Molecular Diagnosis of Thyroid Nodules Using Next‐Generation Sequencing in the Chinese Population

<b>Background:</b> Fine-needle aspiration (FNA) cytology remains a challenge in the diagnosis of indeterminate thyroid nodules. Molecular testing can bridge the gap left by FNA cytology and improve the diagnostic accuracy of FNA. <b>Methods:</b> 786 FNA samples and 40 formalin-fixed paraffin-embedded (FFPE) specimens from thyroid nodules were enrolled in next-generation sequencing (NGS) molecular testing, which included gene mutation and gene fusion analysis. The molecular diagnostic performance was assessed by analyzing sensitivity, specificity, accuracy, negative predictive value (NPV), and positive predictive value (PPV). <b>Results:</b> Among 826 thyroid nodules, 409 were NGS-positive (49.52%), with a high prevalence of <i>BRAF</i> V600E (36.32%, 300/826) and <i>RAS</i> (9.32%, 77/826) mutations, a low prevalence of <i>TERT</i> promoter mutations (1.69%, 14/826), and gene fusions involving <i>RET</i> (1.82%, 15/826), <i>NTRK3</i> (0.73%, 6/826), <i>ALK</i> (0.24%, 2/826), and <i>PAX8-PPARG</i> (0.12%, 1/826). With the analysis of genetic profiles in thyroid nodules, <i>BRAF</i> V600E, <i>TERT</i> mutations, and gene fusions were included in the 6-gene test panel. The overall diagnostic performance of the 6-gene test panel, including sensitivity, specificity, accuracy, NPV, and PPV, was 84.87%, 89.61%, 86.26%, 71.13%, and 95.15%, respectively. For thyroid nodules in Bethesda III, IV, and V, the diagnostic sensitivity, specificity, accuracy, NPV, and PPV of the panel were 85.71%, 88.89%, 86.36%, 61.54%, and 96.77%, respectively. <b>Conclusion:</b> The results reveal that the 6-gene test panel as a "rule in" test in a clinical setting improves the accuracy of FNA cytology, potentially assisting in the diagnosis of the thyroid nodules with indeterminate FNA cytology.