Afirma Genomic Sequencing Classifier and Xpression Atlas Molecular Findings in Consecutive Bethesda III-VI Thyroid Nodules

Abstract

Context Broad genomic analyses among thyroid histologies have been described from relatively small cohorts. Objective Investigate the molecular findings across a large, real-world cohort of thyroid fine needle aspiration (FNA) samples. Design Retrospective analysis of RNA sequencing data files. Setting CLIA laboratory performing Afirma Genomic Sequencing Classifier (GSC) and Xpression Atlas (XA) testing. Participants 50,644 consecutive Bethesda III-VI nodules. Intervention none. Main Outcome Measures Molecular test results. Results Of 48,952 Bethesda III/IV FNAs studied, 66% were benign by Afirma GSC. The prevalence of BRAF V600E was 2% among all Bethesda III/IV FNAs and 76% among Bethesda VI FNAs. Fusions involving NTRK, RET, BRAF, and ALK were most prevalent in Bethesda V (10%), and 130 different gene partners were identified. Among small consecutive Bethesda III/IV sample cohorts with one of these fusions and available surgical pathology excision data, the positive predictive value of an NTRK or RET fusion for carcinoma or non-invasive follicular thyroid neoplasm with papillary-like nuclear features was >95%, while for BRAF and ALK fusions it was 81% and 67%, respectively. At least one genomic alteration was identified by the expanded Afirma XA panel in 70% of Medullary Thyroid Carcinoma Classifier positive FNAs, 44% of Bethesda III or IV Afirma GSC suspicious FNAs, 64% of Bethesda V FNAs, and 87% of Bethesda VI FNAs. Conclusions This large study demonstrates that almost half of Bethesda III/IV Afirma GSC suspicious and most Bethesda V/VI nodules had at least 1 genomic variant or fusion identified, which may optimize personalized treatment decisions.

Combining molecular testing and the Bethesda category III:VI ratio for thyroid fine‐needle aspirates: A quality‐assurance metric for evaluating diagnostic performance in a cytopathology laboratory

“…In the current study, one of the most notable results is that the rate of NGAs in all 3 indeterminate categories approximated their suggested RoM according to TBS, with RAS ‐like mutations predominant in categories III and IV and BRAF V600E identified in nearly one‐half of specimens in category V. The observed rates of RAS and BRAF mutations across indeterminate TBS categories in the current study approximate those reported in previous studies 53‐55 . The observed rates of BRAF mutation across indeterminate TBS categories in the current study are particularly concordant with those in a multi‐institutional study comprising nearly 50,000 samples, although none of those institutions reported their AUS rates or III:VI ratios 56 . The observed rate of BRAF mutation specifically in TBS category V in the current study approximates a previously calculated, pooled prevalence across multiple studies, although a meta‐analysis revealed wide interstudy variation 57 .…”

“…[53][54][55] The observed rates of BRAF mutation across indeterminate TBS categories in the current study are particularly concordant with those in a multi-institutional study comprising nearly 50,000 samples, although none of those institutions reported their AUS rates or III:VI ratios. 56 The observed rate of BRAF mutation specifically in TBS category V in the current study approximates a previously calculated, pooled prevalence across multiple studies, although a meta-analysis revealed wide interstudy variation. 57 Observed rates of RAS and BRAF mutations specifically in TBS category VI also approximate those in previous studies.…”

“…64 Both are subject to change in myriad ways in their next iterations, including changes to morphologic criteria and suggested risks and types of malignancy within and among categories, as well as the expansion of MT to a broader array of lesions. Indeed, Veracyte now offers an MT that it markets for thyroid aspirates in TBS category V. 56,65,66 Laboratories have also reported widely variable AUS rates, including some that are significantly higher than those suggested by TBS, as well as widely variable rates of thyroid aspirates falling into TBS category I (nondiagnostic), which has implications for the analytic sensitivity of currently available molecular tests. [67][68][69] The advantage of the approach presented in the current study is its plasticity.…”

NTRK‐rearranged papillary thyroid carcinoma demonstrates frequent subtle nuclear features and indeterminate cytologic diagnoses

“…Interestingly, we discerned extracellular hyalinelike materials in the FNA of 1 solid variant of PTC harboring VIM-NTRK3 fusion with the correlated histomorphology. This rare fusion variant has been reported in only 1 anaplastic thyroid carcinoma 26 and <0.03% of thyroid aspiration specimens 27 without detailed morphological descriptions. To the best of our knowledge, this finding has not been reported in NTRK-rearranged PTC, and whether it could be a specific cytologic feature of this fusion type requires further validation.…”

Thyroid nodules of indeterminate cytology in Hispanic/Latinx patients

“…10,11 A recent study of TN describes a genomic landscape with increasing mutations as FNA cytopathology progresses from Bethesda III (atypia of undetermined significance, AUS; follicular lesion of undetermined significance, FLUS; 41.5%) to Bethesda VI (malignant; 86.6%). 12 Based on this gradation, commercial molecular analytic platforms are commonly used to interrogate fine needle aspirate (FNA) samples of thyroid nodules (TN) with indeterminate cytopathology (TN-IC, Bethesda III and IV) to improve the distinction of benign form suspicious TN and inform surgical decisions. 13,14 However, the results of these and other studies have not been stratified by ethnicity.…”