Circulating cell-free DNA fragmentomics distinguishes pancreatic ductal adenocarcinoma from non-malignant conditions

Pancreatic ductal adenocarcinoma (PDAC) has poor survival rates due to late diagnosis and limited early detection methods. Existing serum biomarkers have inadequate sensitivity and specificity. This study assessed whether circulating cell-free DNA (cfDNA) fragmentomic features could distinguish PDAC from chronic pancreatitis (CP) and healthy controls. In this prospective single-center study, 83 participants were enrolled: 56 with histologically confirmed PDAC, 12 with CP, and 15 healthy controls. Plasma cfDNA was extracted from blood samples collected before intervention. cfDNA concentration and fragment length were analyzed. Diagnostic performance was evaluated using receiver operating characteristic (ROC) analysis. PDAC patients had significantly shorter cfDNA fragments (165 bp) than healthy controls (169 bp; p = 0.009), whereas no significant difference was observed compared with CP patients (166 bp; p = 0.900). cfDNA concentration was significantly higher in PDAC (45.6 ng/mL) than in CP (21.8 ng/mL; p = 0.026) and healthy controls (20.2 ng/mL; p = 0.002). ROC analysis demonstrated moderate diagnostic accuracy for fragment length (AUC 0.778) and concentration (AUC 0.737–0.796). Shorter cfDNA fragment length and higher concentration may help distinguish PDAC from CP and healthy individuals, supporting further investigation of cfDNA fragmentomics as a minimally invasive diagnostic tool.