For both PLCO and NHS, analyses of population stratification were conducted using approximately 10,000 unlinked SNP markers [51], [52]. Individual European, Asian and African admixture proportions were estimated by STRUCTURE [53] applied to CGEMS data augmented by the HapMap CEU, CHB+JPT and YRI samples. Subjects with significant non-European admixture were excluded for PLCO and NHS. Residual within-Europe population stratification was estimated using the top three (PLCO) or four (NHS) principal components of genetic variation, as calculated using EIGENSTRAT [54].
