Genome-wide analyses of exonic copy number variants in a family-based study point to novel autism susceptibility genes
Open accessAbstract
The genetics underlying the autism spectrum disorders (ASDs) is complex and remains poorly understood. Previous work has demonstrated an important role for structural variation in a subset of cases, but has lacked the resolution necessary to move beyond detection of large regions of potential interest to identification of individual genes. To pinpoint genes likely to contribute to ASD etiology, we performed high density genotyping in 912 multiplex families from the Autism Genetics Resource Exchange (AGRE) collection and contrasted results to those obtained for 1,488 healthy controls. Through prioritization of exonic deletions (eDels), exonic duplications (eDups), and whole gene duplication events (gDups), we identified more than 150 loci harboring rare variants in multiple unrelated probands, but no controls. Importantly, 27 of these were confirmed on examination of an independent replication cohort comprised of 859 cases and an additional 1,051 controls. Rare variants at known loci, including exonic deletions at NRXN1 and whole gene duplications encompassing UBE3A and several other genes in the 15q11-q13 region, were observed in the course of these analyses. Strong support was likewise observed for previously unreported genes such as BZRAP1, an adaptor molecule known to regulate synaptic transmission, with eDels or eDups observed in twelve unrelated cases but no controls (p = 2.3x10(-5)). Less is known about MDGA2, likewise observed to be case-specific (p = 1.3x10(-4)). But, it is notable that the encoded protein shows an unexpectedly high similarity to Contactin 4 (BLAST E-value = 3x10(-39)), which has also been linked to disease. That hundreds of distinct rare variants were each seen only once further highlights complexity in the ASDs and points to the continued need for larger cohorts.
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Deletions and/or duplications at specific loci including 1q21.1, 15q11.2-13.1, 15q13.2-13.3, 16p11.2, 17q12, and 22q11.2 show evidence for association with ASD.
“These include deletions and/or duplications at specific loci, including: 1q21.1, 15q11.2-13.1, 15q13.2-13.3, 16p11.2, 17q12, and 22q11.2”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as Bucan et al., 2009
Recurrent structural variations involving NRXN1, CNTN4, NLGN1, ASTN2, PTCHD1, and DDX53 show evidence for association with ASD.
“recurrent structural variations involving one or a small number of genes, including: Neurexin 1 (NRXN1), Contactin 4 (CNTN4), Neuroligin 1 (NLGN1), Astrotactin 2 (ASTN2), and the contiguous genes Patched Domain Containing 1 (PTCHD1) and DEAD box Protein 53 (DDX53)”
From Multiple recurrent de novo CNVs, including duplications of the 7q11.23 Williams syndrome region, are strongly associated with autism (2011) · cites this paper as Bucan et al., 2009
Copy number variants associated with psychiatric disorders usually contain multiple genes.
“they usually contain multiple genes (with a few exceptions (Bucan et al., 2009; Talkowski et al., 2011))”
From Defining the genetic, genomic, cellular, and diagnostic architectures of psychiatric disorders (2019) · cites this paper as Bucan et al., 2009
Neurexin 1 CNV are observed in about 50% of unaffected carriers and across several neurodevelopmental disorders.
“as well as Neurexin 1 CNV, which are observed in about 50% of unaffected carriers [36], and observed across several neurodevelopmental disorders (Table 1).”
From Genetics of autism spectrum disorders (2011) · cites this paper as [36]
Not all de novo CNV are necessarily causal or fully penetrant.
“So all such CNV are not necessarily causal or fully penetrant [36].”
From Genetics of autism spectrum disorders (2011) · cites this paper as [36]
De novo CNV are found in 5-10% of ASD probands and in 1-2% of unaffected controls.
“First, de novo CNV are observed in 5–10% of ASD probands, but they are also observed in 1–2% of unaffected controls.”
From Genetics of autism spectrum disorders (2011) · cites this paper as [36]
These results replicate and extend earlier composite pathway analyses of putative ASD susceptibility genes from the literature and CNV pathway analyses in AGRE and other cohorts.
“These results replicate and extend earlier composite pathway analysis of putative ASD susceptibility genes compiled from the literature [68], and CNV pathway analysis in the Autism Genetic Resource Exchange (AGRE) and other cohorts [32, 36].”
From Genetics of autism spectrum disorders (2011) · cites this paper as [36]
Rare de novo CNV considered causal may have intermediate effects and variable penetrance, so they must interact with other factors.
“For example, although rare de novo CNV are considered causal mutations, it is clear that mutations may have intermediate effect sizes and variable penetrance, as mentioned above [36, 42] so such mutations must be interacting with other factors.”
