Subjects

Abstract

Purpose

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).

Methods

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.

Results

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.

Conclusion

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.

References

  1. 1.

    Lelieveld SH, Reijnders MR, Pfundt R, et al. Meta-analysis of 2,104 trios provides support for 10 new genes for intellectual disability. Nat Neurosci. 2016;19:1194–1196.

  2. 2.

    Deciphering Developmental Disorders Study. Prevalence and architecture of de novo mutations in developmental disorders. Nature. 2017;542:433–438.

  3. 3.

    Iossifov I, O’Roak BJ, Sanders SJ, et al. The contribution of de novo coding mutations to autism spectrum disorder. Nature. 2014;515:216–221.

  4. 4.

    De Rubeis S, He X, Goldberg AP, et al. Synaptic, transcriptional and chromatin genes disrupted in autism. Nature. 2014;515:209–215.

  5. 5.

    Coe BP, Stessman HAF, Sulovari A, et al. Neurodevelopmental disease genes implicated by de novo mutation and CNV morbidity. Nat Genet (in press).

  6. 6.

    Fischbach GD, Lord C. The Simons Simplex Collection: a resource for identification of autism genetic risk factors. Neuron. 2010;68:192–195.

  7. 7.

    Sanders SJ, He X, Willsey AJ, et al. Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci. Neuron. 2015;87:1215–1233.

  8. 8.

    Turner TN, Coe BP, Dickel DE, et al. Genomic patterns of de novo mutation in simplex autism. Cell. 2017;171:710–22 e712.

  9. 9.

    RK CY, Merico D, Bookman M, et al. Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder. Nat Neurosci. 2017;20:602–611.

  10. 10.

    Krumm N, Turner TN, Baker C, et al. Excess of rare, inherited truncating mutations in autism. Nat Genet. 2015;47:582–588.

  11. 11.

    Hallmayer J, Cleveland S, Torres A, et al. Genetic heritability and shared environmental factors among twin pairs with autism. JAMA Psychiatry. 2011;68:1095–1102.

  12. 12.

    Turner TN, Hormozdiari F, Duyzend MH, et al. Genome sequencing of autism-affected families reveals disruption of putative noncoding regulatory DNA. Am J Hum Genet. 2016;98:58–74.

  13. 13.

    Schaaf CP, Sabo A, Sakai Y, et al. Oligogenic heterozygosity in individuals with high-functioning autism spectrum disorders. Hum Mol Genet. 2011;20:3366–3375.

  14. 14.

    Girirajan S, Rosenfeld JA, Cooper GM, et al. A recurrent 16p12.1 microdeletion supports a two-hit model for severe developmental delay. Nat Genet. 2010;42:203–209.

  15. 15.

    Yuen RK, Thiruvahindrapuram B, Merico D, et al. Whole-genome sequencing of quartet families with autism spectrum disorder. Nat Med. 2015;21:185–191.

  16. 16.

    Regier AA, Farjoun Y, Larson D, et al. Functional equivalence of genome sequencing analysis pipelines enables harmonized variant calling across human genetics projects. Nat Commun. 2018;9:4038.

  17. 17.

    Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–595.

  18. 18.

    McKenna A, Hanna M, Banks E, et al. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20:1297–1303.

  19. 19.

    Manichaikul A, Mychaleckyj JC, Rich SS, Daly K, Sale M, Chen WM. Robust relationship inference in genome-wide association studies. Bioinformatics. 2010;26:2867–2873.

  20. 20.

    Sudmant PH, Kitzman JO, Antonacci F, et al. Diversity of human copy number variation and multicopy genes. Science. 2010;330:641–646.

  21. 21.

    Handsaker RE, Korn JM, Nemesh J, McCarroll SA. Discovery and genotyping of genome structural polymorphism by sequencing on a population scale. Nat Genet. 2011;43:269–276.

  22. 22.

    Layer RM, Chiang C, Quinlan AR, Hall IM. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 2014;15:R84.

  23. 23.

    Kronenberg ZN, Osborne EJ, Cone KR, et al. Wham: identifying structural variants of biological consequence. PLoS Comput Biol. 2015;11:e1004572.

  24. 24.

    Abyzov A, Urban AE, Snyder M, Gerstein M. CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing. Genome Res. 2011;21:974–984.

