DNA Methylation Biomarkers Capture Residual Biological Risk Beyond PREVENT

Contemporary cardiovascular disease (CVD) risk equations may not fully capture cumulative biological aging or long-term exposure burden. DNA methylation (DNAm) biomarkers may capture aging- and exposure-related biology, but their incremental prognostic value beyond clinical risk-factor models like PREVENT remains uncertain. To our knowledge, no prior study has benchmarked DNAm-based biomarkers with PREVENT.

Methods

In a population-based cohort study, we analyzed NHANES 1999-2002 participants with DNAm biomarkers and mortality follow-up. We derived a DNAmScore from candidate DNAm biomarkers using elastic-net Cox regression with repeated nested cross-validation. A PREVENT-like clinical model was defined as a Cox model fit in NHANES using PREVENT predictors. Weighted Cox models estimated the association between DNAmScore and mortality after adjustment for PREVENT-like clinical predictors. We then compared the PREVENT-like clinical model, DNAmScore alone, and a combined model (PREVENT-like clinical predictors plus DNAmScore) using cross-fitted C-index, time-dependent AUC, calibration, and Brier score.

Results

Our cohort included 2,282 participants; 597 and 937 deaths occurred by 10 and 15 years, respectively. After adjustment for PREVENT-like clinical predictors, the cross-fitted DNAmScore was strongly associated with all-cause mortality (HR per 1-SD increase, 2.43; 95% CI, 1.97–2.99). At 10 years, AUCs were 0.791 for the PREVENT-like model, 0.791 for DNAmScore, and 0.803 for the combined model. At 15 years, corresponding AUCs were 0.825, 0.822, and 0.835. Compared with the PREVENT-like model, the combined model improved AUC by 0.013 (95% CI, 0.006–0.020) at 10 years and 0.010 (95% CI, 0.004–0.015) at 15 years. The combined model had lower Brier scores at all three horizons with similar calibration. DNAmScore remained associated with CVD mortality after clinical adjustment.

Conclusions

DNAmScore identified residual biological risk beyond PREVENT-like clinical predictors, with strong independent mortality associations and modest, consistent improvements in cross-fitted prediction performance. These findings support development and external validation of CVD-specific DNAm biomarkers.

What Is Known

• Contemporary cardiovascular risk models may not fully capture cumulative biological aging and exposure burden.

• DNA methylation biomarkers are associated with mortality, but their incremental predictive value beyond clinical risk predictors remains uncertain.

What the Study Adds

• In a nationally representative NHANES cohort, a cross-fitted composite DNAmScore remained strongly associated with mortality after adjustment for PREVENT predictors.

• Adding DNAmScore produced modest improvements in discrimination and prediction error at 5, 10, and 15 years, and DNAmScore was also associated with cardiovascular mortality in secondary analyses.