Accurately assessing the risk of schizophrenia conferred by rare copy-number variation affecting genes with brain function
Open accessAbstract
Investigators have linked rare copy number variation (CNVs) to neuropsychiatric diseases, such as schizophrenia. One hypothesis is that CNV events cause disease by affecting genes with specific brain functions. Under these circumstances, we expect that CNV events in cases should impact brain-function genes more frequently than those events in controls. Previous publications have applied "pathway" analyses to genes within neuropsychiatric case CNVs to show enrichment for brain-functions. While such analyses have been suggestive, they often have not rigorously compared the rates of CNVs impacting genes with brain function in cases to controls, and therefore do not address important confounders such as the large size of brain genes and overall differences in rates and sizes of CNVs. To demonstrate the potential impact of confounders, we genotyped rare CNV events in 2,415 unaffected controls with Affymetrix 6.0; we then applied standard pathway analyses using four sets of brain-function genes and observed an apparently highly significant enrichment for each set. The enrichment is simply driven by the large size of brain-function genes. Instead, we propose a case-control statistical test, cnv-enrichment-test, to compare the rate of CNVs impacting specific gene sets in cases versus controls. With simulations, we demonstrate that cnv-enrichment-test is robust to case-control differences in CNV size, CNV rate, and systematic differences in gene size. Finally, we apply cnv-enrichment-test to rare CNV events published by the International Schizophrenia Consortium (ISC). This approach reveals nominal evidence of case-association in neuronal-activity and the learning gene sets, but not the other two examined gene sets. The neuronal-activity genes have been associated in a separate set of schizophrenia cases and controls; however, testing in independent samples is necessary to definitively confirm this association. Our method is implemented in the PLINK software package.
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Permutation-based tests were used to correct for the known bias of CNVs toward large genes in the functional enrichment analysis.
“Enrichment of functional classes of genes was tested using the DAVID software (http://david.abcc.ncifcrf.gov/), followed by two additional permutation-based tests to correct for the known bias of CNVs toward large genes (Raychaudhuri et al., 2010), one implemented as a case-only analysis and a second implemented as a case-control analysis in PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/cnv.s”
From High frequencies of de novo CNVs in bipolar disorder and schizophrenia (2011) · cites this paper as Raychaudhuri et al., 2010
Early gene-set studies did not allow for important confounders, in particular the large size of genes implicated in brain function, and the conclusions that can be drawn are consequently unclear.
“it has been noted that the early gene-set studies did not allow for important confounders, in particular the large size of genes implicated in brain function, and that the conclusions that can be drawn are consequently unclear.19”
From De novo CNV analysis implicates specific abnormalities of postsynaptic signalling complexes in the pathogenesis of schizophrenia (2012) · cites this paper as [19]
Genes highly expressed in the brain, particularly those involved in synaptic function, are longer on average than other genes.
“and genes highly expressed in the brain, particularly those involved in synaptic function, are longer on average than other genes186.”
From Systems biology and gene networks in neurodevelopmental and neurodegenerative disorders (2015) · cites this paper as [186]
Gene-set burden analyses controlled for the total number of genes per subject spanned by rare CNVs to account for global enrichment.
“we controlled for the total number of genes per subject spanned by rare CNVs to account for signal that merely reflects the global enrichment of CNV burden in cases 19.”
From Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects (2017) · cites this paper as [19]
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- Authors
- Raychaudhuri, S., Korn, J. M., McCarroll, S. A., The International Schizophrenia Consortium, Altshuler, D., Sklar, P., Purcell, S., & Daly, M. J.
- Affiliations
- Broad Institute (US)
- Corresponding author
- Purcell, Shaun
- Daly, Mark J.
- ORCID
- Venue
- PLoS Genetics
- Publisher
- Public Library of Science (PLoS)
- Published
- 2010-09-09
- Volume
- 6
- Issue
- 9
- Pages
- e1001097
- ISSN
- 1553-7390 (ISSN-L)
- 1553-7404
- PMC
- PMC2936523
- OpenAlex
- W2114327599
- Cited by
- 131
- References
- 35
- Citations by year
- 2026: 1 · 2025: 1 · 2024: 4 · 2023: 1 · 2022: 4 · 2021: 4 · 2020: 6 · 2019: 4 · 2018: 3 · 2017: 10 · 2016: 11 · 2015: 17 · 2014: 16 · 2013: 9 · 2012: 26
- FWCI
- 8.73
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- PLoS Genetics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Aberdeen University Research Archive (Aberdeen University) (submittedVersion)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion, cc-by-nc-nd)
- Figshare (submittedVersion, cc-by)
- ORCA Online Research @Cardiff (Cardiff University) (submittedVersion)
- Research Explorer (The University of Manchester) (submittedVersion)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (R01HL087676)
- National Human Genome Research Institute (U01HG004171)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK083756, R01DK064869, U01DK062432)
- National Institute of Arthritis and Musculoskeletal and Skin Diseases (K08AR055688)
- National Center for Research Resources
- 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
- copy number variation, schizophrenia, pathway enrichment, case-control association, neuropsychiatric disorders
- MeSH terms
- Brain, Computer Simulation, Genes, Humans, Models, Genetic, Schizophrenia, Genome, Human, Case-Control Studies, Gene Deletion, Risk Assessment, Genetic Predisposition to Disease, Databases, Genetic, DNA Copy Number Variations
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