Attempt to replicate the published osteoarthritis-associated genetic variants in the Newfoundland & Labrador Population

Zhai, Guangju and Aref-Eshghi, Erfan and Rahman, Proton and Zhang, Hongwei and Martin, Glynn and Furey, Andrew and Green, Roger C. and Sun, Guang (2014) Attempt to replicate the published osteoarthritis-associated genetic variants in the Newfoundland & Labrador Population. Journal of Orthopedics & Rheumatology, 1 (3). ISSN 2334-2846

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Abstract

Objective: Over 200 genes have been reported to be associated with osteoarthritis (OA), but most of them have not been replicated in an independent sample. Using the newly collected cohort from a genetically isolated population - the Newfoundland and Labrador population, we attempted to replicate 105 previously reported OAassociated SNPs. Methods: A case-control study design was utilized in this study. Patients undergoing total hip/knee joint replacements due to severe OA were collected as cases. A group of healthy individuals with no evidence of OA was used as control.105 SNPs were genotyped either by Sequenom iPLEX Gold method or Illumina GWAS genotyping platform. The cross-reference was performed on both methods in a subset of samples for genotyping quality control. A logistic regression model was used to test for associations between the SNPs and OA. Results: A total of 126 cases and 348 healthy controls were included in the final analysis. OA Patients were on average 9 years older than healthy controls (p<0.0001), but there was no difference in BMI. We were unable to replicate the previously reported associations. Two SNPs, rs2294995 (COL9A3), and rs1049007 (BMP2) showed an association with p<0.05, but the significance did not survive the Bonferroni multiple testing correction. Conclusion: A lack of replication might be due to study design, complexity of OA, method of OA ascertainment, populations studied, or false positives in the original publications. A study with larger sample is needed to confirm the two possible SNPs with OA.

Item Type: Article
URI: http://research.library.mun.ca/id/eprint/6426
Item ID: 6426
Additional Information: Memorial University Open Access Author's Fund
Keywords: Osteoarthritis, Genetics, Single nucleotide polymorphism, Replication
Department(s): Medicine, Faculty of
Date: 23 April 2014
Date Type: Publication
Geographic Location: Canada--Newfoundland & Labrador
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