Bayesian Genome-wide Polygenic Score Integration with FRAX for Enhanced Fracture Risk Prediction in Postmenopausal
Anqi Liu1, Jianing Liu1, Qing Wu1
1Department of Biomedical Informatics, College of Medicine, The Ohio State University.
Importance:
Current fracture risk prediction tools, including the Fracture Risk Assessment Tool (FRAX), do not incorporate genetic risk factors limiting accuracy and contributing to misclassification and suboptimal care.
Objective:
To develop and validate a novel genome-informed fracture risk assessment tool (Bayes-FRAX) integrating Bayesian genome-wide polygenic scores (GPS) into the established FRAX to enhance major osteoporotic fracture (MOF) prediction.
Design Setting And Participants:
This retrospective cohort study analyzed clinical and genetic data from 6,932 postmenopausal women enrolled in the Women's Health Initiative (1993-1998).
Exposures:
Integration of GPS derived using Polygenic Risk Score Continuous Shrinkage (PRS-CS) and Summary data-based Bayesian regression (SBayesR) into FRAX.
Main Outcomes And Measures:
Primary outcomes included the incidence of MOF. Predictive performance metrics assessed were area under the receiver operating characteristic curve (AUROC), area under the precision-recall curve (AUPRC), calibration slopes, Hosmer-Lemeshow goodness-of-fit tests, net reclassification improvement (NRI), diagnostic sensitivity, decision curve analysis (DCA), and external validation metrics.
Results:
Of 6,932 women, 513 (7.4%) experienced MOF. Bayes-FRAX significantly improved prediction over standard FRAX based solely on clinical risk factors, increasing AUROC from 0.662 to 0.680 for both PRS-CS and SBayesR. AUPRC improved from 0.120 (FRAX) to 0.140 (PRS-CS) and 0.138 (SBayesR). Calibration slopes were ideal (GPS-PRS-CS: 1.00 [95% CI: 0.8569-1.1431]; GPS-SBayesR: 1.00 [95% CI: 0.8560-1.1437]). Bayes-FRAX reclassified 3.5% of women, 34% near the intervention threshold. NRI improved by 4.59% (SBayesR) and 4.34% (PRS-CS), largely from better classification of women who fractured (5.85% and 5.65%). Decision curve analyses demonstrated greater net clinical benefit at clinically relevant thresholds, notably at the 20% threshold. External validation in 852 independent White postmenopausal women confirmed robust generalizability, with GPS significantly associated with fracture risk (PRS-CS OR = 0.148, 95% CI: 0.052-0.411; SBayesR OR = 0.116, 95% CI: 0.040-0.324). Likelihood ratio tests also supported improved model fit after GPS inclusion (PRS-CS: P < 0.001; SBayesR: P <0.001). Sensitivity analysis without BMD demonstrated stable AUROC (0.74).
Conclusions And Relevance:
Integrating GPS into FRAX using Bayesian methods improved fracture risk prediction, reclassification, and decision-making. Bayes-FRAX provides a generalizable tool for personalized osteoporosis care, especially for women near treatment thresholds.
