Fig. 2. GAUDI performance compared to PRSice and pPRS in large EUR simulation studies under different settings.

a–c $p_{\text{shared}}$ (proportion of variants with shared effects across ancestry groups) = 1: no ancestry-differential effects for all causal variants. d–f $p_{\text{shared}}$ = 0.5: half of the causal variants have ancestry-differential effects. a, d Causal variants are common only in AFR ancestry, specifically EUR-MAF < 5% and AFR-MAF > = 5%. b, e Causal variants are common only in EUR ancestry, i.e., EUR-MAF > = 5% and AFR-MAF < 5%. c, f Causal variants are common in both ancestries, i.e., EUR-MAF and AFR-MAF both >= 5%. Each experiment was repeated 10 times (shown in the box plots). The minima, maxima and center represent the minimum, maximum and median test R² across the 10 repeats. The bounds of the boxes represent upper and lower quartiles, with whiskers represent 1.5 times of the interquartile range. The maximum LD R² between causal variants were set to be 0.2 for all settings. The dashed red line denotes heritability. $p_{\text{causal}}$: proportion of causal variants out of all variants. Source data are provided as a Source Data file.