We used two complementary SNP selection strategies, a ‘lowest p-value’ strategy and a ‘rodent candidate gene’ strategy, to prioritize SNPs for follow-up. In total, 139 SNPs were carried forward for genotyping in the follow-up sample. These included all SNPs with a p-value <10-4 (Armitage trend test for autosomes and allelic test for x-chromosome), n=121, of which an assay design was possible for n=120 (see Supplementary Online Content eTable 1), and additional 19 SNPs with at least nominal significance, which would not have been accounted for by the ‘lowest p-value’ approach. These 19 SNPs are among 22 SNPs (three of which were already represented in the aforementioned ‘lowest p-value’ selection) located in human homologs of rat genes showing differential expression in the rat brain following chronic alcohol consumption (for more details see Supplementary Online Content) and therefore have a higher a priori probability of being involved in the aetiology of alcohol dependence.
