GWAS genotypes from all subjects taken separately in each sample group of Yale-Penn 1-3 were compared with the 1000 Genomes Project phase 1 reference panel (6). Eigensoft (7) was used for principal components analysis. The first 10 PC scores served to differentiate European-Americans (EAs) and African-Americans (AAs) through K-means clustering (8). Here, we present GWAS data only for EAs (our previous study presented numerous positive GWAS results in AAs). For each Yale-Penn cohort, genotypes from EAs and AAs were imputed together with Minimac3 implemented in Michigan Imputation Server (https://imputationserver.sph.umich.edu/index.html) with genotyped SNPs and the 1000 Genomes reference phase 3 release that contains haplotypes on 2504 samples (n = 5008 haplotypes for a total of ∼81.2M polymorphic markers). The imputation data for Yale-Penn 1-3 were generated in dosage format separately. Under imputation R2>0.3, there was an average of ∼47.1M variants included in dosage data from Yale-Penn 1-3. The dosage genotypes for each cohort were transformed into hard call genotypes with PLINK1.9 (5). Using hard-call genotypes to analyze imputed GWAS genotypes has been reported previously (9). In our study, the dosage genotypes
