Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
Yuen et al . developed a cloud-based database with 5,205 whole genomes from families with autism spectrum disorder (ASD). They identified 18 new candidate ASD-risk genes and approximately 100 risk genes and copy-number loci, which account for 11% of the cases. They also found that individuals bearin...
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| Published in | Nature neuroscience Vol. 20; no. 4; pp. 602 - 611 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
New York
Nature Publishing Group US
01.04.2017
Nature Publishing Group |
| Subjects | |
| Online Access | Get full text |
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| Abstract | Yuen
et al
. developed a cloud-based database with 5,205 whole genomes from families with autism spectrum disorder (ASD). They identified 18 new candidate ASD-risk genes and approximately 100 risk genes and copy-number loci, which account for 11% of the cases. They also found that individuals bearing mutations in ASD-risk genes had lower adaptive ability.
We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8
de novo
single nucleotide variants and 12.6
de novo
insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (
P
= 6 × 10
−4
). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD. |
|---|---|
| AbstractList | Yuen
et al
. developed a cloud-based database with 5,205 whole genomes from families with autism spectrum disorder (ASD). They identified 18 new candidate ASD-risk genes and approximately 100 risk genes and copy-number loci, which account for 11% of the cases. They also found that individuals bearing mutations in ASD-risk genes had lower adaptive ability.
We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8
de novo
single nucleotide variants and 12.6
de novo
insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (
P
= 6 × 10
−4
). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD. We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10-4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10-4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD. We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 x 10[sup.-4]). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD. We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 10 super(-4)). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD. We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10-4 ). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD. We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10 ). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD. We are performing whole genome sequencing (WGS) of families with Autism Spectrum Disorder (ASD) to build a resource, named MSSNG, to enable the sub-categorization of phenotypes and underlying genetic factors involved. Here, we report WGS of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible in a cloud platform, and through an internet portal with controlled access. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertion/deletions (indels) or copy number variations (CNVs) per ASD subject. We identified 18 new candidate ASD-risk genes such as MED13 and PHF3 , and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (p=6×10 −4 ). In 294/2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried CNV/chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD. |
| Audience | Academic |
| Author | Tasse, Anne-Marie Robinson, James T Vorstman, Jacob Merico, Daniele Thiruvahindrapuram, Bhooma Modi, Bonnie MacKinnon Thompson, Ann Gallagher, Louise Lamoureux, Sylvia Bookman, Matt Tsoi, Fiona J Patel, Rohan V Li, Weili Doyle-Thomas, Krissy Wei, John MacDonald, Jeffrey R Savion-Lemieux, Tal Jilderda, Sanne Glazer, David Liu, Xudong Twigger, Simon Chan, Ada J S Koyanagi, Stephanie Hoang, Ny Zwaigenbaum, Lonnie Carter, Melissa T Scherer, Stephen W Chrysler, Christina Hallmayer, Joachim Roberts, Wendy Fernandez, Bridget A Senman, Lili Malow, Beth A Estes, Annette Xu, Lizhen Deflaux, Nicole Ho, Karen Smith, Isabel M Nicolson, Rob Spence, Sarah J Parr, Jeremy R Elsabbagh, Mayada C Yuen, Ryan K Weksberg, Rosanna Dager, Stephen Wang, Zhuozhi Cytrynbaum, Cheryl Sung, Wilson W L Bingham, Jonathan Woodbury-Smith, Marc Knoppers, Bartha M Higginbotham, Edward J Fedele, Angie Ring, Robert H Nalpathamkalam, Thomas Paton, Tara Cook, Edwin H Whitney, Joe Marshall, Christian R Walker, Susan Szatmari, Peter Kirby, Emily Zarrei, Mehdi Anagnostou, Evdokia Engchuan, W |
| AuthorAffiliation | 17 Departments of Pediatrics and Psychology & Neuroscience, Dalhousie University and Autism Research Centre, IWK Health Centre, Halifax, NS, Canada 41 McLaughlin Centre, University of Toronto, Toronto, ON, Canada 5 Genome Diagnostics, Department Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada 22 Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA 27 Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, UK 23 Department of Radiology, University of Washington, Seattle, WA, USA 39 Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada 12 Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada 9 BioTeam Inc., Middleton, MA, USA 25 Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland 13 Department of Pediatrics, University of Alberta, Edmonton, AB Canada 24 Department of Speech and Hearing Science |
