Figure 3.

Performance of P + T, EN, and LDpred2 methods on different variant sets in INTERVAL

Using conditional analysis variants as a base set, we added in the selected variant sets with LD thinning and p value thresholding to form different sizes of expanded variant sets for each trait. We used the CA variant set as the starting point and then observed the performance of P + T, EN, and LDpred2 on these expanded variant sets. Note that in this figure, P + T refers to the method that directly applies the weighted sum on a given variant set with effect sizes from GWAS.

See Figure S2 for similar performance comparison in UKB.