Further dissection of such loci will likely require deep sequencing of the genome for many individuals and additional large-scale studies. One general limitation of hybridization based arrays is that detection of low expression genes is difficult, which may be overcome by RNA sequencing in the future. In addition to both of these technological developments, eQTL surveys such as the one presented here will need to be repeated as the number of SNPs nominated by GWAS studies increases. This is perhaps particularly true for brain related phenotypes. Although we did not find that there were significantly more eQTLs for brain phenotypes using brain expression data, the number of replicated GWAS ‘hits’ for neurological and psychiatric conditions is still quite small and we might expect the brain to be more sensitive as the number of replicated loci increases. We have not tested all possible SNPs in the current analysis to maintain power to detect significant associations, but such analyses could be performed on an ad hoc basis for nominated SNPs in future GWAS without the loss of power caused by testing the whole genome.
