That so few (<6.0%) of the markers associated with the comorbid phenotype at p<10−3 met the same criteria in the analysis of alcohol dependent-only individuals is intriguing. However, 45.0% (391/868) of our significant SNPs met much less stringent criteria (p<0.05) in the alcohol dependent-only analysis. P-values were significantly correlated across the analyses (p=0.0016, F=10.0, adjusted r2=0.010), suggesting not only that the comorbid phenotype and alcohol dependence alone are highly correlated, but also that the former is also influenced by many genetic variants that are not independently associated with alcohol dependence on its own. Thus, many of the variants reported here might be specific to susceptibility for only the comorbid phenotype, while others predispose to alcohol dependence or depressive syndrome in the absence of the other. This finding is consistent with previous reports. Many genes have been associated with alcohol dependence or depression but not the other (for reviews, see (Gelernter et al., 2009; Levinson, 2006), and some genes – notably those related to monoaminergic neurotransmitters – have been associated with both (for a review, see (Saraceno et al., 2009). Our
