Using molecular testing to improve the management of thyroid nodules with indeterminate cytology: an institutional experience with review of molecular alterations

Impact of Molecular Testing on Surgical Decision-Making in Indeterminate Thyroid Nodules: A Systematic Review and Meta-Analysis of Recent Advancements

Background: The management of indeterminate thyroid nodules (Bethesda III/IV) has evolved with molecular testing, aiming to reduce unnecessary surgeries. However, the comparative effectiveness of different platforms in influencing surgical decision-making remains unclear. This systematic review and meta-analysis evaluate the impact of molecular testing on surgical avoidance rates. Methods: A systematic literature search was conducted across eight electronic databases, including Embase, PubMed, and Cochrane Library, from January 2019 to December 2024, following PRISMA guidelines to encompass most recent advancements in the last 5 years. Studies evaluating Afirma Gene Expression Classifier (GEC), Afirma Genomic Sequencing Classifier (GSC), ThyroSeq V2, ThyroSeq V3, and ThyGenX/ThyraMIR were included. The primary outcome was surgical avoidance, analyzed using a random-effects model. Results: Thirty-one studies comprising 4464 indeterminate thyroid nodules met inclusion criteria. Pooled surgical avoidance rates varied across platforms: ThyroSeq V2 (50.3%, 95% CI: 20.8-79.6%), ThyroSeq V3 (62.5%, 95% CI: 54.8-70.0%), Afirma GEC (58.8%, 95% CI: 43.6-73.1%), Afirma GSC (50.6%, 95% CI: 34.3-66.8%), and ThyGenX/ThyraMIR (68.6%, 95% CI: 63.1-73.9%). ThyGenX/ThyraMIR had the highest surgical avoidance rate and lowest heterogeneity (I2 = 51.2%), while ThyroSeq showed improvement from V2 to V3. Conclusions: Molecular testing reduces unnecessary thyroid surgeries, with avoidance rates ranging from 50.3% to 68.6%. While ThyGenX/ThyraMIR showed the highest avoidance rate, its limited representation warrants cautious interpretation. Standardized protocols are needed to optimize clinical application. Further prospective studies should compare platforms and assess long-term outcomes and cost-effectiveness.

Evaluating the clinical performance of an updated microRNA classifier in indeterminate and RAS-mutated thyroid nodule management: A multi-institutional study

BACKGROUND

Integrating microRNA markers with next-generation sequencing panels may enhance risk assessment of cytologically indeterminate thyroid nodules. The ThyGeNEXT-ThyraMIRv1 multiplatform test version 1 demonstrated limited utility in risk-stratifying RAS-mutated indeterminate thyroid nodules. We sought to validate the updated ThyraMIRv2 platform in clinical practice.

METHODS

ThyGeNEXT/ThyraMIRv2, a 3-tiered microRNA classifier, were evaluated using a previously studied multi-institutional cohort of Bethesda III/IV nodules, with positive results having risk of malignancy ≥10%. In addition, ThyraMIRv2's clinical utility in RAS-mutated indeterminate thyroid nodules was assessed.

RESULTS

In 366 indeterminate thyroid nodules, ThyraMIRv2 platform yielded a 30.3% positive-call rate. ThyraMIRv2 platform + nodules had greater operative rates (63.9% vs 36.1%, P < .0001) and cancer/noninvasive follicular thyroid neoplasm with papillary-like nuclear features diagnosis (65.9% vs 25.0%, P < .0001) than ThyraMIRv2 platform nodules. Compared with multiplatform test version 1, ThyraMIRv2 platform's diagnostic testing parameters did not improve significantly. Among 68 RAS-mutated nodules, ThyraMIRv2 classified 36.8%, 55.9%, and 7.4% as positive, moderate, and negative, respectively. All moderate nodules had risk of malignancy ≥10% and were combined with the positive cohort. No significant differences existed in operative rate (81.0% vs 60.0%, P = .272) or cancer/noninvasive follicular thyroid neoplasm with papillary-like nuclear features diagnosis (47.6% vs 40.0%, P > .999) between RAS-mutated positive/moderate and negative groups. For RAS-mutated nodules, ThyraMIRv2 demonstrated improved sensitivity (93.8% vs 64.7, P = .003) and decreased specificity (4.5% vs 34.8%, P = .008) compared with ThyGeNEXT-ThyraMIRv1 multiplatform test version 1, with comparable negative predictive value (33.3% vs 40.0%, P = .731) and positive predictive value (58.8% vs 59.5%, P = .864).

