Cited by 302Autism Spectrum Disorder ResearchGenetic Associations and EpidemiologyGenomics and Rare Diseases

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An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

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Werling, Donna M., Brand, Harrison, An, Joon-Yong, Stone, Matthew R., Zhu, Lingxue, Glessner, Joseph T., Collins, Ryan L., Dong, Shan, Layer, Ryan M., Markenscoff-Papadimitriou, Eirene, Farrell, Andrew, Schwartz, Grace B., Wang, Harold Z., Currall, Benjamin B., Zhao, Xuefang, Dea, Jeanselle, Duhn, Clif, Erdman, Carolyn A., Gilson, Michael C., Yadav, Rachita, Handsaker, Robert E., Kashin, Seva, Klei, Lambertus, Mandell, Jeffrey D., Nowakowski, Tomasz J., Liu, Yuwen, Pochareddy, Sirisha, Smith, Louw, Walker, Michael F., Waterman, Matthew J., He, Xin, Kriegstein, Arnold R., Rubenstein, John L., Sestan, Nenad, McCarroll, Steven A., Neale, Benjamin M., Coon, Hilary, Willsey, A. Jeremy, Buxbaum, Joseph D., Daly, Mark J., State, Matthew W., Quinlan, Aaron R., Marth, Gabor T., Roeder, Kathryn, Devlin, Bernie, Talkowski, Michael E., Sanders, Stephan J.·2018·Nature Genetics

DOI 10.1038/s41588-018-0107-yPMC PMC5961723

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Abstract

Genomic association studies of common or rare protein-coding variation have established robust statistical approaches to account for multiple testing. Here we present a comparable framework to evaluate rare and de novo noncoding single-nucleotide variants, insertion/deletions, and all classes of structural variation from whole-genome sequencing (WGS). Integrating genomic annotations at the level of nucleotides, genes, and regulatory regions, we define 51,801 annotation categories. Analyses of 519 autism spectrum disorder families did not identify association with any categories after correction for 4,123 effective tests. Without appropriate correction, biologically plausible associations are observed in both cases and controls. Despite excluding previously identified gene-disrupting mutations, coding regions still exhibited the strongest associations. Thus, in autism, the contribution of de novo noncoding variation is probably modest in comparison to that of de novo coding variants. Robust results from future WGS studies will require large cohorts and comprehensive analytical strategies that consider the substantial multiple-testing burden.

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Additional file 1 of Whole genome sequencing analysis identifies sex differences of familial pattern contributing to phenotypic diversity in autism
Kim, S.-W., Lee, H., Song, D. Y., Lee, G. Q., Ji, J., Park, J. W., Han, J. H., Lee, J. W., Byun, H. J., Son, J. H., et al. (2024) · Figshare · doi:10.6084/m9.figshare.27124213
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Authors: Werling, D. M., Brand, H., An, J.-Y., Stone, M. R., Zhu, L., Glessner, J. T., Collins, R. L., Dong, S., Layer, R. M., Markenscoff-Papadimitriou, E., Farrell, A., Schwartz, G. B., Wang, H. Z., Currall, B. B., Zhao, X., Dea, J., Duhn, C., Erdman, C. A., Gilson, M. C., Yadav, R., Handsaker, R. E., Kashin, S., Klei, L., Mandell, J. D., Nowakowski, T. J., Liu, Y., Pochareddy, S., Smith, L., Walker, M. F., Waterman, M. J., He, X., Kriegstein, A. R., Rubenstein, J. L., Sestan, N., McCarroll, S. A., Neale, B. M., Coon, H., Willsey, A. J., Buxbaum, J. D., Daly, M. J., State, M. W., Quinlan, A. R., Marth, G. T., Roeder, K., Devlin, B., Talkowski, M. E., & Sanders, S. J.
Affiliations: University of California, San Francisco (US)
Broad Institute (US)
Massachusetts General Hospital (US)
Carnegie Mellon University (US)
Harvard University (US)
University of Utah (US)
University of Pittsburgh (US)
University of Chicago (US)
Yale University (US)
Eastern Nazarene College (US)
Icahn School of Medicine at Mount Sinai (US)
Corresponding author: Devlin, Bernie
Talkowski, Michael E.
Sanders, Stephan J.
ORCID: Werling, Donna M.
Brand, Harrison
An, Joon-Yong
Stone, Matthew R.
Zhu, Lingxue
Glessner, Joseph T.
Collins, Ryan L.
Dong, Shan
Layer, Ryan M.
Markenscoff-Papadimitriou, Eirene
Farrell, Andrew
Schwartz, Grace B.
Currall, Benjamin B.
Zhao, Xuefang
Dea, Jeanselle
Duhn, Clif
Gilson, Michael C.
Yadav, Rachita
Handsaker, Robert E.
Kashin, Seva
Klei, Lambertus
Mandell, Jeffrey D.
Nowakowski, Tomasz J.
Liu, Yuwen
Pochareddy, Sirisha
He, Xin
Kriegstein, Arnold R.
Rubenstein, John L.
Sestan, Nenad
McCarroll, Steven A.
Neale, Benjamin M.
Coon, Hilary
Willsey, A. Jeremy
Buxbaum, Joseph D.
Daly, Mark J.
State, Matthew W.
Quinlan, Aaron R.
Marth, Gabor T.
Roeder, Kathryn
Devlin, Bernie
Talkowski, Michael E.
Sanders, Stephan J.
Venue: Nature Genetics
Publisher: Springer Science and Business Media LLC
Published: 2018-04-26
Volume: 50
Issue: 5
Pages: 727-736
ISSN: 1061-4036 (ISSN-L)
1546-1718
DOI: 10.1038/s41588-018-0107-y
PMC: PMC5961723
OpenAlex: W2799448805
Cited by: 293
References: 81
Citations by year: 2026: 11 · 2025: 27 · 2024: 21 · 2023: 40 · 2022: 42 · 2021: 52 · 2020: 40 · 2019: 40 · 2018: 20
FWCI: 22.78
Type: journal article
Language: en
Open access: green
europepmc.org
Licence: www.springer.com/tdm (tdm)
Locations: Nature Genetics (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
eScholarship (California Digital Library) (submittedVersion)
Funders: March of Dimes Foundation
Simons Foundation Autism Research Initiative
National Institutes of Health (388196, GM061354, HD081256)
National Institute of Mental Health (U01MH111661, U01MH100229, R01MH109900, R01MH109904, U01MH111658, R01MH109901, R37MH057881, U01MH100239, U01MH111662, U01MH111660, R01MH110928, U01MH105575)
National Institute of General Medical Sciences (P01GM061354)
National Institute of Neurological Disorders and Stroke (R35NS097305)
National Institute of Dental and Craniofacial Research (K99DE026824)
Eunice Kennedy Shriver National Institute of Child Health and Human Development (R01HD081256)
Topics: Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
Keywords: autism spectrum disorder, whole genome sequencing, de novo mutations, structural variants, insertion-deletion variants, multiple testing correction, genome annotation, regulatory elements, statistical power
MeSH terms: Autism Spectrum Disorder, Female, Humans, Male, Genome, Genetic Predisposition to Disease, Protein Isoforms, Polymorphism, Single Nucleotide, INDEL Mutation, Genome-Wide Association Study

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An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

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