S-PrediXcan Transcriptome-Imputation Based Gene-Level Association

S-PrediXcan is an integrative gene-based association approach that uses summary data and pre-imputed transcriptome levels with models trained in a measured transcriptome dataset (such as GTEx) to identify genes involved in the etiology of the phenotype (33). In S-PrediXcan, the predicted expression levels are used to correlate with the phenotype in the gene association test. In our study, the GWAS summary statistics of the antibiotic subgroup were used to perform transcriptome imputation and gene-based association testing by S-PrediXcan using a pre-trained model based on GTEx v7 data (the GTEx-V7_HapMap-2017-11-29.tar.gz file in the PredictDB). The infrastructure described was used to impute gene expression at the MHC region (Chr6: 28477797~33448354, GRCh37) (33). The whole blood and the seven GI tissues were also examined.