  25. 25.

    Rausch T, Zichner T, Schlattl A, Stutz AM, Benes V, Korbel JO. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics. 2012;28:i333–i339.

  26. 26.

    Lu HC, Tan Q, Rousseaux MW, et al. Disruption of the ATXN1-CIC complex causes a spectrum of neurobehavioral phenotypes in mice and humans. Nat Genet. 2017;49:527–536.

  27. 27.

    Richards S, Aziz N, Bale S, et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015;17:405–424.

  28. 28.

    Turner TN, Yi Q, Krumm N, et al. denovo-db: a compendium of human de novo variants. Nucleic Acids Res. 2017;45:D804–D811.

  29. 29.

    Lopez E, Berenguer M, Tingaud-Sequeira A, et al. Mutations in MYT1, encoding the myelin transcription factor 1, are a rare cause of OAVS. J Med Genet. 2016;53:752–760.

  30. 30.

    Kearney HM, Thorland EC, Brown KK, Quintero-Rivera F, South ST, Working Group of the American College of Medical Genetics Laboratory Quality Assurance Committee. American College of Medical Genetics standards and guidelines for interpretation and reporting of postnatal constitutional copy number variants. Genet Med. 2011;13:680–685.

  31. 31.

    Guo H, Peng Y, Hu Z, et al. Genome-wide copy number variation analysis in a Chinese autism spectrum disorder cohort. Sci Rep. 2017;7:44155.

  32. 32.

    Leppa VM, Kravitz SN, Martin CL, et al. Rare inherited and de novo CNVs reveal complex contributions to ASD risk in multiplex families. Am J Hum Genet. 2016;99:540–554.

  33. 33.

    Joseph B, Wallen-Mackenzie A, Benoit G, et al. p57(Kip2) cooperates with Nurr1 in developing dopamine cells. Proc Natl Acad Sci U S A. 2003;100:15619–15624.

  34. 34.

    Levy J, Grotto S, Mignot C, et al. NR4A2 haploinsufficiency is associated with intellectual disability and autism spectrum disorder. Clin Genet. 2018;94:264–268.

  35. 35.

    Bannai H, Fukatsu K, Mizutani A, et al. An RNA-interacting protein, SYNCRIP (heterogeneous nuclear ribonuclear protein Q1/NSAP1) is a component of mRNA granule transported with inositol 1,4,5-trisphosphate receptor type 1 mRNA in neuronal dendrites. J Biol Chem. 2004;279:53427–53434.

  36. 36.

    Yang CP, Samuels TJ, Huang Y, et al. Imp and Syp RNA-binding proteins govern decommissioning of Drosophila neural stem cells. Development. 2017;144:3454–3464.

  37. 37.

    Chen DT, Jiang X, Akula N, et al. Genome-wide association study meta-analysis of European and Asian-ancestry samples identifies three novel loci associated with bipolar disorder. Mol Psychiatry. 2013;18:195–205.

  38. 38.

    Ikeda M, Takahashi A, Kamatani Y, et al. A genome-wide association study identifies two novel susceptibility loci and trans population polygenicity associated with bipolar disorder. Mol Psychiatry. 2017;23:639–647.

  39. 39.

    Weiner DJ, Wigdor EM, Ripke S, et al. Polygenic transmission disequilibrium confirms that common and rare variation act additively to create risk for autism spectrum disorders. Nat Genet. 2017;49:978–985.

  40. 40.

    Mek N, Martin HC, Rice DL, et al. Common genetic variants contribute to risk of rare severe neurodevelopmental disorders. Nature. 2018;562:268–271.

  41. 41.

    Geisheker MR, Heymann G, Wang T, et al. Hotspots of missense mutation identify neurodevelopmental disorder genes and functional domains. Nat Neurosci. 2017;20:1043–1051.

  42. 42.

    Gilissen C, Hehir-Kwa JY, Thung DT, et al. Genome sequencing identifies major causes of severe intellectual disability. Nature. 2014;511:344–347.

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Acknowledgements

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.

Author information

Author notes

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

Affiliations

  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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Consortia

  1. University of Washington Center for Mendelian Genomics

    Disclosure

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

    Corresponding author

    Correspondence to Evan E. Eichler PhD.

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    DOI

    https://doi.org/10.1038/s41436-018-0380-2