AbstractObjectiveTo determine any associations of the PTPN22 R620W single‐nucleotide polymorphism (SNP) with systemic sclerosis (SSc) or with anticentromere antibody (ACA)–positive or anti–topoisomerase I (anti–topo I) antibody–positive SSc, in a case–control study of US white, black, Hispanic, and Choctaw Indian individuals.MethodsA total of 850 white, 130 black, 120 Hispanic, and 20 Choctaw Indian patients with SSc were compared with 430 white, 164 black, 146 Hispanic, and 76 Choctaw Indian control subjects, respectively. All subjects were living in the US. PTPN22 SNP (rs2476601) genotyping was performed by TaqMan 5′ allelic discrimination assay and pyrosequencing.ResultsThe PTPN22 CT/TT genotype showed significant association with anti–topo I antibody–positive SSc in white patients (odds ratio [OR] 2.21, 95% confidence interval [95% CI] 1.3–3.7) and with ACA‐positive white patients with SSc (OR 1.70, 95% CI 1.1–2.7). Frequency of the PTPN22*T allele also showed significant association with anti–topo I antibody–positive SSc in white patients (OR 2.03, 95% CI 1.3–3.2). When data for patients in the 3 ethnic groups (black, white, and Hispanic) were combined, a significant association with both genotype and allele frequencies was observed, suggesting a trend toward association in ACA‐positive and anti–topo I antibody–positive SSc. Stepwise logistic regression analysis (controlled for the confounding effects of sex and race) showed that the PTPN22 CT/TT genotype was associated with a significantly higher risk of SSc compared with the CC genotype (for patients with SSc, OR 1.64, 95% CI 1.2–2.2; for ACA‐positive patients with SSc, OR 1.63, 95% CI 1.0–2.6; for anti–topo I antibody–positive SSc, OR 2.33, 95% CI 1.5–3.7).ConclusionOur results indicate that the PTPN22 R620W polymorphism is associated with ACA‐positive and anti–topo I antibody–positive subsets of SSc and represents a risk factor in both white patients and black patients. The association of subsets of SSc with the PTPN22 R620W polymorphism further strengthens the classification of SSc within the spectrum of autoimmune diseases and strongly suggests the involvement of common susceptibility genes and similarly disordered immunoregulatory pathways.