The variance Vk is inversely proportional to the sample size as long as the effective number of chromosome segments, Me, is the same in every GWAS sample in the analysis.24–26 As in the calculation of the GWAS-equivalent sample size, where we assume that Me is the same in every GWAS sample and in the prediction sample, the expected predictive power of a polygenic score is E(Rk2)=(h2)2h2+Vk, where h2 is the SNP heritability of the trait.28–30 (Note that if Me were to differ greatly across samples, then it would be important to take this into account when calculating the expected predictive power.24,25)
