IlluminaHuman1M-Duov3_B genotyping and QC filtering of African-American samples from the African American Prostate Cancer Study (AAPC) from a total of 11 participating studies was performed as described previously55,53,54. The cleaned dataset includes 9,641 African American subjects and 1,001,899 autosomal SNPs. To limit relatedness among samples we restricted all analyses to a subset of 8,215 samples in which all pairs have genome-wide relatedness of 0.05 or less. We performed local ancestry inference using the RFMix24 with the CEU and YRI HapMap populations as reference ancestral populations. We examined prostate cancer (PC) outcome for each subject. There were 4207 cases and 4008 controls after QC. Due to the admixture signal at the 8q24 locus54, we also estimated heritability removing 8q24 from the SNPs used to estimate the kinship (PC|8q24). For each phenotype we included age and the top 10 principal components as fixed effects. For conversion to the liability scale we used a prevalence of 5%54.
