A GWAS of AD status was performed within each ancestry stratum of each sample using an association model appropriate for the study design (Table 1, Supplementary Table S1). For case/control studies, GWAS was performed using logistic regression with imputed dosages. For family-based studies of small, simple pedigrees (e.g., sibships), association with imputed genotypes was tested using generalized estimating equations (GEE). For more complex pedigrees, imputed genotypes were tested using logistic mixed models. Sex was included as a covariate, along with principal components to control for population structure (Supplementary Information A6, Supplementary Note B2, Supplementary Figures S13–S14).
