Diagnostic performance of next-generation sequencing in thyroid nodules and molecular correlates of tumor aggressiveness in papillary thyroid carcinoma

Abstract

Genetic alterations play a crucial role in the pathogenesis and progression of papillary thyroid carcinoma (PTC). However, the diagnostic and prognostic significance of specific genetic alterations in PTC remains to be elucidated. This study aimed to evaluate the diagnostic performance of next-generation sequencing (NGS)-based genetic testing and to examine associations between genetic alteration subtypes and adverse clinicopathological features in PTC. A total of 279 thyroid specimens with NGS-based genetic testing and pathological diagnoses were enrolled, of which 201 specimens with histopathologically confirmed PTC constituted the primary analytical cohort. Diagnostic performance—sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV)—for predicting malignancy was assessed using postoperative histopathology as the reference standard, with a positive result defined as detection of a pathogenic or likely pathogenic mutation. Alterations were categorized as BRAF -like, RAS -like, or Fusion, and their associations with lymph node metastasis (LNM) and tumor size (cutoffs: 0.5 cm, 1 cm) were evaluated using Pearson’s chi-squared test or Fisher’s exact test. Among the 279 thyroid specimens, 219 had postoperative pathology, of which 203 were malignant, 6 borderline, and 10 benign. BRAF V600E was the most frequent genetic alteration (68.10% overall; 79.10% in PTC). Genetic testing demonstrated high sensitivity (86.21%), specificity (90.00%), and PPV (99.43%), but low NPV (24.32%). The Fusion subtype showed a trend toward association with LNM (OR = 7.23, 95% CI 0.85–61.17, P  = 0.048). BRAF -like and RAS -like subtypes showed no significant associations with LNM. For tumor size, BRAF -like alterations were significantly enriched in tumors > 0.5 cm (OR = 2.60, 95% CI 1.24–5.46, P = 0.0098); no significant associations were observed at the 1 cm cutoff. RAS -like and Fusion subtypes showed no significant associations with tumor size. Genetic testing demonstrated high PPV (99.43%) but a low NPV (24.32%), indicating that a positive result identifies malignancy while a negative result cannot exclude cancer. Gene fusions showed a trend toward association with LNM in PTC. BRAF -like mutations appeared more often in tumors > 0.5 cm, whereas RAS -like alterations bore no clear link to adverse pathological features. These results suggest that genetic profiling may improve diagnosis and risk assessment of PTC.