Abstract

Whole exome sequencing has proven to be a powerful tool for understanding the genetic architecture of human disease. Here we apply it to more than 2,500 simplex families, each having a child with an autistic spectrum disorder. By comparing affected to unaffected siblings, we show that 13% of de novo missense mutations and 43% of de novo likely gene-disrupting (LGD) mutations contribute to 12% and 9% of diagnoses, respectively. Including copy number variants, coding de novo mutations contribute to about 30% of all simplex and 45% of female diagnoses. Almost all LGD mutations occur opposite wild-type alleles. LGD targets in affected females significantly overlap the targets in males of lower intelligence quotient (IQ), but neither overlaps significantly with targets in males of higher IQ. We estimate that LGD mutation in about 400 genes can contribute to the joint class of affected females and males of lower IQ, with an overlapping and similar number of genes vulnerable to contributory missense mutation. LGD targets in the joint class overlap with published targets for intellectual disability and schizophrenia, and are enriched for chromatin modifiers, FMRP-associated genes and embryonically expressed genes. Most of the significance for the latter comes from affected females.

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Acknowledgements

Simons Foundation Autism Research Initiative grants to E.E.E. (SF191889), M.W.S. (M144095 R11154) and M.W. (SF235988) supported this work. Additional support was provided by the Howard Hughes Medical Institute (International Student Research Fellowship to S.J.S.) and the Canadian Institutes of Health Research (Doctoral Foreign Study Award to A.J.W.). E.E.E. is an Investigator of the Howard Hughes Medical Institute. We thank all the families at the participating SSC sites, as well as the principal investigators (A. L. Beaudet, R. Bernier, J. Constantino, E. H. Cook Jr, E. Fombonne, D. Geschwind, D. E. Grice, A. Klin, D. H. Ledbetter, C. Lord, C. L. Martin, D. M. Martin, R. Maxim, J. Miles, O. Ousley, B. Peterson, J. Piggot, C. Saulnier, M. W. State, W. Stone, J. S. Sutcliffe, C. A. Walsh and E. Wijsman) and the coordinators and staff at the SSC sites for the recruitment and comprehensive assessment of simplex families; the SFARI staff for facilitating access to the SSC; and the Rutgers University Cell and DNA Repository (RUCDR) for accessing biomaterials. We would also like to thank the CSHL Woodbury Sequencing Center, the Genome Institute at the Washington University School of Medicine, and Yale Center for Genomic Analysis (in particular J. Overton) for generating sequencing data; E. Antoniou and E. Ghiban for their assistance in data production at CSHL; and T. Brooks-Boone, N. Wright-Davis and M. Wojciechowski for their help in administering the project at Yale. The NHLBI GO Exome Sequencing Project and its ongoing studies produced and provided exome variant calls for comparison: the Lung GO Sequencing Project (HL-102923), the WHI Sequencing Project (HL-102924), the Broad GO Sequencing Project (HL-102925), the Seattle GO Sequencing Project (HL-102926) and the Heart GO Sequencing Project (HL-103010).

Author information

Author notes

    • Ivan Iossifov
    • , Brian J. O’Roak
    • , Stephan J. Sanders
    •  & Michael Ronemus

    These authors contributed equally to this work.

Affiliations

  1. Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA

    • Ivan Iossifov
    • , Michael Ronemus
    • , Dan Levy
    • , Boris Yamrom
    • , Yoon-ha Lee
    • , Ewa Grabowska
    • , Ertugrul Dalkic
    • , Zihua Wang
    • , Steven Marks
    • , Peter Andrews
    • , Anthony Leotta
    • , Jude Kendall
    • , Inessa Hakker
    • , Julie Rosenbaum
    • , Beicong Ma
    • , Linda Rodgers
    • , Jennifer Troge
    • , Giuseppe Narzisi
    • , Seungtai Yoon
    • , Michael C. Schatz
    • , W. Richard McCombie
    •  & Michael Wigler
  2. Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA

    • Brian J. O’Roak
    • , Niklas Krumm
    • , Holly A. Stessman
    • , Kali T. Witherspoon
    • , Laura Vives
    • , Karynne E. Patterson
    • , Joshua D. Smith
    • , Bryan Paeper
    • , Deborah A. Nickerson
    • , Jay Shendure
    •  & Evan E. Eichler
  3. Molecular & Medical Genetics, Oregon Health & Science University, Portland, Oregon 97208, USA

