GCTA-GREML accounts for linkage disequilibrium when estimating genetic variance from genome-wide SNPs

In a recent publication in PNAS, Krishna Kumar et al. (1) claim that “GCTA applied to current SNP data cannot produce reliable or stable estimates of heritability.” We show below that those claims are false due to their misunderstanding of the theory and practice of random-effect models underlying genome-wide complex trait analysis (GCTA) (2). GCTA, more precisely, the genomic-relatedness-based restricted maximum-likelihood (GREML) approach (3)...