Association tests in the GWAS datasets (our own dataset individually in Phase 1, then combined with the SAGE dataset in Phase 2) used linear or logistic association models with generalized estimating equations (GEE) to correct for the correlations among related individuals. We evaluated the replication sample of unrelated individuals–the part of the sample that was genotyped individually only for replication SNPs–using linear and logistic models. All models were adjusted for age, sex, and the first three PCs of ancestry.