    • Brian J. O’Roak
  4. Department of Psychiatry, University of California, San Francisco, San Francisco, California 94158, USA

    • Stephan J. Sanders
    • , Jeanselle Dea
    • , Jeffrey D. Mandell
    • , Michael F. Walker
    • , A. Jeremy Willsey
    •  & Matthew W. State
  5. Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA

    • Stephan J. Sanders
    • , Shan Dong
    • , A. Jeremy Willsey
    •  & Matthew W. State
  6. Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing 100871, China

    • Shan Dong
    •  & Liping Wei
  7. Child Study Center, Yale University School of Medicine, New Haven, Connecticut 06520, USA

    • Luis E. Gonzalez
    • , Michael T. Murtha
    • , Catherine A. Sullivan
    • , Zainulabedin Waqar
    •  & Matthew W. State
  8. Yale Center for Genomic Analysis, Yale University School of Medicine, New Haven, Connecticut 06520, USA

    • Shrikant M. Mane
  9. National Institute of Biological Sciences, Beijing 102206, China

    • Liping Wei
  10. New York Genome Center, New York, New York 10013, USA

    • Ewa Grabowska
    •  & Giuseppe Narzisi
  11. Department of Medical Biology, Bulent Ecevit University School of Medicine, 67600 Zonguldak, Turkey

    • Ertugrul Dalkic
  12. Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, New York 10461, USA

    • Kenny Ye
  13. Howard Hughes Medical Institute, Seattle, Washington 98195, USA

    • Evan E. Eichler
  14. Department of Psychiatry, Yale University School of Medicine, New Haven, Connecticut 06520, USA

    • Matthew W. State

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Contributions

CSHL: I.I., M.R. and M.W. designed the study; I.I., D.L., B.Y., Y.L., E.G., E.D., P.A., A.L., J.K., G.N., S.Y., M.C.S., K.Y. and M.W. analysed the data; M.R., I.H., J.R., B.M., L.R., J.T. and W.R.M. generated the exome data at Cold Spring Harbor Laboratory; I.I., Z.W., S.M. and J.T. confirmed the variants; I.I., M.R. and M.W. wrote the paper. UCSF/Yale: S.J.S. and M.W.S. designed the study; S.J.S., S.D., L.W. and A.J.W. analysed the data; S.J.S., J.D., L.E.G., J.D.M., C.A.S., M.F.W. and Z.W. confirmed the variants; S.M.M. and M.T.M. generated the exome data at Yale Medical Center. UW: B.J.O., J.S. and E.E.E. designed the study; B.J.O. and N.K. analysed the data; B.J.O., H.A.S., K.T.W. and L.V. confirmed the variants; E.E.E. and J.S. revised the manuscript; K.E.P, J.D.S., B.P. and D.A.N. generated the exome data at the University of Washington.

Competing interests

E.E.E. is on the scientific advisory board of DNAnexus, Inc. and was a scientific advisory board member of Pacific Biosciences, Inc. (2009–2013) and SynapDx Corp. (2011–2013). J.S. is a member of the scientific advisory board or serves as a consultant for Adaptive Biotechnologies, Ariosa Diagnostics, Stratos Genomics, GenePeeks, Gen9, Good Start Genetics, Ingenuity Systems and Rubicon Genomics. 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.

Corresponding authors

Correspondence to Jay Shendure or Evan E. Eichler or Matthew W. State or Michael Wigler.

Sequence data used in these work are available from the National Database for Autism Research (http://ndar.nih.gov/), under study DOI:10.15154/1149697.

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    Supplementary Information

    This file contains Supplementary Table 3 (Experimental validation in the 40X target), Supplementary Table 4 (Multiple de novo events), Supplementary Table 8 (Compound non-synonymous hits in targets), Supplementary Table 11 (Validation summary by centre) and Supplementary Table 13 (Median gene lengths) as well as legends for Supplementary Tables 1, 2, 5–7, 9, 10 and 12.

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    Supplementary Data

    This zipped file contains Supplementary Tables 1-2, 5-7, 9, 10 and 12.

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DOI

https://doi.org/10.1038/nature13908

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