CONCLUSION

ThyraMIRv2 platform does not improve indeterminate thyroid nodule malignancy stratification compared to ThyGeNEXT-ThyraMIRv1 multiplatform test version 1. ThyraMIRv2 improves malignant RAS-mutated nodule detection but increases false positives. Future studies encompassing a larger cohort of RAS-mutated with surgical pathology results are warranted to better characterize the performance parameters of this classifier.

THADA-IGF2BP3 gene fusions in thyroid fine needle aspiration is involved in the pathway to "noninvasive follicular thyroid neoplasm with papillary-like nuclear features"

BACKGROUND

The increased usage and adaptation of molecular testing of thyroid fine needle aspirations (FNA) has expanded the variety and number of gene fusions identified. While the identified number of molecular alterations is increasing, the definitive association between preoperative molecular analysis and phenotype has yet to be established. The aim of this study was to examine Thyroid adenoma-associated (THADA)-IGF2BP3 molecular fusions with FNA categorization, surgical pathology diagnosis, and other molecular alterations detected by ThyroSeq Genomic Classifier testing.

METHODS

FNA cytology samples of thyroid nodules from 04/2017 to 01/2023 with the diagnosis of atypia of undetermined significance or follicular lesion of undetermined significance (AUS/FLUS; Bethesda III) or follicular neoplasm suspicious for follicular neoplasm (FN/SFN; Bethesda IV) with associated ThyroSeqV3 testing were reviewed. Parameters including patient demographics, FNA diagnosis, ThyroSeq V3 results, and surgical pathology follow up were examined.

RESULTS

87 out of 249 (35%) FNA specimens of thyroid nodules displayed molecular alterations. 64 cases (74%) had a cytology diagnosis of AUS and 23 (26%) had FN. RAS mutation was observed in 48 cases. On surgical follow-up, 17 (35%) cases showed non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP), while 14 (29%) patients had a malignant diagnosis. THADA-IGF2BP3 fusions were seen in 8 cases, all with NIFTP on surgical pathology follow-up (100%).

CONCLUSIONS

Analysis of THADA-IGF2BP3 fusion, in our institutional series, shows close association with NIFTP cases. THADA-IGF2BP3 fusion, which seems to be a favorable prognostic indicator in general, may serve as a molecular marker for non-invasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP).

Monitoring Outcomes of Indeterminate Thyroid Nodules and Predictive Capabilities of Molecular Testing

OBJECTIVE

This study aimed to compare the effectiveness of reflex molecular testing at identifying thyroid malignancy in indeterminate thyroid nodules (ITNs) since its implementation at our institution.

METHOD

Identified all ITNs at our institution from January 2010 to October 2020. Calculated the sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV) of ThyroSeq since the initiation of universal reflex testing of all first-time ITNs beginning in March 2016. Analyze effect on frequency of diagnostic surgeries.

RESULTS

Study group: March 2016 to October 2020, 378 ITNs underwent ThyroSeq (318 Bethesda III and 60 Bethesda IV). Mean age 52 years, 35.9% male, 61.1% female. 145 surgically excised with overall resection rate of 38.4% (III: 32.7%; IV 68%). Final histology: 49 malignant with overall rate of malignancy (ROM) of ITNs at 33.8% (III: 31.7%; IV: 39%). ThyroSeq sensitivity for ITNs at 84% (III 78.8%, IV 93.8%). ThyroSeq NPV for ITNs at 86% (III 84%, IV 93.3%). ThyroSeq specificity for ITNs at 52% (III 50.7%, IV 56%). ThyroSeq PPV for ITNs at 47% (III 42.6%, IV 57.7%). Control group: From January 2010 to February 2016 there were 242 ITNs (152 Bethesda III, 90 Bethesda IV). Mean age 52.6 years, 25.8% male, 74.2% female. 157 cases were surgically excised, with an overall resection rate of 64.9% (III: 57.2%; IV: 77.8%). Final histology: 32 malignant, with overall ROM of ITNs at 20.4% (III: 27.6%; IV: 11.4%).

