Figure 1.

Simulation TWASs Comparing BGW-TWAS, BVSR with cis-eQTL only, PrediXcan, and TIGAR Methods

Simulation studies used various gene expression heritability $h_e^2=(0.05,0.1,0.2,0.5)$ and various true causal cis-eQTL proportions. Test R² was calculated as the squared correlation between imputed GReX and simulated gene expression values of the test samples.

(A and B) Test R² and TWAS power comparison with 5 true causal eQTL. BGW-TWAS was found to out-perform the alternative methods when a non-negligible proportion of true causal eQTL were from trans-genome regions.

(C and D) Test R² and TWAS power comparison with 22 true causal eQTL. BGW-TWAS was found to out-perform alternative method when >50% of true causal eQTL were from trans-genome regions and $h_e^2>0.1$.