| AuthorAffiliation_xml | – name: 10 Dalla Lana School of Public Health and the Department of Family and Community Medicine, University of Toronto, ON, Canada – name: 35 Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA – name: 22 Institute for Juvenile Research, Department of Psychiatry, University of Illinois at Chicago, Chicago, IL, USA – name: 1 The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada – name: 9 BioTeam Inc., Middleton, MA, USA – name: 38 Department of Psychiatry, University of Toronto, Toronto, ON, Canada – name: 31 Department of Medicine, University of California San Diego, La Jolla, CA, USA – name: 36 Centre of Genomics and Policy, McGill University, Montreal, QC, Canada – name: 28 Department of Neurology, Boston Children’s Hospital, Boston, MA, USA – name: 32 Division of Biostatistics, Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada – name: 30 Department of Electrical and Computer Engineering and Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada – name: 19 Children’s Health Research Institute, London, ON, Canada – name: 34 Regional Genetics Program, The Children’s Hospital of Eastern Ontario, Ottawa, ON, Canada – name: 7 Autism Research Unit, The Hospital for Sick Children, Toronto, ON, Canada – name: 16 Department of Psychiatry, McGill University, Montreal, QC, Canada – name: 29 Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht, the Netherlands – name: 4 Verily Life Sciences, South San Francisco, CA, USA – name: 5 Genome Diagnostics, Department Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, ON, Canada – name: 26 Sleep Disorders Division, Department of Neurology, Vanderbilt University School of Medicine, Nashville, TN, USA – name: 8 Public Population Project in Genomics and Society, McGill University, Montreal, QC, Canada – name: 15 Bloorview Research Institute, University of Toronto, Toronto, ON, Canada – name: 18 Department of Psychiatry, Queen’s University, Kinston, ON, Canada – name: 39 Department of Psychiatry, The Hospital for Sick Children, Toronto, ON, Canada – name: 14 Department of Psychiatry and Behavioural Neurosciences, McMaster University, Hamilton, ON, Canada – name: 12 Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, Toronto, ON, Canada – name: 6 Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada – name: 13 Department of Pediatrics, University of Alberta, Edmonton, AB Canada – name: 20 Western University, London, ON, Canada – name: 3 Google, Mountain View, CA, USA – name: 25 Department of Psychiatry, School of Medicine, Trinity College Dublin, Dublin, Ireland – name: 11 Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, ON, Canada – name: 17 Departments of Pediatrics and Psychology & Neuroscience, Dalhousie University and Autism Research Centre, IWK Health Centre, Halifax, NS, Canada – name: 24 Department of Speech and Hearing Sciences, University of Washington, Seattle, WA, USA – name: 33 Disciplines of Genetics and Medicine, Memorial University of Newfoundland and Provincial Medical Genetic Program, Eastern Health, St. John’s, NF, Canada – name: 21 Autism Speaks, New York, NY, USA – name: 40 Department of Pharmacology & Physiology, Drexel University College of Medicine, Philadelphia, PA, USA – name: 2 Deep Genomics Inc., Toronto, ON, Canada – name: 37 Child Youth and Family Services, Centre for Addiction and Mental Health, Toronto, ON, Canada – name: 41 McLaughlin Centre, University of Toronto, Toronto, ON, Canada – name: 27 Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, UK – name: 23 Department of Radiology, University of Washington, Seattle, WA, USA |
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givenname: Mathew T surname: Pletcher fullname: Pletcher, Mathew T organization: Autism Speaks – sequence: 83 givenname: Stephen W surname: Scherer fullname: Scherer, Stephen W email: stephen.scherer@sickkids.ca organization: The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Department of Molecular Genetics, University of Toronto, McLaughlin Centre, University of Toronto |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/28263302$$D View this record in MEDLINE/PubMed |
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et al
. developed a cloud-based database with 5,205 whole genomes from families with autism spectrum disorder (ASD). They identified 18 new candidate... We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and... We are performing whole genome sequencing (WGS) of families with Autism Spectrum Disorder (ASD) to build a resource, named MSSNG, to enable the... |
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| SubjectTerms | 45 45/23 631/208/514/2254 692/699/476/1373 Animal Genetics and Genomics Autism Autism Spectrum Disorder - genetics Behavioral Sciences Biological Techniques Biomedicine Chromosome Aberrations Databases, Genetic DNA Copy Number Variations Genetic aspects Genetic Predisposition to Disease - genetics Genome-Wide Association Study - methods Genotypes Health aspects Humans Innovations Molecular targeted therapy Mutagenesis, Insertional - genetics Neurobiology Neurosciences Pervasive developmental disorders Phenotype Polymorphism, Single Nucleotide - genetics Psychological aspects resource Risk factors Sequence Deletion - genetics |
| Title | Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder |
| URI | https://link.springer.com/article/10.1038/nn.4524 https://www.ncbi.nlm.nih.gov/pubmed/28263302 https://www.proquest.com/docview/1892718909 https://www.proquest.com/docview/1874787943 https://www.proquest.com/docview/1897374280 https://pubmed.ncbi.nlm.nih.gov/PMC5501701 |
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