Our simulation studies focused on the impact of LD and variability in the estimation of effect sizes, caused by small sample size and admixture, on PRSs, in admixed populations with two ancestral populations (compared to the three ancestral populations of Hispanics/Latinos), CEU (EA) and YRI (African ancestry, AA), for simplicity. Henceforth, we always refer to admixed populations as ADM. When distinction is needed, we add subscripts to denote sample sizes (an integer representing thousands of individuals) and proportions of AA admixture (a number between 0 and 1). We simulated genotypes in a 1Mbp genomic region for a large EA sample (nEA = 50,000), a moderately sized admixed sample (ADM12, with nADM12 = 12,000), and a small admixed sample (ADM5, with nADM5 = 5, 000). Admixture proportions where either 20% or 40% of YRI. These proportions were selected based on observed proportions of African ancestries in HCHS/SOL’s Dominican and Puerto-Rican background groups respectively (see Figure 2 in Conomos et al. (2016)). We simulated quantitative traits under a few potential genetic architectures, assuming one or two causal SNPs, which are either shared
