Abstract

Recent research has uncovered an important role for de novo variation in neurodevelopmental disorders. Using aggregated data from 9,246 families with autism spectrum disorder, intellectual disability, or developmental delay, we found that 1/3 of de novo variants are independently present as standing variation in the Exome Aggregation Consortium's cohort of 60,706 adults, and these de novo variants do not contribute to neurodevelopmental risk. We further used a loss-of-function (LoF)-intolerance metric, pLI, to identify a subset of LoF-intolerant genes containing the observed signal of associated de novo protein-truncating variants (PTVs) in neurodevelopmental disorders. LoF-intolerant genes also carry a modest excess of inherited PTVs, although the strongest de novo–affected genes contribute little to this excess, thus suggesting that the excess of inherited risk resides in lower-penetrant genes. These findings illustrate the importance of population-based reference cohorts for the interpretation of candidate pathogenic variants, even for analyses of complex diseases and de novo variation.

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Acknowledgements

We thank all of the members of the ATGU and the laboratory of D.P.W. for assistance in this endeavor. We thank the families who took part in the Simons Simplex Collection study and the Simons Variation in Individuals Project, as well as the clinicians who collected data at each of the study sites. The authors would like to thank the Exome Aggregation Consortium and the groups that provided exome variant data for comparison. A full list of contributing groups can be found on the ExAC website (see URLs). We also greatly thank A. Byrnes, R. Fine, D. Fronk, A. Martin, C. Nichols, N. Radd, K. Satterstrom, and E. Wigdor for their insightful contributions. Finally, we acknowledge G.A. Barnard for inspiring us to write in a more conversational tone similar to that in his seminal 1947 paper (Biometrika 34, 123–138, 1947). This work was supported by NIH grants U01MH100233, U01MH100209, U01MH100229, and U01MH100239 to the Autism Sequencing Consortium (ASC), and R56 MH097849 and R01 MH097849 to the Population-based Autism Genetics and Environment Study (PAGES). M.J.D., J.A.K., and K.E.S. were supported by grants from the Simons Foundation Autism Research Initiative (SFARI 342292 and a subaward from the Simons Center for the Social Brain at MIT). M.L. and D.G.M.'s work on the ExAC project was funded by U54DK105566 and R01 GM104371 from the National Institutes of Health. K.S. was funded by T32 HG002295/HG/NHGRI. E.B.R. was funded by National Institutes of Mental Health Grant 1K01MH099286 and NARSAD Young Investigator grant 22379.

Author information

Affiliations

  1. Analytic and Translational Genetics Unit (ATGU), Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Jack A Kosmicki
    • , Kaitlin E Samocha
    • , Daniel P Howrigan
    • , Monkol Lek
    • , Konrad J Karczewski
    • , Benjamin M Neale
    • , Daniel G MacArthur
    • , Elise B Robinson
    •  & Mark J Daly
  2. Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.

    • Jack A Kosmicki
    • , Kaitlin E Samocha
    • , Daniel P Howrigan
    • , Kamil Slowikowski
    • , Monkol Lek
    • , Konrad J Karczewski
    • , Benjamin M Neale
    • , Daniel G MacArthur
    • , Elise B Robinson
    •  & Mark J Daly
  3. Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA.

    • Jack A Kosmicki
    • , Kaitlin E Samocha
    • , Daniel P Howrigan
    • , Benjamin M Neale
    • , Elise B Robinson
    •  & Mark J Daly
  4. Program in Bioinformatics and Integrative Genomics, Harvard University, Cambridge, Massachusetts, USA.

    • Jack A Kosmicki
    •  & Kamil Slowikowski
  5. Program in Genetics and Genomics, Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA.

    • Jack A Kosmicki
    •  & Kaitlin E Samocha
  6. Department of Psychiatry, University of California, San Francisco, San Francisco, California, USA.

    • Stephan J Sanders
  7. Divisions of Genetics and Rheumatology, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA.

    • Kamil Slowikowski
  8. Partners Center for Personalized Genetic Medicine, Boston, Massachusetts, USA.

    • Kamil Slowikowski
  9. Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, USA.

    • David J Cutler
  10. Department of Psychiatry, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA.

    • Bernie Devlin
  11. Department of Statistics, Carnegie Mellon University, Pittsburgh, Pennsylvania, USA.

    • Kathryn Roeder
  12. Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Joseph D Buxbaum
  13. Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Joseph D Buxbaum
  14. Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Joseph D Buxbaum
  15. Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Joseph D Buxbaum
  16. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Joseph D Buxbaum
  17. Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Joseph D Buxbaum
  18. Departments of Pediatrics (Systems Medicine), Biomedical Data Science, and Psychiatry (by courtesy), Stanford University, Stanford, California, USA.

    • Dennis P Wall

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Contributions

J.A.K. and E.B.R. performed the analyses. J.A.K., D.P.H., E.B.R., and M.J.D. designed the experiment. J.A.K. and K.S. wrote the code. D.P.W., E.B.R., and M.J.D. supervised the research. J.A.K. and M.J.D. wrote the paper. J.A.K., K.E.S., D.P.H., S.J.S., M.L., K.J.K., D.G.M., and J.D.B. generated data. J.A.K., K.E.S., D.P.H., D.J.C., B.D., K.R., B.M.N., D.G.M., D.P.W., E.B.R., and M.J.D. contributed to analysis concepts and methods. J.A.K. was responsible for the remainder. All authors revised and approved the final manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Mark J Daly.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–4, Supplementary Tables 3–5, 7–21, 23–25, 27–30 and 32–34, and Supplementary Note

Excel files

  1. 1.

    Supplementary Table 1

    ASD and unaffected ASD sibling de novo variants. All 5,856 de novo variants in 3,982 individuals with ASD and 2,545 de novo variants in 2,078 unaffected siblings. Each row in the file represents one de novo variant in an individual. Descriptions of the column names are in the second tab.

  2. 2.

    Supplementary Table 2

    ID/DD de novo variants. All 1,692 de novo variants in 1,284 individuals with ID/DD14-17. As with Supplementary Table 1, each row in the file represents one de novo variant in an individual. As noted in the DDD study, some de novo variants were observed in multiple unrelated individuals14. As with Supplementary Table 1, column name descriptions are in the second tab.

  3. 3.

    Supplementary Table 6

    Congenital heart disease and schizophrenia de novo variants. All 1,281 de novo variants in 362 individuals with congenital heart disease, and 640 de novo variants in 617 individuals with schizophrenia. As with Supplementary Tables 1 and 2, each row in the file represents one de novo variant in an individual. Likewise, descriptions of the column names are in the second tab.

  4. 4.

    Supplementary Table 22

    Gene summary statistics. Counts of class 1 de novo PTVs, transmitted and untransmitted singleton PTVs absent from ExAC, and singleton PTVs absent from ExAC from 404 cases and 3,654 controls grouped by gene. In total, there are 9,637 genes with at least one PTV from these categories. Descriptions of the column names are in the second tab.

  5. 5.

    Supplementary Table 26

    Transmitted and untransmitted PTVs from 4,319 ASD trios. All singleton, LofTee high-confidence PTVs absent from ExAC that were transmitted or untransmitted in 4,319 trios with ASD. Descriptions of the columns are found in the second tab.

  6. 6.

    Supplementary Table 31

    PTVs from Swedish case-control study. All singleton, LofTee high-confidence PTVs absent from ExAC that were present in 404 cases and 3,654 controls from Sweden. Descriptions of the columns are found in the second tab.

About this article

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DOI

https://doi.org/10.1038/ng.3789

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