Simion Chiosea, Steven P Hodak, Linwah Yip, Devaprabu Abraham, Chelsey Baldwin, Zubair Baloch, Seza A Gulec, Zeina C Hannoush, Bryan R Haugen, Lija Joseph, Atil Y Kargi, Elham Khanafshar, Masha J Livhits, Bryan McIver, Kepal Patel, Snehal G Patel, Gregory W Randolph, Ashok R Shaha, Jyotirmay Sharma, Nikolaos Stathatos, Annemieke van Zante, Sally E Carty, Yuri E Nikiforov, Marina N Nikiforova
The Journal of Clinical Endocrinology & Metabolism, Volume 108, Issue 11, November 2023, Pages 2999–3008
https://doi.org/10.1210/clinem/dgad220
Comprehensive genomic analysis of thyroid nodules for multiple classes of molecular alterations detected in a large series of fine needle aspiration (FNA) samples has not been reported.
To determine the prevalence of clinically relevant molecular alterations in Bethesda categories III-VI (BCIII-VI) thyroid nodules.
This retrospective analysis of FNA samples, tested by ThyroSeq v3 using Genomic Classifier and Cancer Risk Classifier at UPMC Molecular and Genomic Pathology laboratory, analyzed the prevalence of diagnostic, prognostic, and targetable genetic alterations in a total of 50 734 BCIII-VI nodules from 48 225 patients.
Among 50 734 informative FNA samples, 65.3% were test-negative, 33.9% positive, 0.2% positive for medullary carcinoma, and 0.6% positive for parathyroid. The benign call rate in BCIII-IV nodules was 68%. Among test-positive samples, 73.3% had mutations, 11.3% gene fusions, and 10.8% isolated copy number alterations. Comparing BCIII-IV nodules with BCV-VI nodules revealed a shift from predominantly RAS-like alterations to BRAF V600E-like alterations and fusions involving receptor tyrosine kinases (RTK). Using ThyroSeq Cancer Risk Classifier, a high-risk profile, which typically included TERT or TP53 mutations, was found in 6% of samples, more frequently BCV-VI. RNA-Seq confirmed ThyroSeq detection of novel RTK fusions in 98.9% of cases.
In this series, 68% of BCIII-IV nodules were classified as negative by ThyroSeq, potentially preventing diagnostic surgery in this subset of patients. Specific genetic alterations were detected in most BCV-VI nodules, with a higher prevalence of BRAF and TERT mutations and targetable gene fusions compared to BCIII-IV nodules, offering prognostic and therapeutic information for patient management.
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