Comparison TWAS/PrediXcan p-values across software.
Comparison of TWAS/PrediXcan p-values calculated by GAMBIT versus S-PrediXcan (cloned from GitHub on April 10, 2020) using GWAS summary statistics for HDL cholesterol from the Global Lipids Genetics Consortium . Results are shown for 25,691 unique genes across 47 tissues using GTEx v7 HapMap predictive weights from PredictDB [6, 7]. Signed -log10(p)-values are shown for p ≥ 10−50; 10 genes with outlying p < 10−50 are not displayed. The squared Pearson correlation between z-scores is 0.995; differences in z-scores between GAMBIT and S-PrediXcan are presumably due to differences in the LD reference data. S-PrediXcan uses precomputed LD files which are packaged together with predictive weights, whereas GAMBIT calculates LD interactively from a reference panel (here, European individuals in the 1000 Genomes Project).