Cited by 1,734Autism Spectrum Disorder ResearchGenetics and Neurodevelopmental DisordersGenomics and Rare Diseases

Patterns and rates of exonic de novo mutations in autism spectrum disorders

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Neale, Benjamin M., Kou, Yan, Liu, Li, Ma’ayan, Avi, Samocha, Kaitlin E., Sabo, Aniko, Lin, Chiao-Feng, Stevens, Christine +51 more·2012·Nature

Abstract

Autism spectrum disorders (ASD) are believed to have genetic and environmental origins, yet in only a modest fraction of individuals can specific causes be identified. To identify further genetic risk factors, here we assess the role of de novo mutations in ASD by sequencing the exomes of ASD cases and their parents (n = 175 trios). Fewer than half of the cases (46.3%) carry a missense or nonsense de novo variant, and the overall rate of mutation is only modestly higher than the expected rate. In contrast, the proteins encoded by genes that harboured de novo missense or nonsense mutations showed a higher degree of connectivity among themselves and to previous ASD genes as indexed by protein-protein interaction screens. The small increase in the rate of de novo events, when taken together with the protein interaction results, are consistent with an important but limited role for de novo point mutations in ASD, similar to that documented for de novo copy number variants. Genetic models incorporating these data indicate that most of the observed de novo events are unconnected to ASD; those that do confer risk are distributed across many genes and are incompletely penetrant (that is, not necessarily sufficient for disease). Our results support polygenic models in which spontaneous coding mutations in any of a large number of genes increases risk by 5- to 20-fold. Despite the challenge posed by such models, results from de novo events and a large parallel case–control study provide strong evidence in favour of CHD8 and KATNAL2 as genuine autism risk factors.

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Crossref · 10.1038/nature11011

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  • TADA requires a mutational model that accounts for gene size and sequence composition to obtain an expectation for mutations per gene given sample size.

    “TADA requires a mutational model (Sanders et al., 2012; Neale et al., 2012; Samocha et al., 2014) which accounts for gene size and sequence composition to obtain an expectation for mutations per gene, given sample size.”

    From Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism (2020) · cites this paper as Neale et al., 2012

    The Methods section, “Expectation of de novo mutation calculation” (page unavailable), describes a mutation model based on trinucleotide context and sums mutation probabilities across captured exome bases. That supports the sequence-composition aspect, but our copy does not state that TADA requires this model or describe calculating expected mutations per gene for a given sample size. (LLM, conf=0.82)

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  • Mutations in chromatin complexes have been observed in schizophrenia where synaptic gene regulation is disrupted, and these mutations are high-confidence genetic risk factors for ASD.

    “mutations in chromatin complexes have been observed in schizophrenia where synaptic gene regulation is disrupted, and these mutations are also high-confidence genetic risk factors for ASD”

    From The clinical use of epigenetics in psychiatry: a narrative review of epigenetic mechanisms, key candidate genes, and precision psychiatry (2025) · cites this paper as [42]

    The paper’s main text (indexed under Abstract; page unavailable) reports strong evidence that mutations in CHD8 and KATNAL2 are ASD risk factors. It does not establish that mutations in chromatin complexes were observed in schizophrenia or that they disrupt synaptic gene regulation there; its mention of schizophrenia concerns broadly shared copy-number-variant risk. (LLM, conf=0.84)

    Experimental — accuracy not yet measured
  • CHD2 is one of the INH-M13 hub genes.

    “One of the INH-M13 hub genes is CHD2, whose de novo variants have been identified in individuals with ASD.42,43”

    From hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data (2023) · cites this paper as [43]

    The citation is attached to the statement that de novo CHD2 variants have been identified in individuals with ASD, rather than to the INH-M13 hub-gene designation. Searches of our copy for CHD2 and for de novo CHD2 variants found no passage addressing that finding. The closest passages (Abstract; page unavailable) discuss CHD8, not CHD2. (LLM, conf=0.72)

    Experimental — accuracy not yet measured
  • CHD2 de novo variants have been identified in individuals with ASD.

