We find high concordance between PrediXcan and S-PrediXcan results indicating that in most cases, we can use the summary version without loss of power to detect associations. Figure 2 shows the comparison of PrediXcan and S-PrediXcan Z-scores for a simulated phenotype (under the null hypothesis), a cellular growth phenotype and two disease phenotypes: type 1 diabetes and bipolar disorder from the WTCCC Consortium21; see Supplementary Notes 1, 2 and 3 for details. For the simulated phenotype, the study sets (in which GWAS is performed) and the reference set (in which LD between SNPs is computed) were African, East Asian, and European subsets from 1000 Genomes. The training set (in which prediction models are trained) was European (DGN Cohort5) in all cases. The high correlation between PrediXcan and S-PrediXcan demonstrates the robustness of our method to mismatches between reference and study sets. Despite the generally good concordance between the summary and individual level methods, there were a handful of false positive results with S-PrediXcan much more significant than PrediXcan. This underscores the need to use closely matched LD information whenever possible. Supplementary Fig. 11 shows S-PrediXcan’s performance on a phenotype simulated under the alternative hypothesis.
