TrustPGS: When can a polygenic score be trusted? A per-individual reliability framework across ancestries

Abstract

Polygenic scores summarise genetic predisposition to a trait, but a population-level accuracy figure cannot tell a clinician whether a given prediction is reliable for the person in front of them. This gap is most consequential for individuals whose ancestry is under-represented in the discovery cohort, precisely the patients for whom a wrong trust call carries the highest clinical cost. We present TrustPGS, a framework that tells clinicians and downstream models which individual predictions can be trusted and which cannot, so that polygenic scores can inform clinical decisions rather than being acted on uniformly regardless of how well-supported each prediction is. The framework rests on two axes calibrated on a discovery cohort, the consensus of a Bayesian posterior-sample ensemble and the directional agreement of the top-magnitude linkage-disequilibrium blocks. We computed SBayesRC posterior-sample scores for ten polygenic traits in the 1000 Genomes Project phase-3 cohort and tested whether the resulting trust labels transfer, without recalibration, to the ancestrally diverse Simons Genome Diversity Project, comparing strict application of the European cutoffs, percentile-rank rescaling, and within-cohort recalibration. Percentile-rank rescaling preserved an enrichment factor above one in non-European populations for five of ten traits (Alzheimer disease, breast cancer, body mass index, LDL cholesterol, and systolic blood pressure), traits whose European and target-cohort distributions were shifted but comparable in shape. Three traits (coronary artery disease, height, and schizophrenia) carried distributions that differed in shape rather than location, a pattern traceable to discovery-cohort bias that recalibration could not repair either, and two further traits (type 2 diabetes and educational attainment) showed intermediate behaviour, present but never enriched in one case, and an apparent success that rank-mapping correctly unmasked as artefactual in the other. Because each of these patterns is detectable before any individual-level claim is made, TrustPGS gives clinicians and downstream models a falsifiable, per-trait basis for deciding when a reliability label can be trusted on a new population, rather than a single portability promise that holds or fails silently.