Uncovering causal gene-tissue pairs and variants through a multivariate TWAS controlling for infinitesimal effects

Yihe Yang, Noah Lorincz-Comi and Xiaofeng Zhu ()
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Yihe Yang: Case Western Reserve University School of Medicine
Noah Lorincz-Comi: Case Western Reserve University School of Medicine
Xiaofeng Zhu: Case Western Reserve University School of Medicine

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: Abstract Transcriptome-wide association studies (TWAS) are commonly used to prioritize causal genes underlying associations found in genome-wide association studies (GWAS) and have been extended to identify causal genes through multivariate TWAS methods. However, recent studies have shown that widespread infinitesimal effects due to polygenicity can impair the performance of these methods. In this report, we introduce a multivariate TWAS method named tissue-gene pairs, direct causal variants, and infinitesimal effects selector (TGVIS) to identify tissue-specific causal genes and direct causal variants while accounting for infinitesimal effects. In simulations, TGVIS maintains an accurate prioritization of causal gene-tissue pairs and variants and demonstrates comparable or superior power to existing approaches, regardless of the presence of infinitesimal effects. In the real data analysis of GWAS summary data of 45 cardiometabolic traits and expression/splicing quantitative trait loci from 31 tissues, TGVIS is able to improve causal gene prioritization and identifies novel genes that were missed by conventional TWAS.

Date: 2025
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DOI: 10.1038/s41467-025-61423-8

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