Cohorts 1 and 2 are almost entirely of European ancestry, reflecting restrictive Australian immigration policies through 1972; however, Eigenstrat analyses (32), which included data from other Australian GWAS series, identified as outliers (operationalized by +/− 6 standard deviations) a small number of families of mixed European and Asian ancestry (principally Chinese, Burmese, Indian or Malaysian), of middle eastern (Lebanese) ancestry; with one or more grandparents of Aboriginal, Torres Strait Islander or Maori ancestry; or with some African heritage (including individuals of self-report Maltese ancestry, consistent with the known population genetics of the Maltese population) (see (29)). A total of 153 individuals from 60 families were thus identified, and excluded from further analyses: this included 34 alcohol dependent and 119 unaffected individuals. In the analyses presented here, we use only data from the approximately 300,000 SNPs that passed quality-control and were available on all platforms. We do not attempt imputation, given the potential for statistical problems in the analysis of imputed data (e.g. biased estimates of effect size) in family-structured data-sets.
