Fourth, we reduced the causal effect size of trait 1 on trait 2 (Figure 3d and Supplementary Table 3h-j). LCV had low power, and other methods had very low power. Fifth, we increased the polygenicity of the causal trait (Figure 3e, Supplementary Table 3k-m). LCV had moderate power while the MR methods had very low power, again owing to the low number of genome-wide significant SNPs. We also simulated a partially genetically causal relationship (gcp=0.25-0.75), with similar results (Supplementary Table 3p-r). We compared our gcp estimates in fully causal simulations with our gcp estimates in partially causal simulations, finding that LCV reliably distinguished the two cases, unlike existing methods (Supplementary Table 3a,p-r).
