Genotyping and the standard quality control filters that were applied are described in greater detail in Medland et al. (29) (see especially Table 1 in that publication). All genotyping was conducted on Illumina platforms, with genotypes called using Illumina BeadStudio software. Quality-control excluded SNPs with mean GenCall score less than 70%, with call rate less than 95%, with deviation from Hardy-Weinberg significant at p<10−6, or Minor Allele Frequency less than 1%. For the present study, Illumina CNV370-Quadv3 GWAS data were available on 4241 individuals (including most alcohol dependent cases) genotyped at CIDR and an additional 2611 individuals genotyped by deCODE for the OZALC project; Illumina 317K data were available for 53 individuals genotyped at the University of Helsinki Genome Center; and Illumina 610 Quad data were available for the remaining individuals genotyped by deCODE. Duplicate samples allowed comparison of genotyping across platforms/locations: a single SNP was identified, genotyped using the CNV370-Quadv3, that was called very differently at CIDR versus deCODE, and therefore deleted from the data-set. Checks were run on genetic relatedness, with misspecified relationships corrected prior to analysis.
