1
|
Schmitz-Abe K, Sanchez-Schmitz G, Doan RN, Hill RS, Chahrour MH, Mehta BK, Servattalab S, Ataman B, Lam ATN, Morrow EM, Greenberg ME, Yu TW, Walsh CA, Markianos K. Homozygous deletions implicate non-coding epigenetic marks in Autism spectrum disorder. Sci Rep 2020; 10:14045. [PMID: 32820185 PMCID: PMC7441318 DOI: 10.1038/s41598-020-70656-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 07/29/2020] [Indexed: 11/09/2022] Open
Abstract
More than 98% of the human genome is made up of non-coding DNA, but techniques to ascertain its contribution to human disease have lagged far behind our understanding of protein coding variations. Autism spectrum disorder (ASD) has been mostly associated with coding variations via de novo single nucleotide variants (SNVs), recessive/homozygous SNVs, or de novo copy number variants (CNVs); however, most ASD cases continue to lack a genetic diagnosis. We analyzed 187 consanguineous ASD families for biallelic CNVs. Recessive deletions were significantly enriched in affected individuals relative to their unaffected siblings (17% versus 4%, p < 0.001). Only a small subset of biallelic deletions were predicted to result in coding exon disruption. In contrast, biallelic deletions in individuals with ASD were enriched for overlap with regulatory regions, with 23/28 CNVs disrupting histone peaks in ENCODE (p < 0.009). Overlap with regulatory regions was further demonstrated by comparisons to the 127-epigenome dataset released by the Roadmap Epigenomics project, with enrichment for enhancers found in primary brain tissue and neuronal progenitor cells. Our results suggest a novel noncoding mechanism of ASD, describe a powerful method to identify important noncoding regions in the human genome, and emphasize the potential significance of gene activation and regulation in cognitive and social function.
Collapse
Affiliation(s)
- Klaus Schmitz-Abe
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Divisions of Newborn Medicine and Manton Center for Orphan Disease Research, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02115, USA
| | - Guzman Sanchez-Schmitz
- Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.,Division of Infectious Diseases, Department of Pediatrics and Precision Vaccines Program, Boston Children's Hospital, Boston, MA, 02115, USA
| | - Ryan N Doan
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - R Sean Hill
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Maria H Chahrour
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Bhaven K Mehta
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Sarah Servattalab
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Bulent Ataman
- Department of Neurobiology, Harvard Medical School, Boston, MA, 02115, USA
| | - Anh-Thu N Lam
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA.,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA
| | - Eric M Morrow
- Department of Molecular Biology, Cell Biology and Biochemistry and Department of Psychiatry and Human Behavior, Brown University, Providence, RI, 02912, USA
| | | | - Timothy W Yu
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA.
| | - Christopher A Walsh
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02115, USA. .,Howard Hughes Medical Institute, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Neurology, Harvard Medical School, Boston, MA, 02115, USA.
| | - Kyriacos Markianos
- Division of Genetics and Genomics, Department of Pediatrics, Boston Children's Hospital, Boston, MA, 02115, USA. .,Department of Pediatrics, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02115, USA. .,Center for Data and Computational Sciences, Cooperative Studies Program, VA Boston Healthcare system, Boston, MA, 02130, USA.
| |
Collapse
|
3
|
Yu T, Chahrour M, Coulter M, Jiralerspong S, Okamura-Ikeda K, Ataman B, Schmitz-Abe K, Harmin D, Adli M, Malik A, D’Gama A, Lim E, Sanders S, Mochida G, Partlow J, Sunu C, Felie J, Rodriguez J, Nasir R, Ware J, Joseph R, Hill R, Kwan B, Al-Saffar M, Mukaddes N, Hashmi A, Balkhy S, Gascon G, Hisama F, LeClair E, Poduri A, Oner O, Al-Saad S, Al-Awadi S, Bastaki L, Ben-Omran T, Teebi A, Al-Gazali L, Eapen V, Stevens C, Rappaport L, Gabriel S, Markianos K, State M, Greenberg M, Taniguchi H, Braverman N, Morrow E, Walsh C. Using whole-exome sequencing to identify inherited causes of autism. Neuron 2013; 77:259-73. [PMID: 23352163 PMCID: PMC3694430 DOI: 10.1016/j.neuron.2012.11.002] [Citation(s) in RCA: 318] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2012] [Indexed: 01/01/2023]
Abstract
Despite significant heritability of autism spectrum disorders (ASDs), their extreme genetic heterogeneity has proven challenging for gene discovery. Studies of primarily simplex families have implicated de novo copy number changes and point mutations, but are not optimally designed to identify inherited risk alleles. We apply whole-exome sequencing (WES) to ASD families enriched for inherited causes due to consanguinity and find familial ASD associated with biallelic mutations in disease genes (AMT, PEX7, SYNE1, VPS13B, PAH, and POMGNT1). At least some of these genes show biallelic mutations in nonconsanguineous families as well. These mutations are often only partially disabling or present atypically, with patients lacking diagnostic features of the Mendelian disorders with which these genes are classically associated. Our study shows the utility of WES for identifying specific genetic conditions not clinically suspected and the importance of partial loss of gene function in ASDs.
