Controls for occult stratification among these subjects and poor technical quality in the nominally-positive SNPs identified here fail to provide alternative explanations for the positive results of comparisons between smokers and controls. Only 837 of the nominally-positive SNPs from the smoker-control comparisons display large allele frequency differences between European- and African-American control individuals. This number is smaller than the 2,223 SNPs that would be expected to have such properties if they were selected by chance. Only 158 of the nominally-positive SNPs from the smoker-control comparisons in these data lie among the SNPs that display the largest variation between pools in data from this and other studies using the same arrays. This number is also smaller than chance values. These comparisons thus fail to support the alternative hypotheses that either occult ethnic stratification in these samples or technical problems with assays for these SNPs provided the basis for the overall results reported here.
