SNP-based heritability estimation: measurement noise, population stratification, and stability

Siddharth Krishna Kumar1 and co-authors claim to have shown that \"GCTA applied to current SNP data cannot produce reliable or stable estimates of heritability.\" Given the numerous recent studies on the genetic architecture of complex traits that are based on this methodology, these claims have important implications for the field. Through an investigation of the stability of the likelihood function under phenotype perturbation and an analysis of its dependence on the spectral properties of the genetic relatedness matrix, our study characterizes the properties of an important approach to the analysis of GWAS data and identified crucial errors in the authors analyses, invalidating their main conclusions.