Principal-components analyses were carried out separately for the European, Asian and African-American subgroups, on the basis of a subset of 37,000 uncorrelated SNPs. For the analyses of European subjects, we included the first six principal components as covariates, together with a seventh component derived specifically for one study (LMBC) for which there was substantial inflation not accounted for by the components derived from the analysis of all studies (this component was set to zero for all other studies). The addition of further principal components did not reduce inflation further. We included two principal components each for the studies in Asian and African-American populations.
