Use of urinary cell-free DNA methylation assay to identify tumor fraction for early detection and recurrence monitoring in urothelial carcinoma.

844 Background: Urothelial carcinoma (UC) remains one of the most common urologic cancers, presenting challenges in both initial diagnosis and follow-up due to the invasive nature of traditional diagnostic procedures. Urinary cell-free DNA (ucfDNA) analysis offers a non-invasive alternative, with DNA methylation patterns providing a promising avenue for identifying tumor-derived cfDNA. This study explores the utility of ucfDNA methylation-based tumor fraction (mTF) for early detection and monitoring recurrence in UC patients. Methods: A case-control study was conducted with 121 participants, analyzing ucfDNA from patients with pathologically confirmed malignant tumors and benign lesions. A panel of UC-specific methylation markers was developed to quantify tumor-derived ucfDNA in a tissue-agnostic manner. The methylation-based tumor fraction (mTF) was then correlated with reference circulating tumor DNA (ctDNA) levels and clinical urine cytology indicators. Results: Our analysis revealed a significantly higher mTF in UC patients compared to controls (Wilcoxon test, p-value = 3.3 x 10 -9 ). Utilizing mTF as an independent biomarker for distinguishing malignant from benign cases achieved a positive predictive value (PPV) of 92% and a negative predictive value (NPV) of 90%. Moreover, relapse signals (mTF > 0.005) were detected in follow-up urine samples from all patients (7/7) who had undergone transurethral resection of bladder tumor (TURBT). Conclusions: The urinary cfDNA methylation-based tumor fraction presents a promising non-invasive biomarker for both early detection and recurrence monitoring of urothelial carcinoma. This approach could significantly improve patient management by providing a valuable tool for diagnosis and ongoing surveillance, underscoring the need for innovative diagnostic strategies in UC.