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

Circulating cell-free DNA (cfDNA) fragmentomics-the analysis of cfDNA 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 AJCC stage II-IV melanoma patients (549 plasma samples) and 11 phenotypic high-risk healthy controls, quantifying six fragment-size ranges by routine capillary electrophoresis. Linear mixed-effects modelling and ROC analyses evaluated associations with disease status; time-dependent ROC 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 tumour-associated nuclease/chromatin processing. Discrimination of active disease versus disease-free samples was modest (AUC up to 0.64), comparable to serum S100 (AUC 0.68) and higher than LDH (AUC 0.60). In resected patients, 250-320 bp variability and short-fragment ratios predicted relapse-free and distant-metastasis-free survival from blood draw (HR ≈ 1.5-2.4 per 1 SD increase) after clinical adjustment, with strongest performance over ∼3-6 months. Correlations with S100/LDH 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 cfDNA assays for risk-adapted follow-up.