To assess whether our results were driven primarily by the alcohol dependence phenotype, rather than by the comorbid phenotype, we ran a parallel analysis comparing N=354 individuals with alcohol dependence but without depressive syndrome to N=407 controls who had neither disorder (the same controls that were used in the primary analysis). We then compared p-values from that analysis to those in our original list of SNPs with p<10−3. Only 52 of the 938 markers reported here met the same criteria in the alcohol dependence-only analysis; 44.3% (416/938) had p<0.05. The direction of the allelic effect was reversed in 12 (of 938) cases, but none of those 12 markers had p<0.05 in the secondary analysis.
