mane1,6,7, Laura E. Mitchell19, Jane W. Newburger10, Michael Parfenov3, Itsik Pe'er20, George Porter21, Amy Roberts10, Ravi Sachidanandam22, Stephan J. Sanders1,23, Howard S. Seiden24, Mathew W. State1,23, Sailakshmi Subramanian22, Irina R. Tikhonova1,6,7, Wei Wang15,25, Dorothy Warburton4,26, Peter S. White14,15, Ismee A. Williams4, Hongyu Zhao1,27, Jonathan G. Seidman3, Martina Brueckner1,28,**, Wendy K. Chung4,30,**, Bruce D. Gelb22,24,31,**, Elizabeth Goldmuntz14,**, Christine E. Seidman3,5,32,**, and Richard P. Lifton1,2,6,7,33,** 1Department of Genetics, Yale University School of Medicine, New Haven, CT, 06510, USA 2Howard Hughes Medical Institute, Yale University, CT, 06510, USA 3Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA 4Department of Pediatrics, Columbia University Medical Center, New York, NY, 10032, USA 5Howard Hughes Medical Institute, Harvard University, Boston, MA, 02115, USA 6Yale Center for Mendelian Genomics, New Haven, CT 06510, USA 7Yale Center for Genome Analysis, Yale University, New Haven, CT, 06511, USA 8Steven and Alexandra Cohen Children's Medical Center of New York, New Hyde Park, NY, 11040, USA 9Department of Computer Science, Yale University, New Haven, CT, 06511, USA 10Department of Cardiology, Children's Hospital Boston, Boston, MA, 02115, USA Correspondence to R.P.L ([email protected]).. *These authors contributed equally **These authors contributed equally Supplementary Information is linked to online version of the paper at www.nature.com/nature Author Contributions. Study design: M.B., W.K.C., B.D.G., E.G., H.H, J.R.K., R.P.L., L.E.M., J.G.S, C.E.S., D.W., P.S.W.; Cohort ascertainment, phenotypic characterization, and recruitment: R.E.B., M.B., W.K.C., J.D., B.D.G., E.G., J.K., R.K., T.L., J.W.N, G.P., A.R.A., H.S.S., C.E.S, I.A.W.; Informatics/data management: R.D.B., R.E.B, N.J.C., M.C., S.D., J.G., H.H., M.J.I., J.L., A.L., S.M.M., J.D.O., M.P., A.E.R., J.G.S., W.W., P.S.W, S.Z.; Exome sequencing production: J.D.O., A.L., R.P.L., S.M.M., M.W.S., I.R.T.; De novo mutation validation: W.K.C, L.M.; Exome sequencing analysis: K.K.B., Y.H.C., M.C., S.D., K.A.F., J.G., J.K.K., R.P.L., I.P., R.S., S.J.S., J.G.S., C.E.S., S.S., W.W., S.Z.; RNA sequence production/analysis: J.J., M.P., C.E.S., J.G.S, H.W.; Statistical analysis: M.C., R.P.L., I.P., A.R., C.E.S, J.G.S, S.Z., H.Z.; Writing of manuscript: M.B., M.C., W.K.C., B.D.G., E.G., J.R.K., R.P.L., C.E.S., S.Z. Author Information mRNA available at NCBI under accession IDs listed in Table S4; mutation data is available at dbSNP under batch accession 1059065. Reprints and permissions information is available at www.nature.com/reprints. The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of the NHLBI. The authors declare no competing financial interests; details accompany the full-text HTML version of the paper at www.nature.com/nature. Zaidi et al. Page 2 11Department of Biostatistics, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA NIH-PA Author Manuscript12 NIH-PA Author ManuscriptDepartment of Cardiology, NIH-PA Author Manuscript University College London, Great Ormond St Hospital, London, WC1N 3JH, UK 13Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA 14Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA 15The Center for Biomedical Informatics, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA 16National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA 17Section of Cardiothoracic Surgery, University of Southern California Keck School of Medicine, Los Angeles, CA, 90089, USA 18Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, 10032, USA 19Division of Epidemiology, Human Genetics and Environmental Sciences, University of Texas School of Public Health, Houston, Texas, 77030, USA 20Department of Computer Science, Columbia University, New York, NY, 10032, USA 21Department of Pediatrics, University of Rochester Medical Center, The School of Medicine and Dentistry, Rochester, NY, 14611, USA 22Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA 23Program on Neurogenetics, Child Study Center, Department of Psychiatry, Yale University, New Haven, CT, 06510, USA 24Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA 25Department of Computer Science, New Jersey Institute of Technology, Newark, NJ, 07102, USA 26Department of Pathology, Columbia University Medical Center, New York, NY, 10032, USA 27Department of Biostatistics, Yale School of Public Health, New Haven, CT, 06510, USA 28Department of Pediatrics Yale University School of Medicine, New Haven, CT, 06510, USA 29Division of Cardiology, The Children's Hospital of Philadelphia, The University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, 19104, USA 30Department of Medicine, Columbia University Medical Center, New York, NY, 10032, USA 31The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA 32Cardiovascular Division, Brigham & Women's Hospital, Harvard University, Boston, MA, 02115, USA 33Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06510, USA Nature. Author manuscript; available in PMC 2013 December 13. Zaidi et al. Page 3 Abstract Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births1. NIH-PA Author Manuscript NIH-PA Author ManuscriptMany cases occur NIH-PA Author Manuscript sporadically and impair reproductive fitness, suggesting a role for de novo mutations. By analysis of exome sequencing of parent-offspring trios, we compared the incidence of de novo mutations in 362 severe CHD cases and 264 controls. CHD cases showed a significant excess of protein-altering de novo mutations in genes expressed in the developing heart, with an odds ratio of 7.5 for damaging mutations. Similar odds ratios were seen across major classes of severe CHD. We found a marked excess of de novo mutations in genes involved in production, removal or reading of H3K4 methylation (H3K4me), or ubiquitination of H2BK120, which is required for H3K4 methylation2–4. There were also two de novo mutations in SMAD2; SMAD2 signaling in the embryonic left-right organizer induces demethylation of H3K27me5. H3K4me and H3K27me mark `poised' promoters and enhancers that regulate expression of key developmental genes6. These findings implicate de novo point mutations in several hundred genes that collectively contribute to ~10% of severe CHD. From more than 5000 probands enrolled in the Congenital Heart Disease Genetic Network Study of the National Heart Lung and Blood Institute Pediatric Cardiac Genomics Consortium7, we selected 362 parent-offspring trios comprising a child (proband) with severe CHD and no first-degree relative with identified structural heart disease. Probands with an established genetic diagnosis were excluded. There were 154 probands with conotruncal defects, 132 with left ventricular obstruction, 70 with heterotaxy and six with other diagnoses (Supplementary Table 1). Genomic DNA samples from trios underwent exome sequencing (see Methods)8. Targeted bases in each sample were sequenced a mean of 107 times by independent reads with 96.0% read eight or more times. In parallel, 264 trios comprising unaffected siblings of autism cases and their unaffected parents (Supplementary Table 1) were sequenced in the same facility using the same protocol and were analyzed as a control group9 (Supplementary Table 2, Supplementary Figure 1). Family relationships were confirmed from sequence data in all trios. High probability de novo variants in probands were identified using a Bayesian quality score (QS; see Methods). Sanger sequencing of 181 putative de novo mutations across the QS spectrum demonstrated strong correlation of confirmation with QS (R2 = 0.89), with 100% confirmation of 90 calls with QS > 50 (Supplementary Table 3, Supplementary Figure 2).