Computational protocol: A Promoter Region Polymorphism in PDCD-1 Gene Is Associated with Risk of Rheumatoid Arthritis in the Han Chinese Population of Southeastern China

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Protocol publication

[…] The deviation from Hardy-Weinberg equilibrium (HWE) was examined in controls by the  χ 2 test. The following statistical analyses were performed using SNPstats software (Availability: []. Based on the logistic regression method, the case-control association of genotypes was tested and the odds ratios (OR) and 95% confidence intervals (95% CI) were given. D′ and r 2 were calculated to evaluate the magnitude of LD. Haplotype frequencies were estimated using the EM algorithm coded into the haplo.stats package ( The association analysis of haplotypes was similar to that of genotypes with logistic regression, and results were shown as OR and 95% CI. The most frequent haplotype was automatically selected as the reference category and rare haplotypes were pooled together in a group. The log-additive inheritance model was assumed by default. The significance level of all these tests was 0.05. The nonparametric Mann-Whitney U test was used for comparisons among groups with small or unequal sample sizes. Results were expressed as the mean ± SEM, and 2-tailed P values less than 0.05 were considered significant. […]

Pipeline specifications

Software tools snpStats, haplo.stats
Application GWAS
Organisms Homo sapiens
Diseases Arthritis, Rheumatoid, Autoimmune Diseases