Routines for aggregating genome-wide SNP counts into composite scores (Fig. S1) were designed using GWAS data from case-control subjects representing European-American (n = 1,274) and African-American (n = 285) populations, as ascertained by the Collaborative Study on the Genetics of Alcoholism (COGA) (Edenberg et al. 2010), a national consortium designed to study the genetic predisposition to develop alcoholism and related phenotypes. Alcoholic probands were recruited from inpatient and outpatient treatment centers, whereas controls were selected from Health Maintenance Organizations (HMOs), drivers’ license records, and dental clinics, with the objective of obtaining representative samples of the communities at each recruitment site (Reich et al. 1998). All cases were diagnosed for DSM-IV alcohol dependence at each clinical assessment if assessed multiple times. To avoid pleiotropic genetic components that contribute to multiple substance abuse phenotypes, non-alcoholic controls did not meet diagnostic criteria for other illicit substance abuse or dependence (although cases could). Furthermore, controls were required to be 25 years or older and to have consumed alcohol at some point in their lives to ensure that their unaffected status was not due to
