Neither controls for occult stratification nor for assay variability appear to provide convincing alternative explanations for most of the data obtained here. When we examined the overlap between the 7620 clustered positive SNPs from the ECA samples and: 1) the 2.5% of the SNPs for which the noise in validating studies was highest and 2) the 2.5% of SNPs that displayed the largest differences between Baltimore African-American vs European American control individuals, we found 15 and 245, respectively, vs 185 expected by chance in each case.
