Whole genome sequencing resource identifies 18 new candidate genes for autism spectrum disorder
Open accessAbstract
We are performing whole-genome sequencing of families with autism spectrum disorder (ASD) to build a resource (MSSNG) for subcategorizing the phenotypes and underlying genetic factors involved. Here we report sequencing of 5,205 samples from families with ASD, accompanied by clinical information, creating a database accessible on a cloud platform and through a controlled-access internet portal. We found an average of 73.8 de novo single nucleotide variants and 12.6 de novo insertions and deletions or copy number variations per ASD subject. We identified 18 new candidate ASD-risk genes and found that participants bearing mutations in susceptibility genes had significantly lower adaptive ability (P = 6 × 10-4). In 294 of 2,620 (11.2%) of ASD cases, a molecular basis could be determined and 7.2% of these carried copy number variations and/or chromosomal abnormalities, emphasizing the importance of detecting all forms of genetic variation as diagnostic and therapeutic targets in ASD.
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The DLX5/6-N-Haplotype frequency in the MSSNG database of ASDs families showed a nonsignificant association (P = 0.16) with ASD.
“we analyzed the DLX5/6-N-Haplotype frequency in the MSSNG database of ASDs families (Yuen et al. 2017), and we found a nonsignificant association (P = 0.16) with the disease.”
From <i>DLX5/6</i> GABAergic Expression Affects Social Vocalization: Implications for Human Evolution (2021) · cites this paper as Yuen et al. 2017
LoF variants in TAOK2 are identified in ASD probands, however it is not a top-ranking ASD risk factor by large genetic screening.
“LoF variants in TAOK2 are identified in ASD probands [93, 94], however it is not a top-ranking ASD risk factor by large genetic screening [85].”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [94]
In humans, mutations in MAPK3 and TAOK2 but not in KCTD13 have been found in ASD cases.
“In humans, mutations in MAPK3 [92] and TAOK2 [93, 94] but not in KCTD13 [85, 95] have been found in ASD cases.”
From 16p11.2 Copy Number Variations and Neurodevelopmental Disorders (2020) · cites this paper as [94]
The genetic architecture in the self-reported SPARK cohort is similar to published, clinically confirmed ASD cohorts.
“We also demonstrated that the genetic architecture in this self-reported cohort is similar to published, clinically confirmed ASD cohorts.3,4,7”
From Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes (2019) · cites this paper as [4]
Over the past decade, genomic studies focused on de novo likely gene disrupting variants have identified about 100 high-confidence ASD risk genes or loci.
“Over the past decade, genomic studies focused on de novo, likely gene disrupting (dnLGD) variants (stopgain, frameshift, and essential splice site) have identified ~100 high-confidence ASD risk genes or loci.3,4”
From Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes (2019) · cites this paper as [4]
PAX5 and FEZF2 are involved in transcription regulation during central nervous system development.
“PAX5 and FEZF2 are involved in transcription regulation during central nervous system development.4,24,37”
From Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes (2019) · cites this paper as [4]
Recent studies have reported additional individuals with ASD and/or NDD with de novo damaging variants in BRSK2, PAX5, NR4A2, RALGAPB, and DPP6.
“Recent studies have reported additional individuals with ASD and/or NDD with de novo damaging variants in these genes including BRSK2,27 PAX5,4,28 NR4A2,29,30 RALGAPB,7,31,32 and DPP6.5,33,34”
From Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes (2019) · cites this paper as [4]
Genome sequencing leaves most ASD cases genetically unsolved.
“even its application leaves the majority of ASD cases “genetically unsolved”2,19–21.”
From Genome-wide detection of tandem DNA repeats that are expanded in autism (2020) · cites this paper as [2]
Over 100 genes and loci are known to increase ASD likelihood.
“more than 100 genes and loci are known to be associated with increased likelihood of ASD2,13.”
From Genome-wide detection of tandem DNA repeats that are expanded in autism (2020) · cites this paper as [2]
This provides compelling evidence for rare expansions in ASD-related phenotypes.
“This provides compelling evidence for the role of rare tandem repeat expansions in ASD-related phenotypes2,39,50.”
