SNP-based heritability is a fundamental quantity in complex trait genetics. As such, SNP-based heritability estimates from GWAS summary statistics are standard results to report in any major GWAS meta-analysis effort. For binary traits, such as case-control disease traits, SNP-based heritability estimates must be converted to the liability scale to be meaningfully interpreted. We demonstrate here that the field standard approach for estimating liability-scale heritability from meta-analytic GWAS summary data can downwardly bias liability-scale heritability estimates by as much as approximately 50% in simulations and approximately 30% in real data. We have therefore proposed a simple procedure for obtaining unbiased estimates of liability-scale SNP-based heritability in these contexts.
