MON-570 Clinical Utility of ThyroSeq v3 Genomic Classifier Test in Detecting Gene Fusions in Thyroid Nodules

Background: Chromosomal rearrangements leading to gene fusions are a known molecular mechanism of thyroid cancer. ThyroSeq Genomic Classifier (GC) allows detecting most of the known fusion types preoperatively by analyzing thyroid fine-needle aspiration (FNA) samples collected from thyroid nodules, but it also facilitates discovery of novel fusion types. The goal of this study was to evaluate the prevalence and types of known and novel fusions detected in thyroid nodules during routing clinical testing and establish histopathologic and clinical correlations. Design: Overall, 6,800 consecutive thyroid nodules were tested by a targeted next-generation sequencing assay (ThyroSeq v3 GC) using material collected by fine-needle aspiration (FNA). In addition, 17 surgically removed tumors were tested for confirmation of fusion subtype. Surgical pathology and clinical follow-up was obtained when available. Immunohistochemistry was performed on selected cases. Results: Gene fusions were identified in 318 (4.68%) of consecutively tested thyroid nodules. The most common fusion type was THADA/IGF2BP3 detected in 121 (38%) cases, followed by RET/PTC in 52 (16%), NTRK3 in 47 (15%), and PPARG in 47 (15%). Other fusions were found at lower prevalence, including BRAF in 14 (4%), ALK in 9 (3%), THADA/TRA2A in 8 (3%), and NTRK1 in 8 (3%) cases. In addition, 12 (4%) of nodules had rare and novel fusions, including PAX8/GLIS fusions. Presence of PAX8/GLIS fusions was confirmed in resected tumor samples. Surgical pathology information was collected on 49 (16%) positive cases and is ongoing. RET/PTC, NTRK3, NTRK1, and ALK fusions were all diagnosed as classic papillary thyroid carcinoma (PTC) or follicular variant of PTC. All 3 ALK-positive PTC and 5 THADA/IGF2BP3 NIFTP showed strong and diffuse immunoreactivity with ALK and IMP3 antibodies, respectively. THADA/IGF2BP3 was found in noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) (50%), PTC (40%) and follicular thyroid carcinoma (FTC) (10%). PPARG fusions were found in FTC (25%), Hurthle cell carcinoma (25%), PTC (25%) and follicular adenomas (25%). One BRAF fusion (SND1/BRAF) was found in follicular adenoma and all other nodules were PTC. All PAX8/GLIS fusions were characteristic of hyalinizing trabecular tumors. Conclusions: ThyroSeq GC detected gene fusions in approximately 5% of thyroid nodules that underwent FNA. ThyroSeq overall correct call rate for fusions was 94.1%, with variation between specific fusion types. Preoperative detection of fusions in FNA samples assists with diagnosis of thyroid nodules and thyroid cancer and informs patient management.