Discrepancy in SNP selection for the follow-up study between the permutation procedure and an alternative PC adjustment strategy.

Note: Under the premise that the top 5% of the testing SNPs ranked by the statistic using a given PC adjustment strategy are to be followed-up to the next stage, the discrepancy the proportion of SNPs selected by this procedure and not selected by the permutation procedure.aPLCOca-PLCOco is the original PLCO prostate cancer study.bPLCOca-NHSco is the reconstructed study with prostate cancer cases from the PLCO, and external controls from NHS.cNHSca-NHSco is the original NHS breast cancer study.dNHSca-PLCOco is the reconstructed study with breast cancer cases from the NHS, and external controls from PLCO.eNo PC adjustment in the association test.fAdjustment for the top 10 PCs ranked by their associated eigenvalues.gAdjustment for the PCs with significant genetic variation (P-value