The effect of the SNP genotypes on the dichotomous celiac disease outcome was analyzed using logistic regression models. For the GWAS analysis, the SNPs were coded as continuous variables, with genotypes coded as 0, 1 or 2 to indicate the number of minor alleles in the SNP. The statistical model included the sex of the individual, and the computed principal components of the genomic kinship matrix. There was no significant age effect observed, so the variable was not included in the GWAS analysis. Odds ratios and 95% confidence intervals were calculated from the computed regression coefficients for the SNP genotype effect and standard errors. The dermatitis herpetiformis and microscopic colitis dichotomous phenotypes were analyzed for association using a logistic regression model. All SNPs were analyzed with all samples using a model that included celiac disease status and the SNP as predictors. A second analysis of the two phenotypes included only the celiac disease cases (case-only analysis) and the genotype was the only predictor in the model. The GenABEL library [15] of the R statistical computing environment was used for all association analysis.
