Multi-ancestry transcriptome prediction with functionally informed variants in TOPMed MESA improves performance of transcriptome-wide association studies

Reliable reference transcriptome prediction models are key to accurate multi-ancestry transcriptome-wide association studies (TWASs). We propose three methods leveraging functionally informed variants (FIVs) for transcriptome prediction models to improve multi-ancestry TWASs. We trained models on 1,287 multi-ancestry participants from the Trans-Omics for Precision Medicine (TOPMed) program Multi-Ethnic Study of Atherosclerosis (MESA) with RNA sequencing (RNA-seq) data from peripheral blood mononuclear cells (PBMCs). We validated models' prediction accuracy on two external independent datasets, Geuvadis and Jackson Heart Study. To test robustness of our methods for TWASs, we integrated models with three multi-ancestry GWASs from blood cell, lipid, and pulmonary function traits, respectively. Our methods presented similar prediction accuracy while using a smaller and functionally informed set of variants compared to the benchmark method, elastic net (EN). Overall, our methods achieved higher power and accuracy (with average improved accuracy of 24% over EN) for TWASs. However, no single proposed method outperformed all GWAS traits. To further improve TWAS performance, we propose an omnibus approach that aggregates TWAS summary statistics from our methods. The omnibus approach yielded the highest number of Bonferroni-significant TWAS genes for all GWAS traits, and it further improved TWAS power and accuracy for blood cell traits. Additionally, the omnibus approach detected some trait-relevant important genes that the EN missed. Our study demonstrates the value of including FIVs in multi-ancestry transcriptome prediction models for improving TWAS performance. Further, the observed TWAS improvement depends on the GWAS trait's relevance to the PBMCs used to build our transcriptome prediction models.