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Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

Nature volume 485, pages 246–250 (2012)Cite this article

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Abstract

It is well established that autism spectrum disorders (ASD) have a strong genetic component; however, for at least 70% of cases, the underlying genetic cause is unknown1. Under the hypothesis that de novo mutations underlie a substantial fraction of the risk for developing ASD in families with no previous history of ASD or related phenotypes—so-called sporadic or simplex families2,3—we sequenced all coding regions of the genome (the exome) for parent–child trios exhibiting sporadic ASD, including 189 new trios and 20 that were previously reported4. Additionally, we also sequenced the exomes of 50 unaffected siblings corresponding to these new (n = 31) and previously reported trios (n = 19)4, for a total of 677 individual exomes from 209 families. Here we show that de novo point mutations are overwhelmingly paternal in origin (4:1 bias) and positively correlated with paternal age, consistent with the modest increased risk for children of older fathers to develop ASD5. Moreover, 39% (49 of 126) of the most severe or disruptive de novo mutations map to a highly interconnected β-catenin/chromatin remodelling protein network ranked significantly for autism candidate genes. In proband exomes, recurrent protein-altering mutations were observed in two genes: CHD8 and NTNG1. Mutation screening of six candidate genes in 1,703 ASD probands identified additional de novo, protein-altering mutations in GRIN2B, LAMC3 and SCN1A. Combined with copy number variant (CNV) data, these results indicate extreme locus heterogeneity but also provide a target for future discovery, diagnostics and therapeutics.

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Figure 1: De novo mutation events in autism spectrum disorder.
Figure 2: Mutations identified in protein–protein interaction (PPI) networks.

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Data deposits

Access to the raw sequence reads can be found at the NCBI database of Genotypes and Phenotypes (dbGaP) and National Database for Autism Research under accession numbers phs000482.v1.p1 and NDARCOL0001878, respectively.

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Acknowledgements

We would like to thank and recognize the following ongoing studies that produced and provided exome variant calls for comparison: NHLBI Lung Cohort Sequencing Project (HL 1029230), NHLBI WHI Sequencing Project (HL 102924), NIEHS SNPs (HHSN273200800010C), NHLBI/NHGRI SeattleSeq (HL 094976), and the Northwest Genomics Center (HL 102926). We are grateful to all of the families at the participating Simons Simplex Collection (SSC) sites, as well as the principal investigators (A. Beaudet, R. Bernier, J. Constantino, E. Cook, E. Fombonne, D. Geschwind, E. Hanson, D. Grice, A. Klin, R. Kochel, D. Ledbetter, C. Lord, C. Martin, D. Martin, R. Maxim, J. Miles, O. Ousley, K. Pelphrey, B. Peterson, J. Piggot, C. Saulnier, M. State, W. Stone, J. Sutcliffe, C. Walsh, Z. Warren and E. Wijsman). We also acknowledge M. State and the Simons Simplex Collection Genetics Consortium for providing Illumina genotyping data, T. Lehner and the Autism Sequencing Consortium for providing an opportunity for pre-publication data exchange among the participating groups. We appreciate obtaining access to phenotypic data on SFARI Base. This work was supported by the Simons Foundation Autism Research Initiative (SFARI 137578 and 191889; E.E.E., J.S. and R.B.) and NIH HD065285 (E.E.E. and J.S.). E.B. is an Alfred P. Sloan Research Fellow. E.E.E. is an Investigator of the Howard Hughes Medical Institute.

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Authors and Affiliations

  1. Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA,

    Brian J. O’Roak, Laura Vives, Santhosh Girirajan, Emre Karakoc, Niklas Krumm, Bradley P. Coe, Roie Levy, Arthur Ko, Choli Lee, Joshua D. Smith, Emily H. Turner, Ian B. Stanaway, Benjamin Vernot, Maika Malig, Carl Baker, Joshua M. Akey, Elhanan Borenstein, Mark J. Rieder, Deborah A. Nickerson, Jay Shendure & Evan E. Eichler

  2. Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, Washington 98195, USA,

    Beau Reilly & Raphael Bernier

  3. Department of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, USA,

    Elhanan Borenstein

  4. Santa Fe Institute, Santa Fe, New Mexico 87501, USA,

    Elhanan Borenstein

  5. Howard Hughes Medical Institute, Seattle, Washington 98195, USA,

    Evan E. Eichler

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Contributions

E.E.E., J.S. and B.J.O. designed the study and drafted the manuscript. E.E.E. and J.S. supervised the study. R.B., B.R. and B.J.O. analysed the clinical information. R.B., L.V., S.G., E.K., N.K. and B.P.C. contributed to the manuscript. S.G., N.K., B.P.C., A.K., C.B., M.M. and L.V. generated and analysed CNV data. B.J.O. and L.V. performed MIP resequencing and mutation validations. I.B.S., E.H.T., B.J.O. and J.S. developed MIP protocol and analysis. B.V. and J.M.A. generated loci-specific mutation rate estimates. R.L. and E.B. performed PPI network analysis and simulations. E.K. performed DADA analysis. C.L. performed Illumina sequencing. J.D.S., I.B.S., E.H.T. and C.L. analysed sequence data. B.P.C. performed IPA analysis. B.J.O., E.K. and N.K. developed the de novo analysis pipelines and analysed sequence data. D.A.N., M.J.R., J.D.S. and E.H.T. supervised exome sequencing and primary analysis.

Corresponding authors

Correspondence to Jay Shendure or Evan E. Eichler.

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Competing interests

E.E.E. is on the scientific advisory boards for Pacific Biosciences, Inc and SynapDx Corp. J.S. is a member of the scientific advisory board or serves as a consultant for Aria Diagnostics, Stratos Genomics, Good Start Genetics, and Adaptive TCR. B.J.O. is an inventor on patent PCT/US2009/30620: mutations in contactin associated protein 2 are associated with increased risk for idiopathic autism.

Supplementary information

Supplementary Information

This file contains Supplementary Discussion; Supplementary Figures 1–13; Supplementary Tables 2, 4, 6-13; and Supplementary References. (PDF 2170 kb)

Supplementary Tables

This file contains Supplementary Tables 1, 3 and 5 which give detailed information on exome capture, sequence coverage, paternal age, de novo mutation sites, and functional annotations. (XLS 203 kb)

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O’Roak, B., Vives, L., Girirajan, S. et al. Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations. Nature 485, 246–250 (2012). https://doi.org/10.1038/nature10989

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