ArticleAmerican journal of human genetics2016
Frequency and Complexity of De Novo Structural Mutation in Autism.
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Article in American journal of human genetics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 66 papers.
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66citing papers in PubMed
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Who cites it
66 citing papers in PubMed.
- Computational strategies for copy number variation detection, disease association, and beyond.Genome biology · 2026Review
- Protocol for identifying genetic modifiers of phenotypes in individuals with disease-associated variants.STAR protocols · 2026Article
- Long-read genome sequencing improves detection and functional interpretation of structural and repeat variants in autism.Cell genomics · 2026Article
- Multi-omics Differential Inference for Functional Interpretation (MoDIFI): A Statistical Framework to Prioritize Cell Lines for Neurodevelopmental Variants.bioRxiv : the preprint server for biology · 2026Article
- Recent Insights Into the Evolutionary Genomics of the Critically Endangered Aye-Aye (Daubentonia madagascariensis).American journal of primatology · 2025Review
- Single-Cell Dissection of the Biological Function and Molecular Features Underlying the Micropeptide LSMEM1 in Kidney.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Generation and characterization of a knockout mouse of an enhancer of EBF3.Biology open · 2025Article
- The Landscape of Structural Variation in Aye-Ayes (Daubentonia madagascariensis).Genome biology and evolution · 2025Article
- De novo and somatic structural variant discovery with SVision-pro.Nature biotechnology · 2025Article
- Optical genome mapping reveals novel structural variations in an autism spectrum disorder cohort.Computational and structural biotechnology journal · 2025Article
- Integrative genetic analysis: cornerstone of precision psychiatry.Molecular psychiatry · 2025Review
- Contribution ofmedRxiv : the preprint server for health sciences · 2024Article
- Proteome-Wide Assessment of Clustering of Missense Variants in Neurodevelopmental Disorders Versus Cancer.medRxiv : the preprint server for health sciences · 2024Article
- The rate of de novo structural variation is increased in in vitro-produced offspring and preferentially affects the paternal genome.Genome research · 2023Article
- Structural Variations Contribute to the Genetic Etiology of Autism Spectrum Disorder and Language Impairments.International journal of molecular sciences · 2023Article
- Genome-wide identification and phenotypic characterization of seizure-associated copy number variations in 741,075 individuals.Nature communications · 2023Article
- Detection of trait-associated structural variations using short-read sequencing.Cell genomics · 2023Article
- Novel correlative analysis identifies multiple genomic variations impacting ASD with macrocephaly.Human molecular genetics · 2023Article
- Identification and characterisation of de novo germline structural variants in two commercial pig lines using trio-based whole genome sequencing.BMC genomics · 2023Article
- Copy Number Variants Are Ovarian Cancer Risk Alleles at Known and Novel Risk Loci.Journal of the National Cancer Institute · 2022Article
6 more citing papers are in PubMed but not listed here.
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Authors and funding
35 authors.
William M BrandlerBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Danny AntakiBeyster 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, 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 GujralBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Amina NoorBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Gabriel RosanioBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Timothy R ChapmanBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Daniel J BarreraBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Guan Ning LinDepartment of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA.
Dheeraj MalhotraBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Amanda C WattsBiomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Lawrence C WongRady Children's Hospital, San Diego, CA 92123, USA.
Jasper A EstabilloRady Children's Hospital, San Diego, CA 92123, USA.
Therese E GadomskiBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Oanh HongBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Karin V Fuentes FajardoBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Abhishek BhandariBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Renius OwenQuest Diagnostics Nichols Institute, San Juan Capistrano, CA 92675, USA.
Michael BaughnBiomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Jeffrey YuanBiomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Terry SolomonBiomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Alexandra G MoyzisBiomedical Sciences Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.
Michelle S MaileBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA.
Stephan J SandersDepartment of Psychiatry, University of California, San Francisco, San Francisco, CA 94143, USA.
Gail E ReinerDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Keith K VauxDepartment of Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Charles M StromQuest Diagnostics Nichols Institute, San Juan Capistrano, CA 92675, USA.
Kang ZhangDepartment of Ophthalmology, University of California, San Diego, La Jolla, CA 92093, USA.
Alysson R MuotriDepartment of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093, USA.
Natacha AkshoomoffRady Children's Hospital, San Diego, CA 92123, USA.
Suzanne M LealCenter for Statistical Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
Karen PierceDepartment of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA.
Eric CourchesneDepartment of Neuroscience, University of California, San Diego, La Jolla, CA 92093, USA.
Lilia M IakouchevaDepartment of Psychiatry, University of California, San Diego, La Jolla, CA 92093, USA.
Christina CorselloRady Children's Hospital, San Diego, CA 92123, USA.
Jonathan SebatBeyster 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, University of California, San Diego, La Jolla, CA 92093, USA. Electronic address: jsebat@ucsd.edu.
Funding
Identifying and Characterizing the Full Spectrum of Haplotype-resolved Structural Variation in Human GenomesU24HG007497 · NHGRI · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Evan Eichler, Jan Oliver Korbel · 2019 to 2026
$17.2MAn Integrative Analysis of Structural Variation for the 1000 Genomes ProjectU41HG007497 · NHGRI · JACKSON LABORATORY · PI LEE, CHARLES · 2013 to 2017
$13.0MTraining Program in Basic Clinical GeneticsT32GM008666 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI HAMILTON, BRUCE A · 1998 to 2021
$8.6MThe Role of Germline Mutation and Parental Age in Autism Spectrum DisordersR01MH076431 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI SEBAT, JONATHAN · 2005 to 2015
$5.5MUC San Diego Genetics Training ProgramT32GM145427 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI BRUCE A HAMILTON · 2022 to 2026
$2.6MEvaluating the effect of splicing mutations on isoform networks in autismR01MH109885 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IAKOUCHEVA, LILIA M, MUOTRI, ALYSSON R. · 2016 to 2020
$2.5MA computational framework for predicting the impact of mutations in autismR01MH105524 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IAKOUCHEVA, LILIA M, RADIVOJAC, PREDRAG · 2014 to 2016
$1.4MA systems biology approach to unravel theunderlying functional modules of ASDR01HD065288 · NICHD · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IAKOUCHEVA, LILIA M · 2009 to 2010
$1.3MProtein network of high risk copy number variants for psychiatric disordersR21MH104766 · NIMH · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI IAKOUCHEVA, LILIA M · 2014 to 2015
$421kNHGRI NIH HHS HG007497NHGRI NIH HHS U24 HG007497NHGRI NIH HHS U41 HG007497NICHD NIH HHS HD065288NICHD NIH HHS R01 HD065288NIGMS NIH HHS T32 GM008666NIGMS NIH HHS T32 GM145427NIMH NIH HHS MH076431NIMH NIH HHS MH104766NIMH NIH HHS MH105524NIMH NIH HHS R01 MH076431NIMH NIH HHS R01 MH105524NIMH NIH HHS R01 MH109885NIMH NIH HHS R21 MH104766
Abstract
Genetic studies of autism spectrum disorder (ASD) have established that de novo duplications and deletions contribute to risk. However, ascertainment of structural variants (SVs) has been restricted by the coarse resolution of current approaches. By applying a custom pipeline for SV discovery, genotyping, and de novo assembly to genome sequencing of 235 subjects (71 affected individuals, 26 healthy siblings, and their parents), we compiled an atlas of 29,719 SV loci (5,213/genome), comprising 11 different classes. We found a high diversity of de novo mutations, the majority of which were undetectable by previous methods. In addition, we observed complex mutation clusters where combinations of de novo SVs, nucleotide substitutions, and indels occurred as a single event. We estimate a high rate of structural mutation in humans (20%) and propose that genetic risk for ASD is attributable to an elevated frequency of gene-disrupting de novo SVs, but not an elevated rate of genome rearrangement.
Indexed as
Gene DeletionGene DuplicationAllelesAmino Acid SequenceAutism Spectrum DisorderBase SequenceCase-Control StudiesChildDNA Copy Number VariationsFemaleGene FrequencyGene RearrangementGenetic LociGenome, HumanGenotyping TechniquesHumans
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