Abstract
We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10−4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.
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Acknowledgements
We thank the families for their participation in the study, The Centre for Applied Genomics and Google for their analytical and technical support, and staff at Autism Speaks for organizational and fundraising support. This work was funded by Autism Speaks, Autism Speaks Canada, the Canadian Institute for Advanced Research, the University of Toronto McLaughlin Centre, Genome Canada/Ontario Genomics Institute, the Government of Ontario, the Canadian Institutes of Health Research (CIHR), NeuroDevNet, Ontario Brain Institute, the Catherine and Maxwell Meighen Foundation and The Hospital for Sick Children Foundation. Special thanks to B. and (the late) S. Wright for their vision in helping to conceptualize and develop this project and to foundational philanthropic supporters C. Dolan, G. Gund, B. Marcus, V. and J. Morgan and S. Wise. R.K.C.Y. is funded by the CIHR Postdoctoral Fellowship, NARSAD Young Investigator award and Thrasher Early Career Award. R.W. is funded by the Ontario Brain Institute and NeuroDevNet. M.U. is funded by the Banting Postdoctoral Fellowship. M.W. is funded by a CIHR (Institute of Genetics) Clinical Investigatorship Award. L.Z. is funded by the Stollery Children's Hospital Foundation Chair in Autism Research. P.S. is funded by the Patsy and Jamie Anderson Chair in Child and Youth Mental Health. B.M.K. is funded by the Canada Research Chair in Law and Medicine. S.W.S. is funded by the GlaxoSmithKline-CIHR Chair in Genome Sciences at the University of Toronto and The Hospital for Sick Children.
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R.K.C.Y. and S.W.S. conceived and designed the experiments. R.K.C.Y., D.M., M.B., B.T., R.V.P., J. Whitney, N.D., J. Bingham, Z.W., S.W. and G.P. processed and analyzed the whole genome sequencing data. S.W., L.D., A.J.S.C., S.K., T.P., E.J.H. and S.L. designed and performed experiments for variant characterization and validation. J.A.B., C.R.M., M.U., M.Z., E.D., S.L.P., W.E., K.H., W.L., J.R.M., T.N., W.W.L.S., F.J.T., J. Wei, L.X., W.V.E., S.T., B.J.F., J.T.R. and L.J.S. helped perform different components of analysis and validation experiments. R.K.C.Y., M.B., J.L.H., R.H.R., D.G., M.T.P. and S.W.S. coordinated the whole genome sequencing experiments. R.K.C.Y., R.H.R., D.G., M.T.P. and S.W.S. conceived and coordinated the project. N.H., A.-M.T., E.K., W.R., I.D., S.J., B.M.M., B.K., M.S., C. Cytrynbaum, R.W., L.Z., M.W.-S., J. Brian, L.S., A.I., K.D.-T., A.T., C. Chrysler, J.L., T.S.-L., I.M.S., X.L., R.N., V.S., A.F., E.H.C., S.D., A.E., L.G., B.A.M., J.R.P., S.J.S., J.V., B.A.F., M.E., M.T.C., J.H., B.M.K., E.A. and P.S. managed, recruited, diagnosed and examined the recruited participants. R.K.C.Y. and S.W.S. wrote the manuscript.
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Integrated supplementary information
Supplementary Figure 1 Ethnicity inference from whole genome sequencing.
(a) Principle component analysis with HapMap samples using PLINK in two dimensions. (b) Principle component analysis with HapMap samples using PLINK in three dimensions.
Supplementary Figure 2 Pedigrees of families with mutations in putative novel ASD-risk genes.
Families exhibiting loss-of-function or de novo missense mutations in (a) MED3, (b) PHF3, (c) PER2 and (d) HECTD4 are shown. The de novo or inherited variant alleles are shown below each family member. ‘‘+’’ indicates the allele containing the reference (presumably wild-type) sequence. Males are denoted by squares and females by circles. Symbol with dash line indicates that the sample was not whole-genome sequenced. NA indicates that no DNA sample was available for testing. Black symbols indicate individuals diagnosed with ASD. Arrows pointing to the symbols indicate ASD probands in each family.
Supplementary Figure 3 Screen captures of MSSNG portal.
(a) Variant search interface. (b) Example of variant search results. (c) Example of gene info search results. (d) Example of read depth search results.
Supplementary Figure 4 Distribution of de novo mutation detection by platforms.
Fraction of samples in different number of de novo mutations detected by Complete Genomics (CG) and Illumina (ILNM) are shown.
Supplementary information
Supplementary Text and Figures
Supplementary Figures 1–4, Supplementary note (PDF 3396 kb)
Supplementary Table 1
Quality of WGS. (XLSX 914 kb)
Supplementary Table 2
Number of de novo SNVs and indels. (XLSX 72 kb)
Supplementary Table 3
All de novo variants detected. (XLSX 7305 kb)
Supplementary Table 4
All de novo LOF variants detected. (XLSX 36 kb)
Supplementary Table 5
All damaging variants in ASD-risk genes. (XLSX 25 kb)
Supplementary Table 6
Genes associated with syndromic or related disorders and their potential drug targets (XLSX 14 kb)
Supplementary Table 7
Summary of all samples included in MSSNG DB4. (XLSX 168 kb)
Supplementary Table 8
Pathogenic CNVs detected. (XLSX 27 kb)
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C Yuen, R., Merico, D., Bookman, M. et al. Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. Nat Neurosci 20, 602–611 (2017). https://doi.org/10.1038/nn.4524
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DOI: https://doi.org/10.1038/nn.4524
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