Population stratification artifacts were assessed in two ways. As described elsewhere (36), including principal components as covariates in a logistic regression model can robustly control stratification effects. To do this, we identified a set of 127,688 SNPs in linkage equilibrium (43) and used the “smartpca” program in EigenSoft (44) to compute 10 principal components for each subject that were included as covariates in logistic regression models (case/control status ∼ SNPi + PC1 + PC2 + … + PC10). We also used a stratified Cochran-Mantel-Haenszel test in PLINK (43) as a complementary approach.
