Polygenic risk score portability for common diseases across genetically diverse populations

• Published in: Human genomics 2024-09, Vol.18 (1), p.93-12, Article 93
• Main Authors: Moreno-Grau, Sonia, Vernekar, Manvi, Lopez-Pineda, Arturo, Mas-Montserrat, Daniel, Barrabés, Míriam, Quinto-Cortés, Consuelo D, Moatamed, Babak, Lee, Ming Ta Michael, Yu, Zhenning, Numakura, Kensuke, Matsuda, Yuta, Wall, Jeffrey D, Ioannidis, Alexander G, Katsanis, Nicholas, Takano, Tomohiro, Bustamante, Carlos D
• Format: Article
• Language: English
• Subjects: Asian people; Asian People - genetics; Biobanks; Black People - genetics; Cardiovascular disease; Datasets; Diabetes; Female; Genetic Predisposition to Disease; Genetic Risk Score; Genome-Wide Association Study; Genomes; Genotype & phenotype; High density lipoprotein; Humans; Hypothyroidism; Lipids; Low density lipoprotein; Models, Genetic; Phenotypes; Phenotypic variations; Polygenic inheritance; Polymorphism, Single Nucleotide; Population genetics; Population studies; Principal components analysis; Quality control; Questionnaires; Triglycerides; Vitamin D; White People - genetics
• ISSN: 1479-7364; 1473-9542; 1479-7364
• DOI: 10.1186/s40246-024-00664-y

Polygenic risk scores (PRS) derived from European individuals have reduced portability across global populations, limiting their clinical implementation at worldwide scale. Here, we investigate the performance of a wide range of PRS models across four ancestry groups (Africans, Europeans, East Asians, and South Asians) for 14 conditions of high-medical interest. To select the best-performing model per trait, we first compared PRS performances for publicly available scores, and constructed new models using different methods (LDpred2, PRS-CSx and SNPnet). We used 285 K European individuals from the UK Biobank (UKBB) for training and 18 K, including diverse ancestries, for testing. We then evaluated PRS portability for the best models in Europeans and compared their accuracies with respect to the best PRS per ancestry. Finally, we validated the selected PRS models using an independent set of 8,417 individuals from Biobank of the Americas-Genomelink (BbofA-GL); and performed a PRS-Phewas. We confirmed a decay in PRS performances relative to Europeans when the evaluation was conducted using the best-PRS model for Europeans (51.3% for South Asians, 46.6% for East Asians and 39.4% for Africans). We observed an improvement in the PRS performances when specifically selecting ancestry specific PRS models (phenotype variance increase: 1.62 for Africans, 1.40 for South Asians and 0.96 for East Asians). Additionally, when we selected the optimal model conditional on ancestry for CAD, HDL-C and LDL-C, hypertension, hypothyroidism and T2D, PRS performance for studied populations was more comparable to what was observed in Europeans. Finally, we were able to independently validate tested models for Europeans, and conducted a PRS-Phewas, identifying cross-trait interplay between cardiometabolic conditions, and between immune-mediated components. Our work comprehensively evaluated PRS accuracy across a wide range of phenotypes, reducing the uncertainty with respect to which PRS model to choose and in which ancestry group. This evaluation has let us identify specific conditions where implementing risk-prioritization strategies could have practical utility across diverse ancestral groups, contributing to democratizing the implementation of PRS.