Fig. 3. Relative performance of different MR methods.

The figure shows performance of MR methods on simulations representing the pleiotropy through linkage disequilibrium (LD) scenario (depicted in Fig. 2b) when 1, 3, 5, or 10 causal expression quantitative trait locus (eQTL) single nucleotide polymorphisms (SNPs) were simulated (“Methods”). a False positive rates (at alpha = 0.05) in scenarios where no causal relationship is simulated. b Power to detect a small causal effect (at alpha = 0.05). c Power to detect a large causal effect (at alpha = 0.05). Note that MR-link is the only MR method that can adjust for pleiotropy when only one or two instrumental variables are available. MR methods that had fewer than 100 out of 1500 estimates in a scenario are not shown (“Methods”). Extended results, including those that are not shown in the figure, can be found in Supplementary Data 3.