De novo mutations in histone-modifying genes in congenital heart disease
Open accessAbstract
Congenital heart disease (CHD) is the most frequent birth defect, affecting 0.8% of live births. Many cases occur sporadically and impair reproductive fitness, suggesting a role for de novo mutations. Here we compare the incidence of de novo mutations in 362 severe CHD cases and 264 controls by analysing exome sequencing of parent-offspring trios. CHD cases show 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 (premature termination, frameshift, splice site) mutations. Similar odds ratios are seen across the main classes of severe CHD. We find a marked excess of de novo mutations in genes involved in the production, removal or reading of histone 3 lysine 4 (H3K4) methylation, or ubiquitination of H2BK120, which is required for H3K4 methylation. There are also two de novo mutations in SMAD2, which regulates H3K27 methylation in the embryonic left-right organizer. The combination of both activating (H3K4 methylation) and inactivating (H3K27 methylation) chromatin marks characterizes 'poised' promoters and enhancers, which regulate expression of key developmental genes. These findings implicate de novo point mutations in several hundreds of genes that collectively contribute to approximately 10% of severe CHD.
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Recent discoveries indicate shared genes and pathways between ASD and congenital heart disease.
“In fact, recent discoveries indicate shared genes and pathways between ASD and congenital heart disease (CHD) (26,93,94).”
From Genetics and genomics of autism spectrum disorder: embracing complexity (2015) · cites this paper as [94]
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- Authors
- Zaidi, S., Choi, M., Wakimoto, H., Ma, L., Jiang, J., Overton, J. D., Romano-Adesman, A., Bjornson, R. D., Breitbart, R. E., Brown, K. K., Carriero, N. J., Cheung, Y. H., Deanfield, J., DePalma, S., Fakhro, K. A., Glessner, J., Hakonarson, H., Italia, M. J., Kaltman, J. R., Kaski, J., Kim, R., Kline, J. K., Lee, T., Leipzig, J., Lopez, A., Mane, S. M., Mitchell, L. E., Newburger, J. W., Parfenov, M., Pe’er, I., Porter, G., Roberts, A. E., Sachidanandam, R., Sanders, S. J., Seiden, H. S., State, M. W., Subramanian, S., Tikhonova, I. R., Wang, W., Warburton, D., White, P. S., Williams, I. A., Zhao, H., Seidman, J. G., Brueckner, M., Chung, W. K., Gelb, B. D., Goldmuntz, E., Seidman, C. E., & Lifton, R. P.
- Affiliations
- Howard Hughes Medical Institute (US)
- Harvard University (US)
- Columbia University Irving Medical Center (US)
- Yale University (US)
- Schneider Children's Hospital (US)
- Boston Children's Hospital (US)
- Columbia University (US)
- Great Ormond Street Hospital (GB)
- Children's Hospital of Philadelphia (US)
- National Institutes of Health (US)
- University of Southern California (US)
- The University of Texas Health Science Center at Houston (US)
- Icahn School of Medicine at Mount Sinai (US)
- New Jersey Institute of Technology (US)
- Brigham and Women's Hospital (US)
- Corresponding author
- Brueckner, Martina
- Chung, Wendy K.
- Gelb, Bruce D.
- Goldmuntz, Elizabeth
- Seidman, Christine E.
- Lifton, Richard P.
- ORCID
- Zaidi, Samir
- Choi, Murim
- Wakimoto, Hiroko
- Ma, Lijiang
- Jiang, Jianming
- Overton, John D.
- Deanfield, John
- Fakhro, Khalid A.
- Glessner, Joseph
- Hakonarson, Hakon
- Italia, Michael J.
- Kaltman, Jonathan R.
- Kaski, Juan
- Kim, Richard
- Kline, Jennie K.
- Lee, Teresa
- Leipzig, Jeremy
- Lopez, Alexander
- Mane, Shrikant M.
- Mitchell, Laura E.
- Newburger, Jane W.
- Pe’er, Itsik
- Roberts, Amy E.
- Sachidanandam, Ravi
- Sanders, Stephan J.
- White, Peter S.
- Zhao, Hongyu
- Seidman, Jonathan G.
- Brueckner, Martina
- Chung, Wendy K.
- Gelb, Bruce D.
- Goldmuntz, Elizabeth
- Seidman, Christine E.
- Lifton, Richard P.
- Venue
- Nature
- Published
- 2013-05-12
- Volume
- 498
- Issue
- 7453
- Pages
- 220-223
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3706629
- OpenAlex
- W2104276565
- Cited by
- 934
- References
- 29
- Citations by year
- 2026: 24 · 2025: 52 · 2024: 74 · 2023: 57 · 2022: 65 · 2021: 66 · 2020: 71 · 2019: 72 · 2018: 74 · 2017: 94 · 2016: 82 · 2015: 100 · 2014: 80 · 2013: 23
- FWCI
- 42.52
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- National Institutes of Health (5t32gm082771-05)
- National Heart, Lung, and Blood Institute (U01HL098153, U01HL098123, U01HL098162, F30HL123238, UM1HL098166, U01HL098188, U01HL098163, U01HL098147)
- National Human Genome Research Institute (U54HG006504, U01HG006546)
- National Institute of General Medical Sciences (T32-GM082771, T32GM007205)
- National Institute of Diabetes and Digestive and Kidney Diseases (P30DK079310)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (P30HD018655)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Congenital heart defects research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Health Sciences › Medicine › Cardiology and Cardiovascular Medicine › Cardiac electrophysiology and arrhythmias
- Keywords
- congenital heart disease, de novo mutations, chromatin modification, H3K4 methylation, H3K27 methylation, Smad2, parent-offspring trios, heart development, poised enhancers, developmental gene regulation
- MeSH terms
- Adult, Child, Chromatin, DNA Mutational Analysis, Enhancer Elements, Genetic, Female, Heart Diseases, Histones, Humans, Lysine, Male, Methylation, Mutation, Promoter Regions, Genetic, Odds Ratio, Case-Control Studies, Genes, Developmental, Exome
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Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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