The Occurrence of Gene Fusions in Thyroid Lesions and the Relation With Chronic Lymphocytic Thyroiditis.

Previously, we concluded that thyroid resections with multifocal, genetically distinct lesions more often showed florid chronic lymphocytic thyroiditis (CLT) than thyroids with clonally related multiple lesions. In this study, we characterized a consecutive cohort of thyroid lesions for molecular drivers and investigated the relationship between the molecular alteration type and florid CLT. Molecular diagnostic data from 414 patients (2016-2025) were retrospectively reviewed, including clinical information and histopathological evaluation. Gene fusion, somatic mutation, and chromosomal LOH/imbalance/copy-number analysis results were available for 342 cases. Eighty-eight gene rearrangements were identified across 86 patients. Most had been previously reported in thyroid neoplasia. Five well-known gene fusions revealed unusual breakpoints. Three gene fusions, previously reported only in nonthyroid malignancies (BRAF-TRIM24, SLC12A7-TERT, PVT1-MYC), were described for the first time in thyroid carcinoma. Three novel gene fusions (TRIM65-RET, FGFR2-WARS1, PPARGC1A-PPARɣ) produced in-frame translation products leading to corresponding mRNA expression. BRAF exon-skipping events were identified in treatment-naïve papillary thyroid carcinomas. Florid CLT (p = 0.002) and younger age (OR = 0.97 per year, p < 0.001) were independently associated with gene fusion-positive tumors. Sex, follicular nodular disease, and Graves' disease were not significant predictors. Our findings suggest an association between fusion-driven thyroid neoplasia and florid CLT, warranting further investigation.