In this work we propose a new approach for estimating h2, which takes as input the phenotypes and genotypes of admixed individuals such as African Americans. We show via analytical derivation as well as extensive simulation over both simulated and real genotype data that heritability explained by local ancestry (hγ2) is related to the total narrow sense heritability h2 via the equation hγ2 = 2FSTCθ(1−θ)h2, where FSTC is a specific measure of weighted allele frequency differences between ancestral populations at causal loci (see Online Methods) and θ is the fraction of European ancestry14,15. Since our approach does not use closely related individuals it is free from bias due to epistasis, gene environment interactions, and shared environment effects. Unlike previous work in which h2 estimates could not be obtained for case-control phenotypes11, our current approach can obtain estimates of h2 for both quantitative and case-control phenotypes, achieving goals (1) and (2). Furthermore, unlike previous methods that provide genome-wide estimates, we are able to estimate h2 for a particular genomic region, such as a chromosome, achieving goal (3). Our approach can be
