Additional subject exclusions were made in dbGaP studies to remove the original study cases [e.g., alcohol dependent cases from the Study of Addiction: Genetics and Environment (SAGE) (Bierut et al. 2010)] (Table 1). No phenotypic exclusions were made for the iControl subjects, since no phenotype information is provided in the iControl database. Following all subject-level QC, genotyped SNPs were excluded due to minor allele frequency (MAF) <1 %, call rate <95 %, or Hardy–Weinberg equilibrium P < 0.0001. Numbers of genotyped subjects and polymorphic SNPs before and after QC are provided in Table 1.
