To perform transcriptome-wide association analysis, we used S-PrediXcan [23] (a version of PrediXcan that uses GWAS summary statistics [59]) to integrate transcriptomic data from GTEx [16] and the Depression Genes and Networks study (DGN) [24] to analyze the summary data from the PAU meta-analysis. Forty-eight tissues with sample size > 70 from GTEx release v7 were analyzed, totaling 10,294 samples. DGN contains RNA sequencing data from whole blood of 992 genotyped individuals. The transcriptome prediction model database and the covariance matrices of the SNPs within each gene model were downloaded from the PredictDB repository (http://predictdb.org/, 2018–01-08 release). Only individuals of European ancestry in GTEx were analyzed. S-PrediXcan was performed for each of the 49 tissues (48 from GTEx and 1 from DGN), for a total of 254,345 gene-tissue pairs. Significant association was determined by Bonferroni correction (p < 1.97 × 10−7).
