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Recent ultra-rare inherited variants implicate new autism candidate risk genes

Nature Genetics volume 53, pages 1125–1134 (2021)Cite this article

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Abstract

Autism is a highly heritable complex disorder in which de novo mutation (DNM) variation contributes significantly to risk. Using whole-genome sequencing data from 3,474 families, we investigate another source of large-effect risk variation, ultra-rare variants. We report and replicate a transmission disequilibrium of private, likely gene-disruptive (LGD) variants in probands but find that 95% of this burden resides outside of known DNM-enriched genes. This variant class more strongly affects multiplex family probands and supports a multi-hit model for autism. Candidate genes with private LGD variants preferentially transmitted to probands converge on the E3 ubiquitin–protein ligase complex, intracellular transport and Erb signaling protein networks. We estimate that these variants are approximately 2.5 generations old and significantly younger than other variants of similar type and frequency in siblings. Overall, private LGD variants are under strong purifying selection and appear to act on a distinct set of genes not yet associated with autism.

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Fig. 1: Overview of private variants in the discovery cohort.
Fig. 2: Burden of private LGD variants in affected children.
Fig. 3: Genetic properties of inherited LGD variant burden.
Fig. 4: PPI network for autism candidate genes.
Fig. 5: Estimate of allele age.

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Data availability

The WGS data used in this study are available from the following resources. The AGRE study is available at the Database of Genotypes and Phenotypes (dbGaP) under accession no. phs001766. Access to the AGRE WGS data is subject to approval by Autism Speaks and AGRE. All sequencing and phenotype data for the SSC are available through SFARI and are available to approved researchers at SFARI Base (accession nos. SFARI_SSC_WGS_p, SFARI_SSC_WGS_1 and SFARI_SSC_WGS_2). The genomic and phenotypic data for the SPARK study are available by request from SFARI Base (accession no. SFARI_SPARK_WES_1). Data from the SAGE study are available at the dbGaP under accession no. phs001740.v1.p1. Data from the TASC study are available at dbGaP under accession no. phs001741. Family-level FreeBayes and GATK VCF files for SAGE, SSC and TASC are available under dbGaP accession no. phs001874.v1.p1 and at SFARI Base under accession no. SFARI_SSC_WGS_2a.

Code availability

All software used in this study is publicly available. The code for the ultra-rare transmitted variant pipeline can be found at https://github.com/EichlerLab/ultra_rare_transmitted.git. The code for the figures and analyses are available upon request.

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Acknowledgements

We thank T. Brown for assistance in editing this manuscript and S. Stray, M. Eng, J. Moore, H. Kortbawi and A. Thornton from the laboratory of Mary-Claire King for the isolation of DNA from whole blood. We thank T. Maniatis and the New York Genome Center for conducting the sequencing and initial quality control. We thank all the families at the participating SSC sites, as well as the principal investigators (A. Beaudet, R. Bernier, J. Constantino, E. Cook, E. Fombonne, D. Geschwind, R. Goin-Kochel, E. Hanson, D. Grice, A. Klin, D. Ledbetter, C. Lord, C. Martin, D. Martin, R. Maxim, J. Miles, O. Ousley, K. Pelphrey, B. Peterson, J. Piggot, C. Saulnier, M. State, W. Stone, J. Sutcliffe, C. Walsh, Z. Warren and E. Wijsman). We thank all the families in SPARK, the SPARK clinical sites and SPARK staff. We appreciate obtaining access to the phenotypic and genetic data on SFARI Base. Approved researchers can obtain the SSC population dataset described in this study (https://www.sfari.org/resource/simons-simplex-collection/) and the SPARK population dataset described in this study (https://www.sfari.org/resource/spark/) by applying at https://base.sfari.org. We gratefully acknowledge the resources provided by the AGRE Consortium and the participating AGRE families. Genomic data for the AGRE cohort was provided by iHART, an initiative led by the Hartwell Foundation and directed by D. Wall and D. Geschwind. This work was supported, in part, by grants from the National Institutes of Health (no. R01 MH101221 to E.E.E.; no. R01 MH100047 to R.A.B.; no. K99 MH117165 to T.N.T.; no. K99 HG011041 to P.H.; and no. UM1 HG008901 to M.C.Z.) and the Simons Foundation (no. SFARI 608045 to E.E.E.). The CCDG is funded by the National Human Genome Research Institute and the National Heart, Lung, and Blood Institute. The Genome Sequencing Program Coordinating Center (no. U24 HG008956) contributed to cross-program scientific initiatives and provided logistical and general study coordination. AGRE is a program of Autism Speaks and is supported in part by grant no. 1U24MH081810 from the National Institute of Mental Health to C. M. Lajonchere. E.E.E. is an investigator of the Howard Hughes Medical Institute.

