Utility of Cell-Free DNA integrity index in differentiating malignant from benign lesions in indeterminate thyroid nodules.

BACKGROUND: Differentiated thyroid cancer (DTC) often presents as a solitary thyroid nodule and fine-needle aspiration cytology (FNAC) is the primary diagnostic tool. However, indeterminate FNAC results (Bethesda III/IV) pose a diagnostic challenge and frequently lead to unnecessary surgery. This study investigated the utility of the circulating cell-free DNA (cfDNA) integrity index (cfDI) as a non-invasive biomarker to distinguish malignant from benign thyroid nodules. METHODS: This prospective study included 240 patients with solitary thyroid nodules and 39 healthy controls (HCs). Plasma cfDNA was extracted and quantified. A quantitative real-time PCR assay targeting the Amyloid Precursor Protein (APP) gene generated amplicons of 67, 180, 306, and 476 bp. cfDI was calculated as the ratio of longer amplicons to the 67 bp fragment. The diagnostic performance of these indices was evaluated, and a cutoff was validated for indeterminate nodules. RESULTS: The 180/67 cfDI index was significantly higher in malignant nodules (median 0.67) than in benign nodules (median 0.44, p < 0.0001). ROC analysis yielded an AUC of 0.69 (95% CI: 0.59–0.79) for the 180/67 index, with a cut-off of 0.54, providing 67.6% sensitivity and 60.5% specificity. In the validation cohort of indeterminate nodules (Bethesda III/IV), this cutoff achieved 65.6% sensitivity and 41.3% specificity. CONCLUSION: The cfDNA integrity index of 180/67 demonstrates moderate diagnostic value in differentiating malignant from benign thyroid nodules and may aid in the evaluation of indeterminate cytology. Although promising, its clinical application warrants further validation in larger cohorts and in combination with existing diagnostic modalities.