Population Substructure and Control Selection in Genome-Wide Association Studies
Figure 3
Q-Q plot based on the test without PC adjustment.
For each of the four analyses, the Q-Q plot is based on P-values (in log10 scale) that correspond to the 1 d.f. Wald test on 475,116 testing autosomal SNPs by assuming an additive risk model (in logit scale) and without PC adjustment. A) Results for the original prostate cancer study (prostate cancer cases and controls from PLCO). B) Result for the reconstructed prostate cancer study using external controls (prostate cancer cases from PLCO, and external controls from NHS). C) Results for the original breast cancer study (breast cancer cases and controls from NHS). D) Results for the reconstructed breast cancer study using external controls (breast cancer cases from NHS, and external controls from PLCO).