to control for the non-independence of related subjects, in parallel to the methods used in the IASPSAD GWAS. In FT12, one twin from MZ pairs was excluded from the GWAS for a total discovery n = 905. In both FT12 and COGA, GWAS of DSM-IV alcohol dependence symptoms have previously been conducted (see Wang et al., 2013; Meyers, 2012); however, we repeat the analyses here because the datasets have been imputed to the 1000 Genomes reference panel since the original reports and additional follow-up assessments have been collected for some participants. No new genome-wide significant SNP associations were found in these analyses. Meta-analyses of the GWAS summary statistics were also conducted for the population-based (ALSPAC+FT12) and ascertained (COGA+IASPSAD) sample results using METAL (Willer et al., 2010), with a sample size-weighted scheme. Additional meta-analyses were run for each pair of samples, within and between sample type, to test for heterogeneity in SNP association statistics between them using a random effects meta-analysis model.
