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Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls
Open accessAbstract
Copy number variants (CNVs) account for a major proportion of human genetic polymorphism and have been predicted to have an important role in genetic susceptibility to common disease. To address this we undertook a large, direct genome-wide study of association between CNVs and eight common human diseases. Using a purpose-designed array we typed approximately 19,000 individuals into distinct copy-number classes at 3,432 polymorphic CNVs, including an estimated approximately 50% of all common CNVs larger than 500 base pairs. We identified several biological artefacts that lead to false-positive associations, including systematic CNV differences between DNAs derived from blood and cell lines. Association testing and follow-up replication analyses confirmed three loci where CNVs were associated with disease-IRGM for Crohn's disease, HLA for Crohn's disease, rheumatoid arthritis and type 1 diabetes, and TSPAN8 for type 2 diabetes-although in each case the locus had previously been identified in single nucleotide polymorphism (SNP)-based studies, reflecting our observation that most common CNVs that are well-typed on our array are well tagged by SNPs and so have been indirectly explored through SNP studies. We conclude that common CNVs that can be typed on existing platforms are unlikely to contribute greatly to the genetic basis of common human diseases.
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“SVs have already been associated with diverse diseases, including autism2,3, schizophrenia4,5 and Crohn’s disease6,7.”
From Mapping copy number variation by population-scale genome sequencing (2011) · cites this paper as [6]
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“This analysis identified a single strong association (r2=.99), between rs10490924, a coding variant in the ARMS2 gene which is the peak of association in 10q26, and a 3′ UTR indel polymorphism associated with ARMS2 mRNA instability40.”
From Seven new loci associated with age-related macular degeneration (2013) · cites this paper as [38]
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Metadata
- Authors
- The Wellcome Trust Case Control Consortium
- Venue
- Nature
- Published
- 2010-04
- Volume
- 464
- Issue
- 7289
- Pages
- 713-720
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC2892339
- OpenAlex
- W2130542470
- Cited by
- 807
- References
- 43
- Citations by year
- 2026: 5 · 2025: 11 · 2024: 14 · 2023: 12 · 2022: 22 · 2021: 17 · 2020: 31 · 2019: 40 · 2018: 36 · 2017: 38 · 2016: 42 · 2015: 78 · 2014: 69 · 2013: 88 · 2012: 112
- FWCI
- 69.81
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature (publishedVersion)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion)
- Lincoln Repository (University of Lincoln) (acceptedVersion)
- White Rose Research Online (University of Leeds, The University of Sheffield, University of York) (acceptedVersion)
- St George's Online Research Archive (St George's University of London) (acceptedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- PEARL (University of Plymouth) (submittedVersion, other-oa)
- HAL (submittedVersion, other-oa)
- Discovery Research Portal (University of Dundee) (submittedVersion)
- Document Server@UHasselt (UHasselt) (submittedVersion)
- ePrints Soton (University of Southampton) (submittedVersion)
- UCL Discovery (University College London) (submittedVersion)
- Figshare (submittedVersion, cc-by)
- Minerva Access (University of Melbourne) (submittedVersion)
- Research Portal (King's College London) (submittedVersion)
- Leicester Research Archive (University of Leicester) (submittedVersion)
- ANU Open Research (Australian National University) (submittedVersion)
- PEARL (University of Plymouth) (submittedVersion)
- University of Birmingham Research Portal (University of Birmingham) (submittedVersion)
- Queen Mary Research Online (Queen Mary University of London) (submittedVersion)
- Bristol Research (University of Bristol) (submittedVersion)
- ResearchSpace (University of Auckland) (submittedVersion)
- Spiral (Imperial College London) (submittedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Newcastle University ePrints (Newcastle Univesity)
- Funders
- Wellcome Trust (85517, 061858, 089989, 090532, 083948)
- National Institute for Health and Care Research (NF-SI-0508-10299, NF-SI-0508-10335)
- British Heart Foundation (RG/08/014/24067, RG/09/012/28096)
- Versus Arthritis (/17552, 18475)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genome Rearrangement Algorithms
- Keywords
- copy number variation, common diseases, genetic susceptibility, Crohn's disease, rheumatoid arthritis, type 1 diabetes, type 2 diabetes, IRGM, HLA, TSPAN8, false positive association, Wellcome Trust Case Control Consortium, genetic polymorphism, de novo mutations
- MeSH terms
- Arthritis, Rheumatoid, Crohn Disease, Diabetes Mellitus, Disease, Gene Frequency, Humans, Nucleic Acid Hybridization, Pilot Projects, Quality Control, Case-Control Studies, Genetic Predisposition to Disease, Oligonucleotide Array Sequence Analysis, Polymorphism, Single Nucleotide, Genome-Wide Association Study, DNA Copy Number Variations
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