The Cancer Genetic Markers of Susceptibility (CGEMS) project has conducted two multi-stage GWAS in breast cancer and prostate cancer [1], [3], [21]. For each disease, the initial genome-wide scan was performed in a nested case-control study drawn from a prospective cohort in self-described European Americans. The CGEMS data provides the opportunity for empirical evaluation of the impact of population stratification in an optimal study design. By exchanging the control groups of the two studies, we have explored the consequences of the non-standard strategy of using external controls. We thus can make comparisons between the two approaches.
