Large-Scale Multi-Omics Enhance Risk Prediction for Type 2 Diabetes

IntroductionPolygenic risk scores (PRS), metabolomics, and proteomics have each shown promise in improving type 2 diabetes risk prediction, but their combined utility beyond established clinical models remains unclear. We aimed to evaluate whether integrating multi-omics biomarkers enhances 10-year type 2 diabetes risk prediction beyond single-omics extensions and the clinical Cambridge Diabetes Risk Score (CDRS), which includes HbA1c measurements. MethodsWe analysed data from 23,325 UK Biobank participants without diagnosed diabetes at baseline. Data for a PRS for type 2 diabetes, 11 metabolites, and 15 proteins were added to the CDRS to develop multi-omics prediction models. Model performance was evaluated using Harrells C-index and the net reclassification index (NRI). ResultsDuring 10 years of follow-up, 719 participants developed incident type 2 diabetes. Among individual omics layers, proteomics contributed the greatest improvement in predictive performance, increasing the C-index from 0.857 (clinical CDRS) to 0.880 ({Delta}C-index; +0.023; P < 0.001), with an NRI of 30.0%. The full multi-omics model, further significantly increased the C- index compared to a model combining the clinical CDRS with proteomics data (C-index, 0.886; {Delta}C-index; +0.006; P < 0.033). ConclusionIntegrating proteomics, metabolomics, and a diabetes-PRS into a clinical model substantially improves type 2 diabetes risk prediction beyond single-omics extensions. However, the C-index difference between the proteomics extended and full multi-omics extended models is small, and the clinical models extended with proteomics data would be easier to translate into routine care because it needs only the measurement of 15 proteins.