There are three phases of the Yale–Penn study defined by genotyping epoch; the first two were incorporated in the PGC study, thus they are included in the meta-analyses. Here, we included Yale–Penn 3 individuals as a separate sample. Lifetime AD was diagnosed based on DSM-IV criteria. Genotyping was performed in the Gelernter laboratory at Yale using the Illumina Multi-Ethnic Global Array, then imputed using Michigan imputation server with Haplotype Reference Consortium reference. We performed PCA analyses to classify EAs (567 cases and 1,074 controls) and AAs (451 cases and 410 controls). Variants with MAF >0.01, HWE P value >1 × 10−6 and imputation quality score (INFO) ≥0.8 were retained for association analyses using linear mixed models implemented in GEMMA72 and corrected for age, sex and ten PCs.
