six to ten SNPs with the strongest false positive associations and a similar number of true positive associations with χ2 values comparable to the false positives were selected for further analysis; 5) the genotypes for the chosen true and false positively associated markers are combined with genotypes for the markers in the selected sets (all 200K SNP markers, 128 In4, 96 In4, 64 In4, 48 In4, and 24 In4), and were tested for association testing correcting for substructure by principal component analysis using EIGENSTRAT (Price, et al., 2006); 6) the positively associated markers were re-analyzed for association using correction for population stratification with an appropriate number of principal components (PC 1 or PC2 depending on the studies population, determined by the plateau of χ2 values).
