In summary, the comparable patterns in population substructure for the two genome-wide scans in PLCO and NHS suggest that controls from one study may reliably be used to contrast with cases from the other study in an association analysis. This similarity is remarkable since the PLCO prostate cancer study was assembled from male volunteers of European origin participating in a cancer screen trial and enrolled at 10 screening centers while the NHS breast cancer study was based on a sample of female registered nurses participating in a long-term epidemiology study originally enrolled from 14 large US states. However, because we have also shown that the two studies have demonstrable genetic background differences, using external controls in association studies requires a careful examination of the confounding effect due to PS. The observed genetic background difference between the two studies could in part be due to the difference in geographic locations of the source populations which were sampled, as people from distinct regions tend to have different genetic background. For example, by using the Kruskal-Wallis test [29], which is the non-parametric version
