Meta-analysis of the discovery and replication PWAS was performed using METAL61. For the hypothesis driven meta-analysis, i.e. meta-analysis of the genes found to be significant in the discovery PWAS, we declared as replicated for genes with meta-analysis p-values lower than the p-values of the discovery dataset and had the same direction of association in both datasets. For the proteome-wide meta-analysis for all genes present in both the discovery and replication PWAS, genes with FDR q <0.05 after the meta-analysis and with the same directions of association in both the discovery and replication datasets were declared replicated. The effective sample size for METAL was calculated using this formula: Neff = 2 / (1/Ncases + 1/Ncontrols)61.
