Concepts, estimation and interpretation of SNP-based heritability

Narrow-sense heritability (h(2)) is an important genetic parameter that quantifies the proportion of phenotypic variance in a trait attributable to the additive genetic variation generated by all causal variants. Estimation of h(2) previously relied on closely related individuals, but recent developments allow estimation of the variance explained by all SNPs used in a genome-wide association study (GWAS) in conventionally unrelated individuals, that is, the SNP-based heritability (h(SNPh)(2)). In this Perspective, we discuss recently developed methods to estimate h(SNPh)(2) for a complex trait (and genetic correlation between traits) using individual-level or summary GWAS data. We discuss issues that could influence the accuracy of h(SNPh)(2), definitions, assumptions and interpretations of the models, and pitfalls of misusing the methods and misinterpreting the models and results.