    “One of the INH-M13 hub genes is CHD2, whose de novo variants have been identified in individuals with ASD.42,43”

    From hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data (2023) · cites this paper as [43]

    The Abstract (page unavailable) reports de novo variants in ASD cases and highlights CHD8, but it does not identify a CHD2 variant. Searches of our copy for “CHD2” and “chromodomain helicase DNA binding protein 2” found no passage establishing the gene-specific claim. (LLM, conf=0.73)

    Experimental — accuracy not yet measured
  • CNVs and SNPs have both been reported to play a major role in autism incidence.

    “CNVs and SNPs have both been reported to play a major role in autism incidence (36–41).”

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Authors
Neale, B. M., Kou, Y., Liu, L., Ma’ayan, A., Samocha, K. E., Sabo, A., Lin, C.-F., Stevens, C., Wang, L.-S., Makarov, V., Polak, P., Yoon, S., Maguire, J., Crawford, E. L., Campbell, N. G., Geller, E. T., Valladares, O., Schafer, C., Liu, H., Zhao, T., Cai, G., Lihm, J., Dannenfelser, R., Jabado, O., Peralta, Z., Nagaswamy, U., Muzny, D., Reid, J. G., Newsham, I., Wu, Y., Lewis, L., Han, Y., Voight, B. F., Lim, E., Rossin, E., Kirby, A., Flannick, J., Fromer, M., Shakir, K., Fennell, T., Garimella, K., Banks, E., Poplin, R., Gabriel, S., DePristo, M., Wimbish, J. R., Boone, B. E., Levy, S. E., Betancur, C., Sunyaev, S., Boerwinkle, E., Buxbaum, J. D., Cook Jr, E. H., Devlin, B., Gibbs, R. A., Roeder, K., Schellenberg, G. D., Sutcliffe, J. S., & Daly, M. J.
Affiliations
  • Harvard University (US)
  • Icahn School of Medicine at Mount Sinai (US)
  • Carnegie Mellon University (US)
  • Broad Institute (US)
  • Baylor College of Medicine (US)
  • University of Pennsylvania (US)
  • Vanderbilt University (US)
  • Johns Hopkins University (US)
  • HudsonAlpha Institute for Biotechnology (US)
  • Centre National de la Recherche Scientifique (FR)
  • University of Pittsburgh (US)
Corresponding author
  • Buxbaum, Joseph D.
  • Roeder, Kathryn
  • Daly, Mark J.
Venue
Nature
Published
2012-04-04
Volume
485
Issue
7397
Pages
242-245
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
OpenAlex
W2024663595
Cited by
1,734
References
27
Citations by year
2026: 32 · 2025: 44 · 2024: 56 · 2023: 56 · 2022: 75 · 2021: 99 · 2020: 110 · 2019: 121 · 2018: 125 · 2017: 144 · 2016: 158 · 2015: 180 · 2014: 245 · 2013: 194 · 2012: 92
FWCI
116.56
Type
journal article
Language
en
Open access
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • HAL (submittedVersion, other-oa)
  • Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
  • Vanderbilt University (UL1 RR024975)
  • National Institutes of Health (MH057881, HD015052, HD055751, RR024975)
  • Vanderbilt Kennedy Center, Vanderbilt University Medical Center
  • National Institute of Mental Health (R01MH061009, R01MH089025, R01MH089175, R01MH089004, R01MH089208, R01MH057881, MH057881, R01MH089482, R01MH084676)
  • National Human Genome Research Institute (U54HG003067, HG003273, U54HG003273)
  • National Institute of General Medical Sciences (T32GM007753, P50GM071558)
  • National Center for Research Resources (RR024975, KL2RR024977, TL1RR024978, UL1RR024975)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (P30HD015052, P50HD055751)
Topics
  • Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Keywords
autism spectrum disorder, genetic heterogeneity, locus heterogeneity, polygenic risk, parent-child trios, exome sequencing, protein-protein interaction network, SCN2A, CHD8, β-catenin signaling, p53 pathway, mutation rate, penetrance, copy number variation, genetic risk
MeSH terms
Autistic Disorder, DNA-Binding Proteins, Exons, Family Health, Humans, Models, Genetic, Mutation, Phenotype, Transcription Factors, Poisson Distribution, Case-Control Studies, Genetic Predisposition to Disease, Multifactorial Inheritance, Exome, Protein Interaction Maps

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