Genome-wide characteristics of de novo mutations in autism
Open accessAbstract
De novo mutations (DNMs) are important in autism spectrum disorder (ASD), but so far analyses have mainly been on the ~1.5% of the genome encoding genes. Here, we performed whole-genome sequencing (WGS) of 200 ASD parent–child trios and characterised germline and somatic DNMs. We confirmed that the majority of germline DNMs (75.6%) originated from the father, and these increased significantly with paternal age only (P=4.2×10−10). However, when clustered DNMs (those within 20 kb) were found in ASD, not only did they mostly originate from the mother (P=7.7×10−13), but they could also be found adjacent to de novo copy number variations where the mutation rate was significantly elevated (P=2.4×10−24). By comparing with DNMs detected in controls, we found a significant enrichment of predicted damaging DNMs in ASD cases (P=8.0×10−9; odds ratio=1.84), of which 15.6% (P=4.3×10−3) and 22.5% (P=7.0×10−5) were non-coding or genic non-coding, respectively. The non-coding elements most enriched for DNM were untranslated regions of genes, regulatory sequences involved in exon-skipping and DNase I hypersensitive regions. Using microarrays and a novel outlier detection test, we also found aberrant methylation profiles in 2/185 (1.1%) of ASD cases. These same individuals carried independently identified DNMs in the ASD-risk and epigenetic genes DNMT3A and ADNP. Our data begins to characterize different genome-wide DNMs, and highlight the contribution of non-coding variants, to the aetiology of ASD.
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ASD individuals have two- to three-fold more rare CNVs and de novo loss-of-function variants than unaffected siblings.
“individuals with ASD have a two- to three-fold increase in the number of rare copy number variations (CNVs) and de novo loss-of-function (nonsense, frameshift, and splice site) variants compared to their unaffected siblings11–14.”
From Genome-wide detection of tandem DNA repeats that are expanded in autism (2020) · cites this paper as [14]
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Li, J., Wang, L., Yu, P., Shi, L., Zhang, K., Sun, Z. S., & Xia, K. (2017) · American Journal of Medical Genetics Part B Neuropsychiatric Genetics · doi:10.1002/ajmg.b.32543 · Cited by 22 · see citing works
Bio-collections in autism research
Reilly, J., Gallagher, L., Chen, J. L., Leader, G., & Shen, S. (2017) · Molecular Autism · doi:10.1186/s13229-017-0154-8 · Cited by 23 · see citing works
APOBEC3A/B-induced mutagenesis is responsible for 20% of heritable mutations in the TpCpW contextPreprint
Seplyarskiy, V. B., Andrianova, M. A., & Bazykin, G. A. (2016) · Genome Research · doi:10.1101/gr.210336.116 · Cited by 22 · see citing works
Ambrozkiewicz, M. C., Cuthill, K. J., Harnett, D., Kawabe, H., & Tarabykin, V. S. (2020) · Cells · doi:10.3390/cells9112455 · Cited by 21 · see citing works
Unni, P. A., Friend, J., Weinberg, J., Okur, V., Hochscherf, J., & Dominguez, I. M. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.851547 · Cited by 21 · see citing works
Whole genome sequencing and mutation rate analysis of trios with paternal dioxin exposure
Tôn, N. Đ., Nakagawa, H., Hà, N. H., Dương, N. T., Vu, N. P., Hiền, L. T. T., Huệ, H. T. T., Hoàng, N. H., Wong, J. H., Nakano, K., et al. (2018) · Human Mutation · doi:10.1002/humu.23585 · Cited by 21 · see citing works
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- Authors
- Yuen, R. K., Merico, D., Cao, H., Pellecchia, G., Alipanahi, B., Thiruvahindrapuram, B., Tong, X., Sun, Y., Cao, D., Zhang, T., Wu, X., Jin, X., Zhou, Z., Liu, X., Nalpathamkalam, T., Walker, S., Howe, J. L., Wang, Z., MacDonald, J. R., Chan, A. J., D’Abate, L., Deneault, E., Siu, M. T., Tammimies, K., Uddin, M., Zarrei, M., Wang, M., Li, Y., Wang, J., Wang, J., Yang, H., Bookman, M., Bingham, J., Gross, S. S., Loy, D., Pletcher, M., Marshall, C. R., Anagnostou, E., Zwaigenbaum, L., Weksberg, R., Fernandez, B. A., Roberts, W., Szatmari, P., Glazer, D., Frey, B. J., Ring, R. H., Xu, X., & Scherer, S. W.
- Affiliations
- Hospital for Sick Children (CA)
- BGI Group (China) (CN)
- University of Toronto (CA)
- Karolinska Institutet (SE)
- Google (United States) (US)
- Autism Speaks (US)
- University of Alberta (CA)
- Memorial University of Newfoundland (CA)
- Corresponding author
- Scherer, Stephen W
- ORCID
- Yuen, Ryan KC
- Merico, Daniele
- Cao, Hongzhi
- Pellecchia, Giovanna
- Alipanahi, Babak
- Thiruvahindrapuram, Bhooma
- Tong, Xin
- Sun, Yuhui
- Cao, Dandan
- Zhang, Tao
- Jin, Xin
- Liu, Xiaomin
- Nalpathamkalam, Thomas
- Walker, Susan
- Wang, Zhuozhi
- MacDonald, Jeffrey R
- D’Abate, Lia
- Tammimies, Kristiina
- Uddin, Mohammed
- Wang, Mingbang
- Li, Yingrui
- Wang, Jun
- Wang, Jian
- Yang, Huanming
- Marshall, Christian R
- Anagnostou, Evdokia
- Zwaigenbaum, Lonnie
- Weksberg, Rosanna
- Fernandez, Bridget A
- Glazer, David
- Ring, Robert H
- Xu, Xun
- Scherer, Stephen W
- Venue
- npj Genomic Medicine
- Published
- 2016-08-03
- Volume
- 1
- Issue
- 1
- Pages
- 160271-1602710
- ISSN
- 2056-7944 (ISSN-L)
- PMC
- PMC4980121
- OpenAlex
- W2484001856
- Cited by
- 216
- References
- 70
- Citations by year
- 2026: 9 · 2025: 6 · 2024: 7 · 2023: 13 · 2022: 28 · 2021: 23 · 2020: 30 · 2019: 33 · 2018: 32 · 2017: 33 · 2016: 2
- FWCI
- 21.21
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- npj Genomic Medicine (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- Autism Speaks
- GlaxoSmithKline
- Genome Canada
- Ontario Brain Institute
- National Alliance for Research on Schizophrenia and Depression
- Stollery Children’s Hospital Foundation
- Children's Hospital Foundation
- Ontario Genomics
- Government of Ontario
- Ontario Genomics Institute
- Sick Kids Foundation
- University of Toronto
- Vetenskapsrådet
- Hospital for Sick Children
- U.S. Public Health Service (140849-1)
- Canadian Institutes of Health Research (140849_1)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Keywords
- de novo mutations, autism spectrum disorder, germline mutations, somatic mutations, paternal age, clustered mutations, copy number variation, non-coding variants, untranslated regions, exon skipping, DNA methylation, DNMT3A, ADNP, mutation rate
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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