For the GWAS analysis in this report, we defined as “cases” those individuals who, in addition to meeting lifetime DSM-IV criteria for alcohol dependence, also met lifetime DSM-IV symptom threshold for a major depressive episode (≥5 out of 9 symptoms within a 2 week period, one of which had to be sadness or anhedonia). Individuals were excluded if symptoms were due to bereavement, but not if symptoms were experienced under the influence of drugs and/or alcohol. For the sake of simplicity, we will refer to the depression phenotype as “depressive syndrome” (as in Nurnberger et al., 2001); the reader should note that cases were required to meet Criterion A for a major depressive episode (in addition to being alcohol dependent) but were not required to have experienced these symptoms independent of alcohol or other substances, and thus do not necessarily meet full criteria for a major depressive episode (see below for additional details). Controls were excluded if they met our criteria for depressive syndrome. Cases and controls differed significantly by age (t=7.87, p<0.001), with controls being older (47.5±.63) than cases
