We compare PRS-CS and PRS-CS-auto with four polygenic prediction methods that rely on GWAS summary statistics in both simulations and real data analyses: polygenic scoring based on all genetic markers (unadjusted PRS), informed LD-pruning (also known as LD-clumping) and P-value thresholding (P+T), LDpred and LDpred-inf4. Throughout the paper, we use the 1000 Genomes Project (1 KG) European sample (N = 503) as the external LD reference panel, but also assess the impact of using an in-sample LD reference panel on prediction accuracy in Supplementary Information.
