Single-cell polygenic risk scores dissect cellular and molecular heterogeneity of complex human diseases

Abstract Polygenic risk scores (PRSs) predict an individual’s genetic risk for complex diseases, yet their utility in elucidating disease biology remains limited. We introduce scPRS, a graph neural network-based framework that computes single-cell-resolved PRSs by integrating reference single-cell chromatin accessibility profiles. scPRS outperforms traditional PRS approaches in genetic risk prediction, as demonstrated across multiple diseases including type 2 diabetes, hypertrophic cardiomyopathy, Alzheimer disease and severe COVID-19. Beyond risk prediction, scPRS prioritizes disease-critical cells and, when combined with a layered multiomic analysis, links risk variants to gene regulation in a cell-type-specific manner. Applied to these diseases, scPRS fine-maps causal cell types and cell-type-specific variants and genes, demonstrating its ability to bridge genetic risk with cell-specific biology. scPRS provides a unified framework for genetic risk prediction and mechanistic dissection of complex diseases, laying a methodological foundation for single-cell genetics.