Polygenic transcriptome risk scores (PTRS) can improve portability of polygenic risk scores across ancestries
Yanyu Liang, Milton Pividori, Ani Manichaikul, Abraham A. Palmer, Nancy J. Cox, Heather E. Wheeler, Hae Kyung Im
Abstract
BACKGROUND: Polygenic risk scores (PRS) are valuable to translate the results of genome-wide association studies (GWAS) into clinical practice. To date, most GWAS have been based on individuals of European-ancestry leading to poor performance in populations of non-European ancestry. RESULTS: We introduce the polygenic transcriptome risk score (PTRS), which is based on predicted transcript levels (rather than SNPs), and explore the portability of PTRS across populations using UK Biobank data. CONCLUSIONS: We show that PTRS has a significantly higher portability (Wilcoxon p=0.013) in the African-descent samples where the loss of performance is most acute with better performance than PRS when used in combination.