GWAS was completed for five composite quantitative clinical phenotypes, which were derived using a hierarchical factor analytic approach as described in Hicks et al. (Hicks, Schalet, Malone, Iacono, & McGue, 2011), which also provides additional details on the development of the clinical phenotypes. The five phenotypes (brief description) are: 1) Nicotine (composite of measures of quantity and frequency of nicotine use and symptoms of nicotine dependence), 2) Alcohol Consumption (composite of measures of alcohol use frequency and quantity), 3) Alcohol Dependence (composite of DSM symptoms of alcohol dependence/abuse and non-diagnostic alcohol-related problems), 4) Illicit Drugs (composite of frequency of use of 11 different drug classes and DSM symptoms of drug dependence), and 5) Behavioral Disinhibition (composite of measures non-substance use behavioral disinhibition including symptoms of conduct disorder and aggression). As expected, the clinical phenotypes were significantly and moderately intercorrelated (ranging from .46 to .71; Supplemental Table S1).
