Microdeletions of 3q29 confer high risk for schizophrenia
Open accessAbstract
Schizophrenia (SZ) is a severe psychiatric illness that affects approximately 1% of the population and has a strong genetic underpinning. Recently, genome-wide analysis of copy-number variation (CNV) has implicated rare and de novo events as important in SZ. Here, we report a genome-wide analysis of 245 SZ cases and 490 controls, all of Ashkenazi Jewish descent. Because many studies have found an excess burden of large, rare deletions in cases, we limited our analysis to deletions over 500 kb in size. We observed seven large, rare deletions in cases, with 57% of these being de novo. We focused on one 836 kb de novo deletion at chromosome 3q29 that falls within a 1.3-1.6 Mb deletion previously identified in children with intellectual disability (ID) and autism, because increasing evidence suggests an overlap of specific rare copy-number variants (CNVs) between autism and SZ. By combining our data with prior CNV studies of SZ and analysis of the data of the Genetic Association Information Network (GAIN), we identified six 3q29 deletions among 7545 schizophrenic subjects and one among 39,748 controls, resulting in a statistically significant association with SZ (p = 0.02) and an odds ratio estimate of 17 (95% confidence interval: 1.36-1198.4). Moreover, this 3q29 deletion region contains two linkage peaks from prior SZ family studies, and the minimal deletion interval implicates 20 annotated genes, including PAK2 and DLG1, both paralogous to X-linked ID genes and now strong candidates for SZ susceptibility.
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The three significant schizophrenia regions correspond to CNVs previously implicated in schizophrenia at 3q29, 7q36.3, and 16p11.2.
“In schizophrenia, three genomic regions were significant (Table S6B), all corresponding to CNVs that have been previously implicated in schizophrenia at 3q29 (Mulle et al., 2010), 7q36.3 (Vacic et al., 2011), and 16p11.2 (McCarthy et al., 2009).”
From High frequencies of de novo CNVs in bipolar disorder and schizophrenia (2011) · cites this paper as Mulle et al., 2010
Several individual CNV loci have been strongly implicated as risk factors for schizophrenia.
“several individual CNV loci have been strongly implicated as risk factors for schizophrenia with high degrees of statistical confidence. These include deletions at 1q21.1, NRXN1, 3q29, 15q11.2, 15q13.3, 22q11.2 and duplications at VIPR2, 16p11.2, 16p13.1 and 15q11-q13.2, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [6]
CNVs spanning DLG1 and DLG2 have been reported before in schizophrenia.
“CNVs spanning DLG1 and DLG2 have been reported before in schizophrenia4, 6, 17”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [6]
Even the largest genome-wide scans, typically under 10,000 samples, remain underpowered to robustly confirm genetic association for most pathogenic CNVs reported so far, particularly those with low frequencies or intermediate effect sizes.
“yet even the largest genome-wide scans (sample sizes typically <10,000) remain under-powered to robustly confirm genetic association for the majority of pathogenic CNVs reported so far, particularly for those with low frequencies (<0.5% in cases) or intermediate effect sizes (odds ratios 2–10).”
From Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects (2017) · cites this paper as [8]
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- Authors
- Mulle, J. G., Dodd, A. F., McGrath, J. A., Wolyniec, P. S., Mitchell, A. A., Shetty, A. C., Sobreira, N. L., Valle, D., Rudd, M. K., Satten, G., Cutler, D. J., Pulver, A. E., & Warren, S. T.
- Affiliations
- Emory University (US)
- Johns Hopkins University (US)
- Icahn School of Medicine at Mount Sinai (US)
- Centers for Disease Control and Prevention (US)
- Corresponding author
- Mulle, Jennifer Gladys
- Warren, Stephen T.
- ORCID
- Venue
- The American Journal of Human Genetics
- Publisher
- Elsevier BV
- Published
- 2010-08
- Volume
- 87
- Issue
- 2
- Pages
- 229-236
- ISSN
- 0002-9297 (ISSN-L)
- PMC
- PMC2917706
- OpenAlex
- W2094942174
- Cited by
- 223
- References
- 46
- Citations by year
- 2026: 8 · 2025: 4 · 2024: 8 · 2023: 10 · 2022: 5 · 2021: 9 · 2020: 9 · 2019: 8 · 2018: 15 · 2017: 12 · 2016: 9 · 2015: 19 · 2014: 16 · 2013: 31 · 2012: 30
- FWCI
- 16.39
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- The American Journal of Human Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- National Institute of Mental Health (F32MH080583, R01MH080129, R01MH083722)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (F31HD068133)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Health Sciences › Medicine › Psychiatry and Mental health › Schizophrenia research and treatment
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- schizophrenia, copy number variation, de novo deletion, Ashkenazi Jews, genetic susceptibility, PAK2, DLG1, intellectual disability, autism spectrum disorder
- MeSH terms
- Chromosomes, Human, Pair 3, Humans, Schizophrenia, Reproducibility of Results, Case-Control Studies, Sequence Deletion, Genetic Predisposition to Disease, Base Pairing, Physical Chromosome Mapping, Young Adult, Genetic Loci, DNA Copy Number Variations
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