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Rates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder

Nature Neuroscience 20, 1217–1224 (2017) | Download Citation

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Abstract

We systematically analyzed postzygotic mutations (PZMs) in whole-exome sequences from the largest collection of trios (5,947) with autism spectrum disorder (ASD) available, including 282 unpublished trios, and performed resequencing using multiple independent technologies. We identified 7.5% of de novo mutations as PZMs, 83.3% of which were not described in previous studies. Damaging, nonsynonymous PZMs within critical exons of prenatally expressed genes were more common in ASD probands than controls (P < 1 × 10−6), and genes carrying these PZMs were enriched for expression in the amygdala (P = 5.4 × 10−3). Two genes (KLF16 and MSANTD2) were significantly enriched for PZMs genome-wide, and other PZMs involved genes (SCN2A, HNRNPU and SMARCA4) whose mutation is known to cause ASD or other neurodevelopmental disorders. PZMs constitute a significant proportion of de novo mutations and contribute importantly to ASD risk.

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Acknowledgements

We are grateful to all the families who participated in the research, including the Simons Foundation Autism Research Initiative (SFARI) Simplex Collection (SSC), the Autism Sequencing Consortium (ASC) and Autism Speaks. We acknowledge the clinicians and organizations that contributed to samples used in this study, including the ASC and SSC principal investigators; the coordinators and staff at the ASC and SSC sites for the recruitment and comprehensive assessment of simplex families; and the ASC, SFARI and NDAR staff for facilitating access to the data sets. This work was supported by a grant from the Simons Foundation (178093, C.A.W.); the National Institutes of Health (NIH) grants R01MH083565, RC2MH089952 and U01MH106883 to C.A.W.; grants R01MH097849, U01MH100233, U01MH100209, U01MH100229, U01MH100239, U01MH111661, U01MH111660, U01MH111658, U01MH111662 and R01MH097849 to the Autism Sequencing Consortium; grants from the Centre for Applied Genomics, the University of Toronto McLaughlin Centre, Genome Canada and Autism Speaks (S.W.S.); Simons Foundation grant (368485, G.M.C.); SRPBS and Brain/MINDS grants from AMED (I.K., B.A., N.O.); grants from the Spanish Ministry of Economy and Competitiveness (M.P.), Instituto de Salud Carlos III (M.P.), PI10/02989 (M.P.), CIBERSAM (M.P.) and ERA-NET NEURON (M.P., C.M.F.), Network of European Funding for Neuroscience Research (M.P.), and Fundación María José Jove and The Institute of Health Carlos III-Fondo de Investigaciones Sanitarias grant project PI13/01136 (A.C.) and the Seaver Foundation. We thank A. Hossain and N. Hatem for their help with sample preparation; F. Zhao and C. Stevens for their help with reprocessing the BAM files; and M. Daly, S. McCarroll, G. Genovese and J. Hirschhorn for comments and suggestions. Research reported in this paper was supported by the Office of Research Infrastructure of the National Institutes of Health under award number S10OD018522. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. This work was supported in part through the computational resources and staff expertise provided by the Department of Scientific Computing at the Icahn School of Medicine at Mount Sinai. Additional computing support was provided by the Harvard Medical School's Orchestra High-Performance Computing Group, which is partially supported by NIH grant NCRR 1S10RR028832-01. 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). C.A.W. is an Investigator of the Howard Hughes Medical Institute; S.W.S. is funded by the GlaxoSmithKline-Canadian Institutes of Heath Research Chair in Genome Sciences at the Hospital for Sick Children and University of Toronto; A.M.D. is supported by the NIGMS (T32GM007753) and NRSA (5T32 GM007226-39); S.D.R. is supported by the Seaver Foundation.

Author information

Affiliations

  1. Division of Genetics and Genomics, Manton Center for Orphan Disease Research and Howard Hughes Medical Institute, Boston Children's Hospital, Boston, Massachusetts, USA.

    • Elaine T Lim
    • , Anne S Kamumbu
    • , Xiaochang Zhang
    • , Alissa M D'Gama
    • , Sonia N Kim
    • , Robert Sean Hill
    •  & Christopher A Walsh

  2. Departments of Pediatrics and Neurology, Harvard Medical School, Boston, Massachusetts, USA.

    • Elaine T Lim
    • , Anne S Kamumbu
    • , Xiaochang Zhang
    • , Alissa M D'Gama
    • , Sonia N Kim
    • , Robert Sean Hill
    •  & Christopher A Walsh

  3. Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

    • Elaine T Lim
    • , Yingleong Chan
    • , Anne S Kamumbu
    • , Xiaochang Zhang
    • , Alissa M D'Gama
    • , Sonia N Kim
    • , Robert Sean Hill
    • , George M Church
    •  & Christopher A Walsh

  4. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA.

    • Elaine T Lim
    • , Yingleong Chan
    •  & George M Church

  5. Mohammed Bin Rashid University of Medicine and Health Sciences, College of Medicine, Dubai, United Arab Emirates.

    • Mohammed Uddin

  6. Seaver Autism Center for Research and Treatment, Icahn School of Medicine at Mount Sinai,New York, New York, USA.

    • Silvia De Rubeis
    • , Arthur P Goldberg
    • , Christopher Poultney
    • , Alexander Kolevzon
    • , Menachem Fromer
    •  & Joseph D Buxbaum

  7. Department of Psychiatry, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Silvia De Rubeis
    • , Arthur P Goldberg
    • , Christopher Poultney
    • , Alexander Kolevzon
    • , Menachem Fromer
    •  & Joseph D Buxbaum

  8. Department of Psychiatry, Center For Excellence in Autism Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.

    • Nancy J Minshew

  9. Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.

