Logistic regression analyses performed in PLINK software,36 which included smartpca-derived PCs in models to control for admixture, examined the association between the log-additive effects of minor allele dosage and case status. We separately compared 1459 heroin-dependent cases (888 male, 571 female; mean [SD] age, 36.5 [8.6] years) with 531 neighborhood controls (235 male, 296 female; mean [SD] age, 34.7 [10.5] years) and 1495 ATR controls (972 male, 523 female; mean [SD] age, 45.0 [9.5] years). Because of uncertainty regarding the most appropriate control group for the current investigation and given within-group differences in the neighborhood controls observed in stage 1 analyses,27 we compared heroin-dependent cases with subgroups of neighborhood controls who were not dependent on the following: (1) any illicit drugs (N=340); (2) any illicit drugs or alcohol (N=275); and (3) any illicit drugs, alcohol, or nicotine (N=207). We also conducted a within-group comparison of neighborhood controls who were and were not illicit drug dependent. A conservative Bonferroni correction for multiple testing yielded a revised significance threshold of P = 3.9 × 10−6 (i.e., .05 /1430 SNPs/ 9 phenotypic comparisons:
