Interpreting SNP heritability in admixed populations.

ABSTRACT: Single-nucleotide polymorphism (SNP) heritability (hsnp2) is defined as the proportion of phenotypic variance explained by genotyped SNPs and is believed to be a lower bound of heritability (h2), being equal to it if all causal variants are genotyped. Despite the simple intuition behind hsnp2, its interpretation and equivalence to h2 is unclear, particularly in the presence of admixture and assortative mating. Here, we use analytical theory and simulations to describe the behavior of h2 and three widely used random-effect estimators of hsnp2-genome-wide restricted maximum likelihood, Haseman-Elston regression, and LD score regression-in admixed populations. We show that hsnp2 estimates can be biased in admixed populations, even if all causal variants are genotyped and in the absence of con

SUBMITTER: Huang J 

PROVIDER: S-EPMC12273224 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature