Cases, neighborhood controls, and ATR controls all consisted primarily of individuals of European ancestry. The former two groups also included some individuals of Asian ancestry. Principal components analyses (PCAs) were conducted using the smartpca program in the Eigensoft version 3.0 statistical software package35 to determine the appropriate admixture correction for each analysis. The kill r2 setting of 0.8 was used to remove some SNPs in high linkage disequilibrium (LD) with others in the panel with data from 1123 of the 1430 SNPs retained for PCA. Because ancestry-informative markers (AIMs) were included in the PCA, Tracy-Widom statistics could not be used to determine the number of principal components. Separate PCA indicated that comparisons of cases to neighborhood controls required no inclusion of principal components (PCs) as covariates, while that comparing cases with ATR controls found at least a trend-level significance for 4 principal components (PCs) (for details and PC plots, see the article by Nelson et al 27). For analyses that divided the neighborhood controls on the basis of lifetime licit and illicit drug dependence, a separate PCA run for each
