Robust identification of mosaic variants in congenital heart disease
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Mosaicism due to somatic mutations can cause multiple diseases including cancer, developmental and overgrowth syndromes, neurodevelopmental disorders, autoinflammatory diseases, and atrial fibrillation. With the increased use of next generation sequencing technology, multiple tools have been developed to identify low-frequency variants, specifically from matched tumor-normal tissues in cancer studies. To investigate whether mosaic variants are implicated in congenital heart disease (CHD), we developed a pipeline using the cancer somatic variant caller MuTect to identify mosaic variants in whole-exome sequencing (WES) data from a cohort of parent/affected child trios (n = 715) and a cohort of healthy individuals (n = 416). This is a novel application of the somatic variant caller designed for cancer to WES trio data. We identified two cases with mosaic KMT2D mutations that are likely pathogenic for CHD, but conclude that, overall, mosaicism detectable in peripheral blood or saliva does not account for a significant portion of CHD etiology.
The authors are grateful to the patients and families who participated in this research and team members who supported subject recruitment and sequencing D.Awad, C. Breton, K. Celia, C. Duarte, D. Etwaru, N.Rishman, M. Daspakova, J. Kline, R. Korsin, A. Lanz, E. Marquez, D. Queen, A. Rodriguez, J. Rose, J.K. Sond, D. Warburton, A. Wilpers and R. Yee [Columbia Medical School]; B. McDonough, A. Monafo, J. Stryker [Harvard Medical School]; N. Cross [Yale School of Medicince]; S. M. Edman, J.L. Garbarini, J.E. Tusi, S.H. Woyciechowski (Children’s Hospital of Philadelphia); J. Ellashek and N. Tran (Children’s Hospital of Los Angeles); K. Flack, L. Panesar, N. Taylor (University College London); D. Gruber and N. Stellato (Steve and Alexandra Cohen Children’s Medical Center of New York); D. Guevara, A. Julian, M. MacNeal, C. Mintz (Icahn School of Medicine at Mount Sinai); and E. Taillie (University of Rochester School of Medicine and Dentistry]). We also thank the Simons Foundation for Autism Research for the contribution of control exome trios.
Funding was provided by the National Heart, Blood and Lung Institute from the following grants: U01-HL098147, U01-HL098123, U01-HL098162, U01-HL098153, U01-HL098163, and U01-HL098188.
Compliance with ethical standards
Conflict of interest
The authors declare that they have no conflict of interest.
All procedures performed in studies involving human participants were in accordance with the ethical standards of the Institutional Review Boards listed and with the 1964 Helsinki declaration and its later amendments or comparable ethical standards. Institutional IRBs: Boston Children’s Hospital, Brigham and Women’s Hospital, Great Ormond Street Hospital, Children’s Hospital of Los Angeles, Children’s Hospital of Philadelphia, Columbia University Medical Center, Icahn School of Medicine at Mount Sinai, Rochester School of Medicine and Dentistry, Steven and Alexandra Cohen Children’s Medical Center of New York, and Yale School of Medicine.
Informed consent was obtained from all individual participants or their parent/guardian included in this study.
The PCGC datasets analyzed during the current study are available from dbGAP (https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000571.v1.p1). Approved researchers can obtain the SSC population dataset used as controls in this study by applying at SFARI Base (https://base.sfari.org/).