Investigation of genetic variation across PTPN22 in UK rheumatoid arthritis (RA) patients.

OBJECTIVE: The aim of this study was to investigate SNPs across the PTPN22 gene region in a UK cohort of RA patients to look for evidence of disease associations independent of the well-characterised R620W variant (rs2476601). METHODS: 951 UK RA cases satisfying ARA criteria and 448 population controls were genotyped for 11 SNPs across the PTPN22 gene region using Sequenom MassArray MassEXTEND technology. Allele, genotype and estimated haplotype frequencies of cases and controls were compared. RESULTS: In addition to the R620W (rs2476601) SNP, three SNPs were associated with RA in this study. The sole haplotype on which the associated T allele of R620W occurred was associated with RA, no other haplotypes showed a significant difference in frequencies between RA cases and controls. CONCLUSION: In contrast to a study of US RA patients we found no evidence of association to PTPN22 independent of the well-characterised R620W variant, suggesting that in UK RA patients this variant alone explains the association with the PTPN22 gene.