Exploring global cfDNA fragmentomics as a biomarker in real-world patients with melanoma

Circulating cell-free DNA fragmentomics-the analysis of cell-free DNA fragment-length profiles-has been explored as a biomarker across cancers, but evidence in melanoma is limited. We conducted a longitudinal prospective study of 235 patients with American Joint Committee on Cancer stages II-IV melanoma (549 plasma samples) and 11 phenotypic high-risk healthy controls, quantifying 6 fragment-size ranges by routine capillary electrophoresis. Linear mixed-effects modeling and receiver operating characteristic analyses evaluated associations with disease status; time-dependent receiver operating characteristic and mixed-effects Cox regression assessed prognostic value in resected patients. Active-disease samples showed a fragmentation shift: enrichment and increased heterogeneity of short (20-150 bp) and short-dinucleosome (250-320 bp) fragments, with depletion of mononucleosome fragments (160-180 bp), consistent with tumor-associated nuclease/chromatin processing. Discrimination of active disease versus disease-free samples was modest (area under the curve up to 0.64), comparable with serum S100 (area under the curve 0.68) and higher than lactate dehydrogenase (area under the curve 0.60). In resected patients, 250-320 bp variability and short-fragment ratios predicted relapse-free and distant-metastasis-free survival from blood draw (hazard ratio ≈ 1.5-2.4 per 1 SD increase) after clinical adjustment, with strongest performance over ∼3-6 months. Correlations with S100/lactate dehydrogenase were weak, supporting independent biological information. Low-cost electrophoresis-based fragmentomics captures clinically meaningful shifts and provides complementary short-term prognostic information, supporting integration into higher-resolution or multimodal cell-free DNA assays for risk-adapted follow-up.