Detection and correction for population stratification using various numbers of SNPs for PCA in the reconstructed study comparing prostate cancer cases from PLCO with controls from NHS.

aSNPs are randomly (except that the large set contains the smaller set) selected from the panel of 12,898 PS inference SNPs that are common to both the Illumina and Affymetrix commercial platforms.bThese PCs have a significantly large genetic variation (with P-values less than 0.05 based on the Tracy Wildom test).cThese PCs have a significantly different distribution between case and control groups (with P-value less than 0.05 based on the Wilcoxon rank-sum test).dThese PCs were chosen by the proposed permutation procedure for the correction of PS.eThe over dispersion factor was estimated by applying the 1-df Wald test statistic with the adjustment for the chosen PCs on the set of 241,238 genomic control SNPs.