From Genetics of autism spectrum disorders (2011) · cites this paper as [36]
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- Authors
- Bucan, M., Abrahams, B. S., Wang, K., Glessner, J. T., Herman, E. I., Sonnenblick, L. I., Alvarez Retuerto, A. I., Imielinski, M., Hadley, D., Bradfield, J. P., Kim, C., Gidaya, N. B., Lindquist, I., Hutman, T., Sigman, M., Kustanovich, V., Lajonchere, C. M., Singleton, A., Kim, J., Wassink, T. H., McMahon, W. M., Owley, T., Sweeney, J. A., Coon, H., Nurnberger, J. I., Li, M., Cantor, R. M., Minshew, N. J., Sutcliffe, J. S., Cook, E. H., Dawson, G., Buxbaum, J. D., Grant, S. F. A., Schellenberg, G. D., Geschwind, D. H., & Hakonarson, H.
- Affiliations
- University of California, Los Angeles (US)
- Children's Hospital of Philadelphia (US)
- University of Pennsylvania (US)
- Autism Speaks (US)
- National Institutes of Health (US)
- University of Iowa (US)
- University of Utah (US)
- University of Illinois Chicago (US)
- University of Pittsburgh (US)
- Vanderbilt University (US)
- Icahn School of Medicine at Mount Sinai (US)
- Corresponding author
- Hakonarson, Hakon
- ORCID
- Glessner, Joseph T.
- Imielinski, Marcin
- Hadley, Dexter
- Lajonchere, Clara M.
- Singleton, Andrew
- Kim, Junhyong
- Wassink, Thomas H.
- Sweeney, John A.
- Coon, Hilary
- Li, Mingyao
- Cantor, Rita M.
- Minshew, Nancy J.
- Sutcliffe, James S.
- Cook, Edwin H.
- Buxbaum, Joseph D.
- Grant, Struan F. A.
- Schellenberg, Gerard D.
- Geschwind, Daniel H.
- Hakonarson, Hakon
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2009-06-26
- Volume
- 5
- Issue
- 6
- Pages
- e1000536
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC2695001
- OpenAlex
- W2125432692
- Cited by
- 424
- References
- 60
- Citations by year
- 2026: 12 · 2025: 9 · 2024: 9 · 2023: 13 · 2022: 9 · 2021: 15 · 2020: 16 · 2019: 16 · 2018: 18 · 2017: 24 · 2016: 24 · 2015: 24 · 2014: 39 · 2013: 36 · 2012: 46
- FWCI
- 25.74
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- PLoS Genetics (publishedVersion, public-domain)
- PubMed Central (publishedVersion, public-domain)
- PubMed (publishedVersion)
- D-Scholarship@Pitt (University of Pittsburgh) (acceptedVersion)
- Carolina Digital Repository (University of North Carolina at Chapel Hill) (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- DukeSpace (Duke University) (submittedVersion, cc-by-nc-nd)
- eScholarship (California Digital Library) (submittedVersion)
- eScholarship (California Digital Library) (submittedVersion, public-domain)
- Figshare (submittedVersion, cc-by)
- UNC Libraries
- Funders
- U.S. Department of Health and Human Services
- Autism Speaks
- Massachusetts General Hospital
- Yale University
- Children's Hospital of Philadelphia (UL1-RR-024134)
- University of Pennsylvania
- Emory University
- George Washington University
- National Alliance for Research on Schizophrenia and Depression
- Cotswold Foundation
- National Institutes of Health (Z01-AG000949)
- National Institute on Aging (K24AG000949, Z01AG000949)
- National Institute of Mental Health (U24MH081810, MH081754, R01MH081754, R01MH604687)
- National Institute of General Medical Sciences (P20GM069012, P20-GM69012)
- National Center for Research Resources (UL1-RR024134-03, UL1RR024134)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (P50HD055784)
- Topics
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetics and Neurodevelopmental Disorders
- Keywords
- autism spectrum disorder, copy number variation, exon deletion, autism susceptibility genes, structural variants, multiplex families, NRXN1, UBE3A, 15q11-q13, rare variants, gene prioritization
- MeSH terms
- Adolescent, Autistic Disorder, Calcium-Binding Proteins, Child, Child, Preschool, Exons, Female, Humans, Male, Nerve Tissue Proteins, Pedigree, Cohort Studies, Cell Adhesion Molecules, Neuronal, Case-Control Studies, Sequence Deletion, Gene Dosage, Neural Cell Adhesion Molecules, Genetic Predisposition to Disease, Gene Duplication, Ubiquitin-Protein Ligases, Genome-Wide Association Study, Young Adult
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.
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