To further study the effect of sample size on prediction performance, we simulated traits using SNPs of chromosome 1, chromosomes 1 and 2, chromosomes 1 to 4 and the whole genome while keeping the same proportion of causal variants and heritability to mimic the situation of increasing sample size. The corresponding relative sample sizes (NMMs, where N is the number of individuals, M is the total number of variants and Ms is the number of variants used in simulation) for the four scenarios are ~135K, ~67K, 37K and ~11K. For each effective sample size, we simulated traits under four settings: h2 = 0.25, p = 0.001; h2 = 0.25, p = 0.01; h2 = 0.5, p = 0.001; h2 = 0.5, p = 0.01, where p represents the proportion of causal variants (Fig 1).
