Autism spectrum disorder (ASD) is genetically heterogeneous, with evidence for hundreds of susceptibility loci. Previous microarray and exome-sequencing studies have examined portions of the genome in simplex families (parents and one ASD-affected child) having presumed sporadic forms of the disorder. We used whole-genome sequencing (WGS) of 85 quartet families (parents and two ASD-affected siblings), consisting of 170 individuals with ASD, to generate a comprehensive data resource encompassing all classes of genetic variation (including noncoding variants) and accompanying phenotypes, in apparently familial forms of ASD. By examining de novo and rare inherited single-nucleotide and structural variations in genes previously reported to be associated with ASD or other neurodevelopmental disorders, we found that some (69.4%) of the affected siblings carried different ASD-relevant mutations. These siblings with discordant mutations tended to demonstrate more clinical variability than those who shared a risk variant. Our study emphasizes that substantial genetic heterogeneity exists in ASD, necessitating the use of WGS to delineate all genic and non-genic susceptibility variants in research and in clinical diagnostics.

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We thank S.S. Gross, M. Bookman and D. Glazer from Google for the development of the MSSNG database. We thank the families for their participation in the study and we thank The Centre for Applied Genomics for informatics support. We would also like to acknowledge the Autism Sequencing Consortium (AASC) principal investigators for the use of data. This work was supported by Autism Speaks (S.W.S., R.K.C.Y.), Autism Speaks Canada (S.W.S.), Neurodevelopment Network (NeuroDevNet) (S.W.S.), the Canadian Institutes for Advanced Research (S.W.S.), the University of Toronto McLaughlin Centre (S.W.S.), Genome Canada and Ontario Genomics Institute (S.W.S.), the government of Ontario (S.W.S., P.S.), the Canadian Institutes of Health Research (S.W.S., P.S.), and The Hospital for Sick Children Foundation (S.W.S.). R.K.C.Y. holds the Autism Speaks Meixner Postdoctoral Fellowship in Translational Research and a NARSAD Young Investigator award. K.T. holds a fellowship from the Swedish Research Council. E.D. holds the Banting Postdoctoral Fellowship. P.S. holds the Patsy and Jamie Anderson Chair in Child and Youth Mental Health. S.W.S. holds the GlaxoSmithKline–Canadian Institutes of Health Research (CIHR) Chair in Genome Sciences at the University of Toronto and The Hospital for Sick Children.

Author information


  1. The Centre for Applied Genomics, Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.

    • Ryan K C Yuen
    • , Bhooma Thiruvahindrapuram
    • , Daniele Merico
    • , Susan Walker
    • , Kristiina Tammimies
    • , Thomas Nalpathamkalam
    • , Giovanna Pellecchia
    • , Yi Liu
    • , Matthew J Gazzellone
    • , Lia D'Abate
    • , Eric Deneault
    • , Jennifer L Howe
    • , Richard S C Liu
    • , Mehdi Zarrei
    • , Mohammed Uddin
    • , Christian R Marshall
    •  & Stephen W Scherer
  2. Department of Women's and Children's Health, Pediatric Neuropsychiatry Unit, Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND), Karolinska Institutet, Stockholm, Sweden.

    • Kristiina Tammimies
  3. Department of Pediatrics, Division of Clinical and Metabolic Genetics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada.

    • Ny Hoang
    • , Rosanna Weksberg
    •  & Melissa T Carter
  4. Department of Psychiatry and Behavioural Neurosciences, Offord Centre for Child Studies, McMaster University, Hamilton, Ontario, Canada.

    • Christina Chrysler
    •  & Ann Thompson
  5. Jinan Pediatric Research Institute, Qilu Children's Hospital of Shandong University, Shandong, China.

    • Yi Liu
  6. Department of Molecular Genetics, Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada.

    • Christian R Marshall
    •  & Peter N Ray
  7. Autism Speaks, Princeton, New Jersey, USA.

    • Robert H Ring
  8. Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada.

    • Lonnie Zwaigenbaum
  9. Department of Paediatrics and Genetics and Genome Biology Program, The Hospital for Sick Children and Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada.

    • Rosanna Weksberg
  10. Autism Research Unit, The Hospital for Sick Children, Toronto, Ontario, Canada.

    • Melissa T Carter
    • , Wendy Roberts
    •  & Peter Szatmari
  11. Disciplines of Genetics and Medicine, Memorial University of Newfoundland, St. John's, Newfoundland, Canada.

    • Bridget A Fernandez
  12. Provincial Medical Genetic Program, Eastern Health, St. John's, Newfoundland, Canada.

    • Bridget A Fernandez
  13. Child Youth and Family Services, Centre for Addiction and Mental Health, Toronto, Ontario, Canada.

    • Peter Szatmari
  14. Department of Psychiatry, University of Toronto, Toronto, Ontario, Canada.

    • Peter Szatmari
  15. Department of Molecular Genetics and McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada.

    • Stephen W Scherer


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R.K.C.Y. and S.W.S. conceived and designed the experiments. R.K.C.Y., B.T., D.M. and T.N. processed and analyzed the whole genome sequencing data. S.W. and K.T. designed and performed experiments for variants characterization and validation. N.H., C.C., J.L.H. and A.T. collected phenotypic information from the participants. G.P., Y.L., M.J.G., L.D., E.D., R.S.C.L., M.Z., M.U. and C.R.M. helped perform different components of whole genome sequencing analysis and validation experiments. R.K.C.Y., R.H.R. and S.W.S. conceived and coordinated the project. L.Z., P.N.R., R.W., M.T.C., B.A.F., W.R. and P.S. recruited, diagnosed and examined the recruited participants. R.K.C.Y. and S.W.S. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Stephen W Scherer.

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