Author reply to A Commentary on Pitfalls of predicting complex traits from SNPs

We thank de los Campos and Sorensen (D&S) for their Correspondence, which follows their recent work1. D&S agree that maximum prediction accuracy depends on h2M, defined as the variance explained by genotyped markers in the population. They claim that estimates of h2M in a finite sample (h2G-BLUP or h2G) may overestimate h2M, and that this is exacerbated for unrelated individuals. We respond by showing how and why we disagree with these claims. h2G and h2G-BLUP are estimates of the same parameter from equivalent models3–6 and so, for the same dataset, they must have the same value. Both measure the proportion of the phenotypic variance that is explained by the markers. This proportion depends on linkage disequilibrium (LD) between the SNPs and causal variants or quantitative trait loci (QTL). If the LD is imperfect, then h2M will be less than the conventional heritability, h2, which is the proportion of variance explained by all causal variants. The extent of LD depends on th