The analyses of empirical data generated from the CGEMS project suggest that the effect of PS in the GWAS of prostate and breast cancers conducted in European American is small when the study is epidemiologically well designed, but can be substantial when controls and cases are drawn from separate studies. The elevated confounding effect of PS due to the use of less desirable controls can be effectively mitigated by methods such as the one proposed here. The impact of using convenience controls on the power for the detection of disease related markers needs to be further investigated, especially in recently admixed populations.
