To maximize the discovery of potentially pathogenic variants to better understand the diagnostic utility of genome sequencing (GS) and to assess how the presence of multiple risk events might affect the phenotypic severity in autism spectrum disorders (ASD).


GS was applied to 180 simplex and multiplex ASD families (578 individuals, 213 patients) with exome sequencing and array comparative genomic hybridization further applied to a subset for validation and cross-platform comparisons.


We found that 40.8% of patients carried variants with evidence of disease risk, including a de novo frameshift variant in NR4A2 and two de novo missense variants in SYNCRIP, while 21.1% carried clinically relevant pathogenic or likely pathogenic variants. Patients with more than one risk variant (9.9%) were more severely affected with respect to cognitive ability compared with patients with a single or no-risk variant. We observed no instance among the 27 multiplex families where a pathogenic or likely pathogenic variant was transmitted to all affected members in the family.


The study demonstrates the diagnostic utility of GS, especially for multiple risk variants that contribute to the phenotypic severity, shows the genetic heterogeneity in multiplex families, and provides evidence for new genes for follow up.

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Data availability

The SAGE genome sequencing data is available at the database of Genotypes and Phenotypes (dbGaP) under accession: phs001740.v1.p1.


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We thank Sunday Stray, Mary Eng, James Moore, Hannah Kortbawi and Anne Thornton from the laboratory of Mary-Claire King for isolation of DNA from whole blood and Tonia Brown for manuscript editing. We are especially grateful to the families who participated in the SAGE study. This work was supported by the following grants: the Simons Foundation Autism Research Initiative (SFARI 303241) and National Institutes of Health (NIH R01MH101221) to E.E.E., NIH (R01MH100047) to R.A.B., and NIH (1K99MH117165) to T.N.T. This work was also supported by the NYGC CCDG (UM1HG008901) and the Genome Sequencing Program (GSP) Coordinating Center (U24HG008956). The CCDG is funded by the National Human Genome Research Institute and the National Heart, Lung, and Blood Institute. The GSP Coordinating Center contributed to cross-program scientific initiatives and provided logistical and general study coordination. Exome sequencing was provided by the University of Washington Center for Mendelian Genomics (UW-CMG) and was funded by NHGRI and NHLBI grants UM1 HG006493 and U24 HG008956. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. E.E.E. is an investigator of the Howard Hughes Medical Institute.

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Author notes

  1. These authors contributed equally: Hui Guo and Michael H. Duyzend


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

    • Hui Guo PhD
    • , Michael H. Duyzend PhD
    • , Bradley P. Coe PhD
    • , Carl Baker BSc
    • , Kendra Hoekzema MSc
    • , Tychele N. Turner PhD
    • , Shwetha C. Murali MSc
    • , Bradley J. Nelson MSc
    • , Deborah A. Nickerson PhD
    •  & Evan E. Eichler PhD
  2. Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China

    • Hui Guo PhD
  3. Department of Psychiatry, University of Washington, Seattle, WA, USA

    • Jennifer Gerdts PhD
    • , Jennifer S. Beighley PhD
    •  & Raphael A. Bernier PhD
  4. New York Genome Center (NYGC), New York, NY, USA

    • Michael C. Zody PhD
  5. Department of Pediatrics, University of Washington School of Medicine, Seattle, WA, USA

    • Michael J. Bamshad MD
  6. Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA

    • Evan E. Eichler PhD


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  1. University of Washington Center for Mendelian Genomics


    E.E.E. is on the scientific advisory board (SAB) of DNAnexus, Inc. The other authors declare no conflicts of interest.

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    Correspondence to Evan E. Eichler PhD.

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