Xiangyu Zhang, Lijun Wang, Jia Zhao, Hongyu Zhao (2025). Knockoff procedure improves causal gene identifications in conditional transcriptome-wide association studies. bioRxiv 2025.02.05.636660; doi: https://doi.org/10.1101/2025.02.05.636660
TWASKnockoff is a new knockoff-based framework designed to identify causal genes for the trait of interest using GWAS summary statistics and gene expression-mapping data. TWASKnockoff extends the knockoff inference to identify disease-causing genes. Unlike the marginal testing performed in traditional TWAS methods, TWASKnockoff examines the conditional independence for each gene-trait pair, considering both correlations in cis-predicted expression across genes and correlations between gene expression levels and genotypes of genetic variants.
