Cross-ancestry information transfer framework improves protein abundance prediction and protein-trait association identification

Genetics-informed proteome-wide association studies (PWASs) provide an effective way to uncover proteomic mechanisms underlying complex diseases. PWAS relies on an ancestry-matched reference panel to model the impact of genetically determined protein expression on phenotype. However, reference panels from underrepresented populations remain relatively limited. We developed a multi-ancestry framework to enhance protein prediction in these populations by integrating diverse information-sharing strategies into a Multi-Ancestry Best-performing Model (MABM). Results indicated that MABM increased the prediction performance with higher performance observed in both cross-validation and an external dataset. Leveraging the Biobank Japan, we identified three times as many significant PWAS associations using MABM as using Lasso model. Notably, 47.5% of the MABM specific associations were reproduced in independent East Asian datasets with concordant effect sizes. Furthermore, MABM enhanced decision-making in gene/protein prioritization for functional validation for complex traits by validating well-established associations and uncovering novel trait-related candidates. The benefits of MABM were further validated in additional ancestries and demonstrated in brain tissue-based PWAS, underscoring its broad applicability. Our findings close critical gaps in multi-omics research among underrepresented populations and facilitate trait-relevant protein discovery in underrepresented populations.