Author information

Author notes

  1. Tychele N. Turner

    Present address: Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA

Authors and Affiliations

  1. Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA

    Amy B. Wilfert, Tychele N. Turner, Shwetha C. Murali, PingHsun Hsieh, Arvis Sulovari, Tianyun Wang, Bradley P. Coe, Hui Guo, Kendra Hoekzema, William Harvey & Evan E. Eichler

  2. Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA

    Shwetha C. Murali & Evan E. Eichler

  3. Center for Medical Genetic & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, China

    Hui Guo

  4. Allen Institute for Brain Science, Seattle, WA, USA

    Trygve E. Bakken

  5. New York Genome Center, New York, NY, USA

    Lara H. Winterkorn, Uday S. Evani, Marta Byrska-Bishop & Michael C. Zody

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

    Rachel K. Earl & Raphael A. Bernier

  7. Department of Systems Biology, Columbia University, New York, NY, USA

    Xueya Zhou, Chang Shu, Joseph Obiajulu & Yufeng Shen

  8. Department of Pediatrics, Columbia Medical Center, New York, NY, USA

    Xueya Zhou, Chang Shu, Joseph Obiajulu & Wendy K. Chung

  9. Simons Foundation, New York, NY, USA

    Pamela Feliciano, Jacob Hall, Irina Astrovskaya, Simon Xu, Jessica Wright, Olena Marchenko, Chris Fleisch, LeeAnne Green Snyder, Sarah D. Barns, Bing Han, Natalia Volfovsky & Wendy K. Chung

  10. Department of Psychiatry, University of Iowa Carver College of Medicine, Iowa City, IA, USA

    Leo Brueggeman & Jacob Michaelson

  11. Program in Neurogenetics, David Geffen School of Medicine, Los Angeles, CA, USA

    Timothy S. Chang & Daniel Geschwind

  12. Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA

    Timothy S. Chang & Daniel Geschwind

  13. Department of Molecular & Medical Genetics, Oregon Health & Science University, Portland, OR, USA

    Andrew Nishida & Brian J. O’Roak

  14. Division of Genetics and Genomics, Boston Children’s Hospital, Boston, MA, USA

    Ryan Doan, Aubrey Soucy & Timothy W. Yu

  15. Department of Pediatrics, Harvard Medical School, Boston, MA, USA

    Ryan Doan, Aubrey Soucy & Timothy W. Yu

  16. The Broad Institute, Cambridge, MA, USA

    Timothy W. Yu

  17. Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA

    Daniel Geschwind

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  1. Amy B. Wilfert
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  2. Tychele N. Turner
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  3. Shwetha C. Murali
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  17. Evan E. Eichler
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Consortia

The SPARK Consortium

  • Xueya Zhou
  • , Tianyun Wang
  • , Pamela Feliciano
  • , Jacob Hall
  • , Irina Astrovskaya
  • , Shwetha C. Murali
  • , Simon Xu
  • , Chang Shu
  • , Joseph Obiajulu
  • , Leo Brueggeman
  • , Jessica Wright
  • , Olena Marchenko
  • , Chris Fleisch
  • , Timothy S. Chang
  • , LeeAnne Green Snyder
  • , Sarah D. Barns
  • , Tychele N. Turner
  • , Bing Han
  • , William Harvey
  • , Andrew Nishida
  • , Ryan Doan
  • , Aubrey Soucy
  • , Brian J. O’Roak
  • , Timothy W. Yu
  • , Daniel Geschwind
  • , Jacob Michaelson
  • , Natalia Volfovsky
  • , Evan E. Eichler
  • , Yufeng Shen
  •  & Wendy K. Chung

Contributions

A.B.W. and E.E.E. designed and conceived the study. L.H.W. and M.C.Z. coordinated the sampling and sequencing for the CCDG cohorts. The SPARK Consortium coordinated the samples and sequencing for the SPARK cohort. A.B.W., T.N.T., S.C.M., A.S., T.W., B.P.C., U.S.E., M.B.-B. and H.G. called the variants and ran the quality control. K.H. performed the Sanger validations. A.B.W., T.N.T., S.C.M., P.H., A.S. and T.W. conducted the analyses and data interpretation. T.E.B. and A.B.W. performed the gene expression analyses. A.B.W., R.A.B. and R.K.E. performed the phenotypic analyses. A.B.W. and E.E.E. wrote the manuscript with input from coauthors.

Corresponding author

Correspondence to Evan E. Eichler.

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Competing interests

The authors declare no competing interests.

Additional information

Peer review information Nature Genetics thanks Anders Børglum, Thomas Bourgeron and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Supplementary information

Supplementary Information

Supplementary Note and Figs. 1–24

Reporting Summary

Supplementary Tables

Supplementary Tables 1–22

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Wilfert, A.B., Turner, T.N., Murali, S.C. et al. Recent ultra-rare inherited variants implicate new autism candidate risk genes. Nat Genet 53, 1125–1134 (2021). https://doi.org/10.1038/s41588-021-00899-8

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