As another assessment of the performance of the AIM sets, we examined whether these AIMs could correct for false-positive association results in models for population specific disease susceptibility loci. Using 200K genotypes from the I-control database and additional genotypes available from other ongoing studies (see Methods) we specified specific genotypes as disease surrogates and identified true (located in a close genetic position to the modeled SNP) and false (unlinked) associated SNPs. These population sets included genotypes for each of the 128 In4 AIMs since each is included within the Illumina 300K array. Three disease gene models were specified using the surrogate phenotypes defined by SNPs in strong LD with 1) a nonsynonymous genetic substitution in SLC24A5 on chromosome 15 under strong positive selection in Europeans, 2) lactase tolerance phenotype on chromosome 2 that is under strong positive selection in northern European populations and 3) a nonsynonymous coding variant in ADH1B under positive selection in East Asian populations (see Methods for additional details).
