Filtering on MAF differences between the Hapmap and the study genotypes is another possible approach to control false positives. In Table 3 and Supplementary Table S1, we provided results filtered by MAF difference at 0.01, 0.1 and 0.2 for European Americans and African Americans, respectively. Filtering by MAF difference of 0.01 resulted in a reduction of false positives, but retained less than 25% of the SNPs. In contrast, filtering with a MAF difference of 0.1 or 0.2 retained many false positives.
