The implications of molecular alterations in cytologically benign thyroid nodules

Ablation of benign thyroid nodules has gained clinical favor. However, reliably excluding malignancy remains a diagnostic challenge. We assessed the frequency and spectrum of molecular abnormalities in cytologically benign nodules.

This retrospective cohort study of national and institutional cohorts reviewed nodules with cytologically benign fine-needle aspiration results referred for next-generation sequencing-based molecular testing (2017-2024). Frequency/type of molecular abnormalities, histopathology, and clinical variables predictive of positive molecular testing were evaluated.

Among 825 cases in the national cohort, 121 (15%) tested positive, including 97 (80%) for low-risk RAS/RAS-like alterations, 19 (16%) for intermediate-risk BRAF V600E and BRAF V600E-like alterations, and 5 (4%) for high-risk molecular profiles including TERT and TP53. Twenty-four nodules with intermediate- or high-risk molecular alterations represented 20% of cytologically benign molecular testing-positive nodules and 3% of all nodules. Among 36 patients with surgical outcomes, 16 (44%) nodules were malignant, and 3 (8%) were noninvasive follicular thyroid neoplasm with papillary-like nuclear features. Among 38 cases in the institutional cohort, 11 (29%) tested positive, 7 (64%) carried low-risk, 2 (18%) carried intermediate-risk, and 2 (18%) carried high-risk alterations. Intermediate- or high-risk alterations were present in 36% of nodules with positive molecular testing and 11% of all nodules. Age <55 years (odds ratio, 13.4) and history of nodule growth (odds ratio, 13.6) were independent predictors of positive molecular testing. Of 9 molecular testing-positive nodules managed with surgery, 4 (44%) were malignant.

Among thyroid nodules with benign cytology referred for molecular testing, 3%-11% demonstrated intermediate- or high-risk alterations. Considering this molecular heterogeneity, further investigation of clinicopathologic factors is warranted to inform nonoperative or preablation molecular risk stratification and ensure accurate exclusion of malignancy.