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Brandler WM, Antaki D, Gujral M, Kleiber ML, Whitney J, Maile MS, Hong O, Chapman TR, Tan S, Tandon P, Pang T, Tang SC, Vaux KK, Yang Y, Harrington E, Juul S, Turner DJ, Thiruvahindrapuram B, Kaur G, Wang Z, Kingsmore SF, Gleeson JG, Bisson D, Kakaradov B, Telenti A, Venter JC, Corominas R, Toma C, Cormand B, Rueda I, Guijarro S, Messer KS, Nievergelt CM, Arranz MJ, Courchesne E, Pierce K, Muotri AR, Iakoucheva LM, Hervas A, Scherer SW, Corsello C, Sebat J. Paternally inherited cis-regulatory structural variants are associated with autism. Science 2018; 360:327-331. [PMID: 29674594 DOI: 10.1126/science.aan2261] [Citation(s) in RCA: 137] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Revised: 08/07/2017] [Accepted: 02/27/2018] [Indexed: 12/15/2022]
Abstract
The genetic basis of autism spectrum disorder (ASD) is known to consist of contributions from de novo mutations in variant-intolerant genes. We hypothesize that rare inherited structural variants in cis-regulatory elements (CRE-SVs) of these genes also contribute to ASD. We investigated this by assessing the evidence for natural selection and transmission distortion of CRE-SVs in whole genomes of 9274 subjects from 2600 families affected by ASD. In a discovery cohort of 829 families, structural variants were depleted within promoters and untranslated regions, and paternally inherited CRE-SVs were preferentially transmitted to affected offspring and not to their unaffected siblings. The association of paternal CRE-SVs was replicated in an independent sample of 1771 families. Our results suggest that rare inherited noncoding variants predispose children to ASD, with differing contributions from each parent.
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Affiliation(s)
- William M Brandler
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Human Longevity, Inc., San Diego, CA 92121, USA
| | - Danny Antaki
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA.,Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA 92093, USA
| | - Madhusudan Gujral
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Morgan L Kleiber
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Joe Whitney
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Michelle S Maile
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Oanh Hong
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Timothy R Chapman
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Shirley Tan
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Prateek Tandon
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Timothy Pang
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Rady Children's Hospital, San Diego, CA 92123, USA
| | - Shih C Tang
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA.,Rady Children's Hospital, San Diego, CA 92123, USA
| | - Keith K Vaux
- Department of Medicine, University of California San Diego, La Jolla, CA 92093, USA
| | - Yan Yang
- Oxford Nanopore Technologies, Inc., NY 10013, USA
| | | | - Sissel Juul
- Oxford Nanopore Technologies, Inc., NY 10013, USA
| | | | - Bhooma Thiruvahindrapuram
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Gaganjot Kaur
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Zhuozhi Wang
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, Canada
| | - Stephen F Kingsmore
- Rady Children's Institute for Genomic Medicine, Rady Children's Hospital, San Diego, CA 92123, USA
| | - Joseph G Gleeson
- Howard Hughes Medical Institute, Rady Children's Institute of Genomic Medicine, Department of Neurosciences, University of California San Diego, La Jolla, CA 92093, USA
| | | | | | | | - J Craig Venter
- Human Longevity, Inc., San Diego, CA 92121, USA.,J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Roser Corominas
- Genetics Unit, Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
| | - Claudio Toma
- Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain.,Neuroscience Research Australia, Sydney, Australia.,School of Medical Sciences, University of New South Wales, Sydney, Australia
| | - Bru Cormand
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain.,Departament de Genètica, Microbiologia i Estadística, Facultat de Biologia, Universitat de Barcelona, Catalonia, Spain.,Institut de Biomedicina de la Universitat de Barcelona (IBUB), Catalonia, Spain.,Institut de Recerca Sant Joan de Déu (IR-SJD), Esplugues, Catalonia, Spain
| | - Isabel Rueda
- Department of Psychiatry, Hospital Sant Joan de Déu, Barcelona, Spain
| | - Silvina Guijarro
- Child and Adolescent Mental Health Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | - Karen S Messer
- Division of Biostatistics and Bioinformatics, Department of Family Medicine and Public Health, University of California, San Diego, La Jolla, CA 92093, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Maria J Arranz
- Research Laboratory Unit, Fundacio Docencia I Recerca Mutua Terrassa, Barcelona, Spain
| | - Eric Courchesne
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA 92093, USA
| | - Karen Pierce
- Autism Center of Excellence, Department of Neuroscience, University of California San Diego, La Jolla, CA 92093, USA
| | - Alysson R Muotri
- Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
| | - Lilia M Iakoucheva
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA
| | - Amaia Hervas
- Child and Adolescent Mental Health Unit, Hospital Universitari Mútua de Terrassa, Barcelona, Spain
| | - Stephen W Scherer
- The Centre for Applied Genomics, Genetics, and Genome Biology, The Hospital for Sick Children, Toronto, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Canada.,McLaughlin Centre, University of Toronto, Toronto, Canada
| | - Christina Corsello
- Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Rady Children's Hospital, San Diego, CA 92123, USA
| | - Jonathan Sebat
- Beyster Center for Genomics of Psychiatric Diseases, University of California San Diego, La Jolla, CA 92093, USA. .,Department of Psychiatry, University of California San Diego, La Jolla, CA 92093, USA.,Department of Cellular and Molecular Medicine and Pediatrics, University of California San Diego, La Jolla, CA 92093, USA
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