Population Substructure and Control Selection in Genome-Wide Association Studies
Figure 5
SNP ranking correlation in prostate cancer studies.
In each plot, SNPs' rankings based on the 1 d.f. Wald test on 475,116 testing autosomal SNPs without PC adjustment are compared with their rankings based on the 1 d.f. Wald test with adjustment for PCs chosen by the permutation procedure. The SNPs in blue are ranked among the top 5% by tests both with and without PC adjustment. The SNPs in green and orange are ranked among the top 5% by only one of the tests. A) Results based on the original prostate cancer study (prostate cancer cases and controls from PLCO). The 1st PC was chosen for PS correction. B) Results based on the reconstructed prostate cancer study using external controls (prostate cancer cases from PLCO, and external controls from NHS). The 1st, 2nd and 4th PCs were chosen for PS correction.