Collapse
Affiliation(s)
- T.W. Yu
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- The Autism Consortium, Boston, Massachusetts, USA, 02115
- Harvard Medical School, Boston, Massachusetts, USA, 02115
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA, 02114
| | - M.H. Chahrour
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- The Autism Consortium, Boston, Massachusetts, USA, 02115
- Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - M.E. Coulter
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - S. Jiralerspong
- Department of Human Genetics and Pediatrics, McGill University, Montreal Children’s Hospital Research Institute, Montreal, Quebec, Canada, H3H1P3
| | - K. Okamura-Ikeda
- Institute for Enzyme Research, The University of Tokushima, Tokushima, Japan
| | - B. Ataman
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - K. Schmitz-Abe
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - D.A. Harmin
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - M. Adli
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Virginia, Charlottesville, Virginia, USA, 22908
| | - A.N. Malik
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - A.M. D’Gama
- Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - E.T. Lim
- Analytic and Translational Genetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, Massachusetts, USA, 02114
| | - S.J. Sanders
- Department of Genetics, Center for Human Genetics and Genomics and Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, 06510
| | - G.H. Mochida
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Harvard Medical School, Boston, Massachusetts, USA, 02115
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA, 02114
| | - J.N. Partlow
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
| | - C.M. Sunu
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
| | - J.M. Felie
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
| | - J. Rodriguez
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
| | - R.H. Nasir
- Harvard Medical School, Boston, Massachusetts, USA, 02115
- Division of Developmental Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
| | - J. Ware
- Harvard Medical School, Boston, Massachusetts, USA, 02115
- Division of Developmental Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
| | - R.M. Joseph
- The Autism Consortium, Boston, Massachusetts, USA, 02115
- Department of Anatomy and Neurobiology, Boston University School of Medicine, Boston, Massachusetts, USA, 02118
| | - R.S. Hill
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - B.Y. Kwan
- Schulich School of Medicine and Dentistry, Western University, London, Ontario, Canada, N6A 5C1
| | - M. Al-Saffar
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Department of Paediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - N.M. Mukaddes
- Istanbul Faculty of Medicine, Department of Child Psychiatry, Istanbul University, Istanbul, Turkey
| | - A. Hashmi
- Armed Forces Hospital, King Abdulaziz Naval Base, Jubail, Kingdom of Saudi Arabia
| | - S. Balkhy
- Department of Neurosciences and Pediatrics, King Faisal Specialist Hospital and Research Center, Jeddah, Kingdom of Saudi Arabia
| | - G.G. Gascon
- Department of Neurology, Massachusetts General Hospital, Boston, Massachusetts, USA, 02114
- Istanbul Faculty of Medicine, Department of Child Psychiatry, Istanbul University, Istanbul, Turkey
- Clinical Neurosciences and Pediatrics, Brown University School of Medicine, Providence, Rhode Island, 02912
| | - F.M. Hisama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Washington, USA, 98195
| | - E. LeClair
- Harvard Medical School, Boston, Massachusetts, USA, 02115
- Division of Developmental Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
| | - A. Poduri
- Harvard Medical School, Boston, Massachusetts, USA, 02115
- Department of Neurology, Boston Children’s Hospital, Boston, Massachusetts, USA,02115
| | - O. Oner
- Department of Child and Adolescent Psychiatry, Dr Sami Ulus Childrens’ Hospital, Telsizler, Ankara, Turkey
| | - S. Al-Saad
- Kuwait Center for Autism, Kuwait City, Kuwait
| | | | - L. Bastaki
- Kuwait Medical Genetics Center, Kuwait City, Kuwait
| | - T. Ben-Omran
- Section of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
- Departments of Pediatrics and Genetic Medicine, Weil-Cornell Medical College, New York and Doha, Qatar
| | - A. Teebi
- Section of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, Doha, Qatar
- Departments of Pediatrics and Genetic Medicine, Weil-Cornell Medical College, New York and Doha, Qatar
| | - L. Al-Gazali
- Department of Paediatrics, Faculty of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - V. Eapen
- Academic Unit of Child Psychiatry South West Sydney (AUCS), University of New South Wales, Sydney, New South Wales, Australia
| | - C.R. Stevens
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA, 02142
| | - L. Rappaport
- The Autism Consortium, Boston, Massachusetts, USA, 02115
- Harvard Medical School, Boston, Massachusetts, USA, 02115
- Division of Developmental Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
| | - S.B. Gabriel
- Program in Medical and Population Genetics, Broad Institute of Massachusetts Institute of Technology and Harvard University, Cambridge, Massachusetts, USA, 02142
| | - K. Markianos
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - M.W. State
- Department of Genetics, Center for Human Genetics and Genomics and Program on Neurogenetics, Yale University School of Medicine, New Haven, Connecticut, USA, 06510
| | - M.E. Greenberg
- Department of Neurobiology, Harvard Medical School, Boston, Massachusetts, USA, 02115
| | - H. Taniguchi
- Institute for Enzyme Research, The University of Tokushima, Tokushima, Japan
| | - N.E. Braverman
- Department of Human Genetics and Pediatrics, McGill University, Montreal Children’s Hospital Research Institute, Montreal, Quebec, Canada, H3H1P3
| | - E.M. Morrow
- The Autism Consortium, Boston, Massachusetts, USA, 02115
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, 02912
- Department of Psychiatry and Human Behavior, Brown University, Providence, Rhode Island, 02912
| | - C.A. Walsh
- Division of Genetics, Department of Medicine, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Manton Center for Orphan Disease Research, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA, 02115
- The Autism Consortium, Boston, Massachusetts, USA, 02115
- Harvard Medical School, Boston, Massachusetts, USA, 02115
| |
Collapse
|