A multicenter prospective clinical trial reveals cell free DNA methylation markers for early esophageal cancer.

Background: Current methods for detecting esophageal cancer (EC) are generally invasive or exhibit limited sensitivity and specificity, especially for the identification of early-stage tumors.

Methods: We identified potential methylated DNA markers (MDM) from multiple genomic regions in a discovery cohort and a diagnostic model was developed and verified in a model-verification cohort of 297 participants. The accuracy of the MDM panel was validated in a multicenter, prospective cohort (n = 1429). The clinical performance of identified MDMs were compared with current tumor-associated protein markers.

Results: From 31 significant differentially methylated EC-associated regions identified in the marker discovery, we trained and validated a 3-MDM diagnostic model that could discriminate among EC patients and Non-EC volunteers in a multicenter clinical prospective cohort with a sensitivity of 85.5% and a specificity of 95.3%. This panel showed higher sensitivity in diagnosing early-stage tumors, with sensitivities of 56% for Stage 0 and 77% for Stage I, comparing with the performance of current biochemical markers. In population with high risk for EC, the sensitivity and specificity are 85.68% and 93.61% respectively.

Conclusion: The assessment of tumor-associated methylation status in blood samples can facilitate non-invasive, and reliable diagnosis of early-stage EC, which warrants further development to expand screening and reduce mortality rates.

Trial registration number: ChiCTR2400083525.