In the Phase 2 analyses described below, we included publically available GWAS data from SAGE (http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000092.v1.p1) (15). The SAGE dataset contained 1,311 AA and 2,750 EA unrelated individuals (Table 2). SAGE includes individuals from the Collaborative Study on the Genetics of Alcoholism (COGA) (5), the Family Study of Cocaine Dependence (FSCD) (6), and the Collaborative Genetic Study of Nicotine Dependence (COGEND) (15). The COGA sample is a set of unrelated individuals recruited in Indiana, New York, St. Louis, Connecticut, Iowa, and San Diego selected for genotyping from a larger set of 8,000 subjects. Cases met criteria for DSM-IV AD. FSCD contained cases and controls from the greater St. Louis metropolitan area. All cases met criteria for DSM-IV AD and most also met criteria for DSM-IV CD. Controls were from the same communities and had consumed alcohol, but had no lifetime history of substance dependence. A subgroup of FSCD subjects was not alcohol dependent, but had a lifetime diagnosis of DSM-IV cannabis dependence or dependence on another illicit drug. COGEND subjects were recruited in MO and MI. Cases met criteria for
