Josep M. Mercader

Open access Sep 2026

Evaluation of functional annotation-informed and ancestry-specific polygenic risk scores for ischemic stroke

Ischemic stroke (IS) is a leading cause of morbidity and mortality, and predicting events remains challenging. Polygenic risk scores (PRSs) aggregate genetic variants, but performance varies across ancestries and remains modest, particularly in non-European populations. We compared Bayesian PRS methods incorporating functional annotations and expanded linkage disequilibrium reference panels for IS prediction. PRSs were generated using PRS-CS with HapMap3 and TagIt panels, and SBayesRC integrating functional priors. Scores were optimized in 1,403 European ancestry (EA) and 6,342 African ancestry (AA) participants from the Reasons for Geographic and Racial Differences in Stroke (REGARDS) study and independently validated in All of Us participants (78,155 EA and 29,594 AA participants), a REGARDS holdout cohort (11,459 EA participants), and the Genetics of Hypertension Associated Treatments (GenHAT) study (6,908 AA participants). Predictive performance was evaluated using logistic regression adjusted for age, sex, the top 10 genetic principal components, and antihypertensive treatment assignment where applicable. Performance was assessed using odds ratios per standard deviation (OR/SD), liability-scale R 2 , and area under the curve (AUC). Among EA participants, SBayesRC demonstrated the largest effect size and liability R 2 in the REGARDS holdout validation cohort (OR/SD = 1.24, 95% CI 1.12–1.36, R 2 = 2.42%). PRS-CS using the expanded TagIt panel (OR/SD = 1.11, 95% CI 1.00–1.22) showed numerically stronger performance than the HapMap3 panel (OR/SD = 1.09, 95% CI 0.98–1.20). Performance was consistent across the All of Us EA cohort, with OR/SD ranging from 1.10 to 1.16 across methods. Among AA participants, associations and predictive metrics were attenuated, with no significant associations observed in All of Us. A modest association was observed for PRS-CS-TagIt in GenHAT (for an all-stroke outcome). PRSs modestly improved discrimination beyond covariate models among EA participants (AUCs up to 66.6%), but showed little to no improvement among AA participants (AUCs 62.7%–66.7%). High PRS percentile groups (e.g., top 2% versus 98%) showed modest stroke enrichment with high specificity and limited sensitivity. Functional annotation-informed PRSs and expanded reference panels modestly improved prediction, particularly among EA participants. Limited performance among AA participants underscores the need for larger, more diverse genomic datasets and integrative models incorporating genetic, clinical, lifestyle, and social determinants of health.

N. Armstrong, V. Srinivasasainagendra, Amit Patki et al. · Frontiers in Bioinformatics · 0 citations

Open access Jul 2026

Improving performance of polygenic risk scores for hypertension across two ancestry groups

Polygenic risk score (PRS) methods are evolving, and the benefit of adding functional annotations to the variant weights has been especially promising. However, less attention has been given to how the linkage disequilibrium (LD) reference panel used affects the score performance. In the current study, we compared two Bayesian approaches, one that incorporates functional annotations (LDpred-funct) and one that does not (PRS-CS), extending these applications to the hypertension (HTN) trait across two ancestry groups (European Americans EA, and African Americans, AA). In PRS-CS we used the standard HapMap 3 LD (HM3) reference panel, as well as a modified multi-ancestry reference panel (TagIt) with better coverage of variants from multiple ancestries. Individual-level data in 1,533 EA (58% with HTN) and 8,603 AA (71% with HTN) participants from the Reasons for Geographic and Racial Differences in Stroke Study (REGARDS) was used to optimize scores across the two approaches. PRS performance metrics including R2 and odds ratios (OR) per standard deviation (SD) were then used to assess PRS performance in 1,270 EA (55% with HTN) and 1,896 AA (69% with HTN) participants from the Hypertension Genetic Epidemiology Network Study (HyperGEN). Among EAs in HyperGEN we observed an R2 of 6.0% for LDpred-funct and R2 of 7.3% for PRS-CS-TagIt versus R2 of 1.4% for PRS-CS-HM3. The magnitude of the OR per SD for HTN was also higher for PRS-CS-TagIt OR=2.17 (95% CI 1.65–2.85, p = 3.0*10−8) and LDpred-funct OR=2.14 (95% CI 1.61–2.85, p = 1.46*10−7) versus PRS-CS-HM3 (OR=1.40; 95% CI 1.07–1.82, p = 1.19*10−2). Among AAs in HyperGEN, the improvements were more modest, where we observed R2 of 1.9% for LDpred-funct and R2 of 2.9% for PRS-CS-TagIt versus 0.7% for PRS-CS-HM3. We found that both annotations and the updated LD panel improved the scores in both ancestry groups, but did not make the scores more equitable across the groups.

Marguerite R Irvin, V. Srinivasasainagendra, N. Armstrong et al. · PLoS ONE · 0 citations