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Replication of a rare risk haplotype on 1p36.33 for autism spectrum disorder

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Abstract

Hundreds of genes have been implicated in autism spectrum disorders (ASDs). In genetically heterogeneous conditions, large families with multiple affected individuals provide strong evidence implicating a rare variant, and replication of the same variant in multiple families is unusual. We previously published linkage analyses and follow-up exome sequencing in seven large families with ASDs, implicating 14 rare exome variants. These included rs200195897, which was transmitted to four affected individuals in one family. We attempted replication of those variants in the MSSNG database. MSSNG is a unique resource for replication of ASD risk loci, containing whole genome sequence (WGS) on thousands of individuals diagnosed with ASDs and family members. For each exome variant, we obtained all carriers and their relatives in MSSNG, using a TDT test to quantify evidence for transmission and association. We replicated the transmission of rs200195897 to four affected individuals in three additional families. rs200195897 was also present in three singleton affected individuals, and no unaffected individuals other than transmitting parents. We identified two additional rare variants (rs566472488 and rs185038034) transmitted with rs200195897 on 1p36.33. Sanger sequencing confirmed the presence of these variants in the original family segregating rs200195897. To our knowledge, this is the first example of a rare haplotype being transmitted with ASD in multiple families. The candidate risk variants include a missense mutation in SAMD11, an intronic variant in NOC2L, and a regulatory region variant close to both genes. NOC2L is a transcription repressor, and several genes involved in transcription regulation have been previously associated with ASDs.

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Acknowledgements

This study was supported by National Institute of Mental Health Grant R01MH094293. We greatly appreciate the time and effort given by the family members who participated in both our local study and the MSSNG database. The authors also wish to acknowledge the resources of MSSNG (http://www.mss.ng), Autism Speaks and The Centre for Applied Genomics at The Hospital for Sick Children, Toronto, Canada. We thank the donors who supported this program for their generosity.

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Authors and Affiliations

  1. Division of Medical Genetics, Department of Medicine, University of Washington, Box 359460, Seattle, WA, 98195, USA

    N. H. Chapman, E. M. Blue, W. H. Raskind & Ellen M. Wijsman

  2. Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA, 98195, USA

    R. A. Bernier, S. J. Webb, J. Munson & W. H. Raskind

  3. Center on Human Development and Disability, University of Washington, Seattle, WA, 98195, USA

    R. A. Bernier, S. J. Webb & J. Munson

  4. Department of Neurology, University of Washington, Seattle, WA, 98195, USA

    D.-H. Chen & E. Heigham

  5. Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA

    W. H. Raskind & Ellen M. Wijsman

  6. Department of Biostatistics, University of Washington, Seattle, WA, 98195, USA

    Ellen M. Wijsman

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  1. N. H. Chapman
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  2. R. A. Bernier
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  4. J. Munson
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  5. E. M. Blue
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  6. D.-H. Chen
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  7. E. Heigham
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  8. W. H. Raskind
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  9. Ellen M. Wijsman
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Correspondence to Ellen M. Wijsman.

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439_2018_1939_MOESM1_ESM.doc

Tables S1, S2 and S3 show Vineland Adaptive Behavior Scales II scores, Adaptive Behavior Assessment System II scores and Social Responsiveness Scale 2 scores, respectively, for affected individuals where available (DOC 26 KB)

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Chapman, N.H., Bernier, R.A., Webb, S.J. et al. Replication of a rare risk haplotype on 1p36.33 for autism spectrum disorder. Hum Genet 137, 807–815 (2018). https://doi.org/10.1007/s00439-018-1939-3

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  • DOI: https://doi.org/10.1007/s00439-018-1939-3

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