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Background  OA is a complex disease caused by environmental and genetic risk factors. The purpose of this study is to identify candidate copy number variations (CNVs) associated with OA.    Methods  We performed a genome-wide association study of CNV to identify potential loci that confer susceptibility to or protection from OA. CNV genotyping was conducted using NimbleGen HD2 3 × 720K comparative hybridization array and included samples from 371 OA patients and 467 healthy controls. The putative CNV regions identified were confirmed with a TaqMan assay.    Results  We identified six genomic regions associated with OA encompassing CNV loci. None of six loci had previously been reported in genome-wide association studies with OA, although a genetic analysis suggested that they have functional effects. The protein product of a candidate risk gene for obesity,  TNKS , targets Wnt inhibition, and this gene was significantly associated with hand and knee OA. Copy number deletion on  TNKS  was associated with a 1.37-fold decreased risk for OA. In addition,  CA10 , which shows a strong association with osteoporosis, was also significant in our study. Copy number deletion on this gene was associated with a 1.69-fold decreased risk for OA.    Conclusion  We identified several CNV loci that may contribute to OA susceptibility in Koreans. Further functional investigations of these genes are warranted to fully characterize their putative association.    Electronic supplementary material  The online version of this article (doi:10.1186/s12891-015-0531-4) contains supplementary material, which is available to authorized users.

A genome-wide association study of copy-number variation identifies putative loci associated with osteoarthritis in Koreans