Background: Thyroid nodules are highly prevalent, with fine‐needle aspiration (FNA) commonly used as the standard preoperative tool for their diagnosis. However, the method classifies some of the samples as indeterminate, leading to unnecessary surgery. In this study, we evaluated the value of next‐generation sequencing (NGS) for cancer diagnosis in indeterminate thyroid nodules.Materials and methods: We performed a prospective, blinded cohort study on 189 patients, with 196 Bethesda III/IV nodules. Specifically, we analyzed DNA mutations and RNA fusions across the FNA samples using NGS, then reviewed follow‐up reports from 84 nodules following definitive surgery, to determine the assay performance.Results: Enough DNA and RNA were obtained in 188 nodules, revealing mutations or fusions in 34.6% of them. The most frequently mutated genes were RAS, followed by BRAF V600E. Based on surgical pathology, 39% (33/84) and 4.8% (4/84) of the nodules were malignant and intermediate, respectively. According to the risk stratification criteria, 28 cases were categorized High‐Risk group, all of the resected nodules (n = 20) were malignant. Twenty‐four thyroid nodules were in the Low‐Risk group, 28.6% (4/14) surgically removed nodules were malignant. In the Benign‐Like category, 18.0% (9/50) were malignant. Five out of 13 nodules with benign mutations were resected, including SPOP, EZH1, and ZNF148, all of them were benign. If genetic alterations annotated with High‐Risk or Low‐Risk was considered as positive, and negative if Benign‐Like. Multigene testing revealed sensitivity, specificity, positive predictive values (PPV), and negative predictive value (NPV) of 73%, 80%, 71%, and 82%, respectively. In addition, if four intermediate nodules were counted as malignant, the PPV and NPV were 71% and 74%.Conclusion: Our results allow for further stratification of Bethesda III/IV thyroid nodules based on the risk of their malignancy. SPOP, EZH1, and ZNF148 mutations may be used as benign markers.

Thyroglobulin measurement with fine-needle aspiration (Tg-FNA) is a sensitive method for detecting metastatic papillary thyroid carcinoma (PTC). However, the diagnostic threshold is not well established and the influence of the thyroid gland on the cutoff value is also controversial. In this study, patients were classified into two groups according to the presence or absence of thyroid tissue, to determine an appropriate cutoff value for clinical practice. Patients with a history of thyroid nodules or surgery for PTC and with enlarged cervical lymph nodes on an FNA examination were enrolled for Tg-FNA detection. One hundred ninety-six lymph nodes (189 patients) were included: 100 from preoperative patients, 49 from patients treated with partial thyroid ablation, and 47 from patients with total thyroid ablation. In 149 lymph nodes from patient with thyroids, the cutoff value for Tg-FNA was 55.99 ng/mL (sensitivity, 95.1%; specificity, 100%), whereas in 47 lymph nodes from patients without a thyroid, it was 9.71 ng/mL (sensitivity, 96.7%; specificity, 100%). Thus, the cutoff value for Tg-FNA was higher in patients with thyroids than in patients without thyroids. The cutoff value for Tg-FNA is influenced by residual thyroid tissue, and a higher cutoff value is recommended for patients with thyroids than for patients without thyroids.