From Genome-wide detection of tandem DNA repeats that are expanded in autism (2020) · cites this paper as [2]
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Exome sequencing of 457 autism families recruited online provides evidence for autism risk genes
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Genome-wide detection of tandem DNA repeats that are expanded in autism
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Paternally inherited cis-regulatory structural variants are associated with autism
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SHANK2 mutations associated with autism spectrum disorder cause hyperconnectivity of human neurons
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Self-citation16p11.2 Copy Number Variations and Neurodevelopmental Disorders
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- Authors
- C Yuen, R. K., Merico, D., Bookman, M., L Howe, J., Thiruvahindrapuram, B., Patel, R. V., Whitney, J., Deflaux, N., Bingham, J., Wang, Z., Pellecchia, G., Buchanan, J. A., Walker, S., Marshall, C. R., Uddin, M., Zarrei, M., Deneault, E., D'Abate, L., Chan, A. J. S., Koyanagi, S., Paton, T., Pereira, S. L., Hoang, N., Engchuan, W., Higginbotham, E. J., Ho, K., Lamoureux, S., Li, W., MacDonald, J. R., Nalpathamkalam, T., Sung, W. W. L., Tsoi, F. J., Wei, J., Xu, L., Tasse, A.-M., Kirby, E., Van Etten, W., Twigger, S., Roberts, W., Drmic, I., Jilderda, S., Modi, B. M., Kellam, B., Szego, M., Cytrynbaum, C., Weksberg, R., Zwaigenbaum, L., Woodbury-Smith, M., Brian, J., Senman, L., Iaboni, A., Doyle-Thomas, K., Thompson, A., Chrysler, C., Leef, J., Savion-Lemieux, T., Smith, I. M., Liu, X., Nicolson, R., Seifer, V., Fedele, A., Cook, E. H., Dager, S., Estes, A., Gallagher, L., Malow, B. A., Parr, J. R., Spence, S. J., Vorstman, J., Frey, B. J., Robinson, J. T., Strug, L. J., Fernandez, B. A., Elsabbagh, M., Carter, M. T., Hallmayer, J., Knoppers, B. M., Anagnostou, E., Szatmari, P., Ring, R. H., Glazer, D., Pletcher, M. T., & Scherer, S. W.
- Affiliations
- Hospital for Sick Children (CA)
- Google (United States) (US)
- University of Toronto (CA)
- McGill University (CA)
- Massachusetts Historical Society (US)
- University of Alberta (CA)
- McMaster University (CA)
- Dalhousie University (CA)
- Queen's University (CA)
- Western University (CA)
- Autism Speaks (US)
- University of Illinois Chicago (US)
- University of Washington (US)
- Trinity College Dublin (IE)
- Vanderbilt University (US)
- Newcastle University (GB)
- Boston Children's Hospital (US)
- University Medical Center Utrecht (NL)
- University of California San Diego (US)
- Memorial University of Newfoundland (CA)
- Children's Hospital of Eastern Ontario (CA)
- Stanford Medicine (US)
- Drexel University (US)
- Corresponding author
- Scherer, Stephen W
- ORCID
- C Yuen, Ryan K
- Merico, Daniele
- Thiruvahindrapuram, Bhooma
- Patel, Rohan V
- Deflaux, Nicole
- Wang, Zhuozhi
- Pellecchia, Giovanna
- Walker, Susan
- Marshall, Christian R
- Uddin, Mohammed
- Paton, Tara
- Hoang, Ny
- Engchuan, Worrawat
- Higginbotham, Edward J
- Ho, Karen
- MacDonald, Jeffrey R
- Nalpathamkalam, Thomas
- Sung, Wilson W L
- Wei, John
- Xu, Lizhen
- Kirby, Emily
- Twigger, Simon
- Drmic, Irene
- Szego, Michael
- Cytrynbaum, Cheryl
- Weksberg, Rosanna
- Zwaigenbaum, Lonnie
- Brian, Jessica
- Smith, Isabel M
- Liu, Xudong
- Nicolson, Rob
- Cook, Edwin H
- Dager, Stephen
- Estes, Annette
- Gallagher, Louise
- Malow, Beth A
- Parr, Jeremy R
- Spence, Sarah J
- Vorstman, Jacob
- Strug, Lisa J
- Fernandez, Bridget A
- Elsabbagh, Mayada
- Carter, Melissa T
- Hallmayer, Joachim
- Knoppers, Bartha M
- Anagnostou, Evdokia
- Ring, Robert H
- Glazer, David
- Scherer, Stephen W
- Venue
- Nature Neuroscience
- Published
- 2017-03-06
- Volume
- 20
- Issue
- 4
- Pages
- 602-611
- ISSN
- 1097-6256 (ISSN-L)
- 1546-1726
- PMC
- PMC5501701
- OpenAlex
- W2591909999
- Cited by
- 844
- References
- 71
- Citations by year
- 2026: 38 · 2025: 59 · 2024: 89 · 2023: 67 · 2022: 109 · 2021: 110 · 2020: 140 · 2019: 97 · 2018: 87 · 2017: 46 · 2016: 1
- FWCI
- 58.10
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Neuroscience (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- Scholarship@Western (Western University) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- Canadian Institutes of Health Research (143295_1, 129338_1, 140849_1, 125818_1)
- National Cancer Institute (U24CA210004)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (U54HD083211)
- 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
- autism spectrum disorder, candidate risk genes, de novo mutations, copy number variation, adaptive skills, genetic databases, chromosomal abnormalities
- MeSH terms
- Autism Spectrum Disorder, Chromosome Aberrations, Humans, Phenotype, Mutagenesis, Insertional, Sequence Deletion, Genetic Predisposition to Disease, Polymorphism, Single Nucleotide, Databases, Genetic, Genome-Wide Association Study, DNA Copy Number Variations
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