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Systematic search for single nucleotide polymorphisms in a lymphoid tyrosine phosphatase gene (PTPN22): Association between a promoter polymorphism and type 1 diabetes in Asian populations

The protein tyrosine phosphatase, nonreceptor 22 gene (PTPN22) maps to human chromosome 1p13.3‐p13.1 and encodes an important negative regulator of T‐cell activation, lymphoid‐specific phosphatase (Lyp). Recently, the minor allele of a single‐nucleotide polymorphism (SNP) at nucleotide position 1858 (rs2476601, +1858C > T) was found to be associated with type 1 diabetes. However, the degree of the association is variable among ethnic populations, suggesting the presence of other disease‐associated variants in PTPN22. To examine this possibility, we carried out a systemic search for PTPN22 using direct sequencing of PCR‐amplified products in the Japanese population. Association and linkage studies were also conducted in 1,690 Japanese samples, 180 Korean samples, and 472 Caucasian samples from 95 nuclear families. We identified five novel SNPs, but not the +1858C > T SNP. Of these two frequent SNPs, −1123G > C, and +2740C > T were in strong linkage disequilibrium (LD), and the −1123G > C promoter SNP was associated with acute‐onset but not slow‐onset type 1 diabetes in the Japanese population (odds ratio [OR] = 1.42, 95% CI = 1.07–1.89, P = 0.015). This association was observed also in Korean patients with type 1 diabetes (Mantel–Haenszel χ2 = 6.543, P = 0.0105, combined OR = 1.41 95% CI = 1.09–1.82). Furthermore, the affected family‐based control (AFBAC) association test and the transmission disequilibrium analysis of multiplex families of European descent from the British Diabetes Association (BDA) Warren Repository indicated that the association was stronger in −1123G > C compared to +1858C > T. In conclusion, the type 1 diabetes association with PTPN22 is confirmed, but it cannot be attributed solely to the +1858C > T variant. The promoter −1123G > C SNP is a more likely causative variant in PTPN22. © 2006 Wiley‐Liss, Inc.