On 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, we evaluated the concordance between two sets of follow-up SNPs, namely, those chosen by the test adjusting for PCs selected by the permutation procedure, and those chosen by the test adjusting for PCs selected by an alternative strategy (such as adjusting for the top 10 PCs, or no PC adjustment). In PLCOca-PLCOco, among the follow-up SNPs chosen by test without PC adjustment, approximately 7% of them would not have been chosen by the test with the adjustment of PCs identified by the permutation procedure. The discrepancy increases to 23% in the corresponding study with external controls PLCOca-NHSco (Table 6). A similar pattern was also observed in the breast cancer studies with swapping of internal and external controls. We note that in each of the four studies considered the vast majority of SNPs ranked in the top 1% by the test with PC adjustment were ranked within the top 5% by the
