Fig 4 shows a contour plot for the PGS R2 based on a meta-analysis of 50 studies with a total sample size of 250,000 individuals, with 1k causal SNPs and 100k SNPs in total, and a CGR of 0.8 between both the discovery studies and the hold-out sample. In the plot, various combinations of hSNP2 in the discovery samples and hSNP2 in the hold-out sample are considered. The response of PGS R2 to heritability in the discovery sample and the hold-out sample is quite symmetric, in the sense that a low hSNP2 in the discovery samples and a high hSNP2 in the hold-out sample yield a similar R2 as a high hSNP2 in the discovery sample and a low hSNP2 in the hold-out sample. However, R2 is slightly more sensitive to hSNP2 in the hold-out sample than in the discovery samples. For instance, when SNP heritability in the discovery samples is 50% and 25% in the hold-out sample, the expected R2 is 10%, whereas in case the SNP heritability is 25% in the discovery samples and 50% in the hold-out sample, the expected R2 is 13%.
