e) Controls for the alternative possibilities that results could come from occult racial/ethnic stratification or assay noise. Several alternative hypotheses might explain observed results. To test some of these alternative hypotheses, we compare the clustered- positive SNPs from different samples with SNPs that display the largest allele frequency differences in appropriate control datasets. These comparison datasets include those that contrast allele frequencies in 1) European-American vs African American control individuals from NIDA samples [12]; 2) Japanese vs Han Chinese individuals from HapMap samples (JPT: Japanese from Tokyo and HCB: Han Chinese from Beijing), 3) control individuals sampled in different portions of the United Kingdom [1], and 4) SNPs that display the largest variances from array to array [12]. We can thus compare data from the true comparisons in our experiments to similarly-analyzed data from samples that test alternative hypotheses, providing substantial additional control evidence.