    • Itaru Kushima
    • , Branko Aleksic
    •  & Norio Ozaki

  10. Child and Adolescent Psychiatry Department, Hospital General Universitario Gregorio Marañón, School of Medicine, Universidad Complutense, IiSGM, CIBERSAM, Madrid, Spain.

    • Mara Parellada
    •  & Celso Arango

  11. Child and Adolescent Psychiatry Department, Hospital General Universitario Gregorio Marañón, IiSGM, CIBERSAM, Madrid, Spain.

    • Maria J Penzol

  12. Grupo de Medicina Xenomica, Universidade de Santiago de Compostela, Centro Nacional de Genotipado-Plataforma de Recursos Biomoleculares y Bioinformaticos-Instituto de Salud Carlos III (CeGen-PRB2-ISCIII), Santiago de Compostela, Spain.

    • Angel Carracedo

  13. Grupo de Medicina Xenomica, CIBERER, Fundacion Publica Galega de Medicina Xenomica-SERGAS, Santiago de Compostela, Spain.

    • Angel Carracedo

  14. Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia.

    • Angel Carracedo

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

    • Alexander Kolevzon
    •  & Joseph D Buxbaum

  16. The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Alexander Kolevzon

  17. Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Alexander Kolevzon

  18. Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.

    • Christina M Hultman

  19. Department of Psychiatry and Institute for Human Genetics, University of California, San Francisco, San Francisco, California, USA.

    • Lauren A Weiss

  20. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Menachem Fromer

  21. Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy, Autism Research and Intervention Center of Excellence, University Hospital Frankfurt, Goethe University, Frankfurt am Main, Germany.

    • Andreas G Chiocchetti
    •  & Christine M Freitag

  22. The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada.

    • Stephen W Scherer

  23. Program in Genetics and Genome Biology (GGB), The Hospital for Sick Children, Toronto, Ontario, Canada.

    • Stephen W Scherer

  24. Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.

    • Stephen W Scherer

  25. McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada.

    • Stephen W Scherer

  26. The Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, New York, USA.

    • Joseph D Buxbaum

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  1. Autism Sequencing Consortium

    A list of members and affiliations appears in the Supplementary Note.

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Contributions

E.T.L. and C.A.W. conceived the project and wrote the manuscript. E.T.L. and M.U. performed the spatiotemporal analyses. E.T.L., S.D.R., Y.C., A.S.K., A.M.D. and S.N.K. performed the resequencing and Sanger sequencing experiments. E.T.L., S.D.R. and X.Z. performed the mutagenesis, overexpression and qPCR experiments. E.T.L. and Y.C. performed the permutations and modeling of background rates. R.S.H., A.P.G. and C.P. performed the data processing and annotation of the variant call files. N.J.M., I.K., B.A., N.O., M.P., C.A., M.J.P., A.C., A.K., C.M.H., L.A.W., A.G.C. and C.M.F. provided additional trio exome sequence data and blood samples for resequencing experiments. E.T.L. and M.F. performed the phasing of mutations. G.M.C., S.W.S., J.D.B. and C.A.W. supervised the project, provided critical comments and edited the manuscript. All authors critically reviewed the manuscript for content.

Competing interests

S.W.S., M.U. and the Hospital for Sick Children hold intellectual property used in this analysis, which is also licensed by Lineagen, Inc. M.P. has received educational honoraria from Otsuka, research grants from Fundación Alicia Koplowitz and Mutua Madrileña and travel grants from Otsuka and Janssen. C.A. has been a consultant to or has received honoraria or grants from Abbot, Amgen, AstraZeneca, Bristol-Myers-Squibb, Caja Navarra, CIBERSAM, Fundación Alicia Koplowitz, Instituto de Salud Carlos III, Janssen Cilag, Lundbeck, Merck, Ministerio de Ciencia e Innovación, Ministerio de Sanidad, Ministerio de Economía y Competitividad, Mutua Madrileña, Otsuka, Pfizer, Roche, Servier, Shire, Takeda and Schering-Plough.

Corresponding authors

Correspondence to Elaine T Lim or Christopher A Walsh.

Integrated supplementary information

Supplementary figures

  1. 1.

    RVIS scores for genes with recurrent nonsynonymous PZMs in probands

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figure 1, Supplementary Tables 1, 6–12, 14, 15, and Supplementary Note

  2. 2.

    Supplementary Methods Checklist

Excel files

  1. 1.

    Supplementary Table 2

    Rates of PZMs across ASC datasets, with the median depth and mode allele fraction of the de novos (Group A) in each dataset

  2. 2.

    Supplementary Table 3

    List of all de novo mutations found in the probands and unaffected siblings

  3. 3.

    Supplementary Table 4

    List of all de novo mutations that were validated using the different resequencing approaches

  4. 4.

    Supplementary Table 5

    Quantitative RT-PCR results for assaying copy number variants

  5. 5.

    Supplementary Table 13

    Gene-specific mutation rates for post-zygotic mutations estimated from the rare inherited variants

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DOI

https://doi.org/10.1038/nn.4598