Functionally informed cis and trans proteome-wide association studies prioritize disease-critical genes

Proteome-wide association studies (PWAS) typically link genetically predicted protein levels to disease using cis-pQTLs, which can be limited by low cis-heritability for disease-critical genes under negative selection and by tagging due to co-regulation among nearby genes. Trans-pQTLs provide complementary information when large sample sizes are available to detect weak polygenic effects, enabling associations between trans-predicted protein levels and disease. We developed PolyPWAS, a functionally informed, summary statistics-based framework for associating both cis- and trans-predicted protein levels to disease. PolyPWAS integrates 96 functional annotations with proteome-wide pleiotropy to improve protein prediction, while correcting for PCs of predicted protein levels to limit tagging effects. We applied PolyPWAS to 2.8K plasma proteins measured in 34K UKB-PPP participants, analyzing GWAS summary statistics for 88 diseases and complex traits (average N=336K). Trans-predicted protein levels explained 21% of disease heritability (vs. 9.6% for cis-predicted protein levels), leveraging a 24% relative improvement in trans-prediction accuracy from functional priors. Trans-PWAS identified more significant protein-disease associations (and more conditionally significant associations) than cis-PWAS. Cis and trans associations showed only modest excess overlap (1.18, 95% CI: 1.11-1.26). Accordingly, combining evidence from cis and trans associations improved disease gene prioritization evaluated using gene sets from rare variant association studies (+11% relative improvement) and PoPS (+7.0% relative improvement) relative to cis-only approaches. PWAS associations to disease replicated across protein level cohorts, with strong UKB-PPP/deCODE concordance after adjusting for cohort-specific prediction accuracy. We provide examples where trans-regulatory effects link multiple disease-critical genes, underscoring the importance of integrating cis- and trans-regulatory effects to map protein-mediated disease biology.