CONCLUSION

The initiation of universal Thyroseq (sensitivity 84% and NPV 86%) of ITNs at our institution has significantly decreased our percentage of diagnostic lobectomies, with a decreased resection rate of 26.5%.

Detection of RAS p.Q61R by Immunohistochemistry in Practice: A Clinicopathologic Study of 217 Thyroid Nodules with Molecular Correlates

RAS p.Q61R is the most prevalent hot-spot mutation in RAS and RAS-like mutated thyroid nodules. A few studies evaluated RAS p.Q61R by immunohistochemistry (RASQ61R-IHC). We performed a retrospective study of an institutional cohort of 150 patients with 217 thyroid lesions tested for RASQ61R-IHC, including clinical, cytologic and molecular data. RASQ61R-IHC was performed on 217 nodules (18% positive, 80% negative, and 2% equivocal). RAS p.Q61R was identified in 76% (n = 42), followed by RAS p.Q61K (15%; n = 8), and RAS p.G13R (5%; n = 3). NRAS p.Q61R isoform was the most common (44%; n = 15), followed by NRAS p.Q61K (17%; n = 6), KRAS p.Q61R (12%; n = 4), HRAS p.Q61R (12%; n = 4), HRAS p.Q61K (6%; n = 2), HRAS p.G13R (6%; n = 2), and NRAS p.G13R (3%; n = 1). RASQ61R-IHC was positive in 47% of noninvasive follicular thyroid neoplasms with papillary-like nuclear features (NIFTP; 17/36), 22% of follicular thyroid carcinomas (FTC; 5/23), 10% of follicular thyroid adenomas (FTA; 4/40), and 8% of papillary thyroid carcinomas (PTC; 9/112). Of PTC studied (n = 112), invasive encapsulated follicular variant (IEFVPTC; n = 16) was the only subtype with positive RASQ61R-IHC (56%; 9/16). Overall, 31% of RAS-mutated nodules were carcinomas (17/54); and of the carcinomas, 94% (16/17) were low-risk per American Thyroid Associated (ATA) criteria, with only a single case (6%; 1/17) considered ATA high-risk. No RAS-mutated tumors recurred, and none showed local or distant metastasis (with a follow-up of 0-10 months). We found that most RAS-mutated tumors are low-grade neoplasms. RASQ61R-IHC is a quick, cost-effective, and reliable way to detect RAS p.Q61R in follicular-patterned thyroid neoplasia and, when malignant, guide surveillance.

Use of molecular testing results to analyze the overuse of atypia of undetermined significance in thyroid cytology

INTRODUCTION

The suggested atypia of undetermined significance (AUS) rate for thyroid fine-needle aspiration biopsies is 10% or less. Prompted by a high institutional AUS rate, we examined using molecular testing results (MTR) as a potential quality metric tool to reduce the AUS rate. We correlated MTR with AUS cytologic findings, surgical pathology follow-up, and individual pathologist AUS rates.

MATERIALS AND METHODS

Demographic data, cytologic diagnoses, MTR, and surgical pathology diagnoses were retrospectively obtained. MTR were classified as either positive or negative. AUS rates and MTR proportions were compared among pathologists. The cytomorphologic features of 143 AUS cases were assessed and correlated with MTR.

RESULTS

Between 2017 and 2022, 710 of 3247 thyroid fine-needle aspirations were classified as AUS, with a yearly average rate of 22% (range = 19%-26%). AUS cases included: 331 (47%) with architectural atypia; 204 (29%) with oncocytic (Hürthle cell) atypia; 99 (14%) with combined architectural and cytologic atypia; and 76 (10%) with isolated cytologic atypia. Most AUS cases with molecular testing had negative MTR (360/492, 73%). AUS with cytologic atypia had higher positive MTR risk (logarithm of odds ratio = 1.27, 95% credible interval [0.5-2.04], P = 0.001). The average positive MTR rate by pathologist was 21.5% (range 0%-35%); higher positive MTR rates had better correlation with subsequent neoplastic/malignant histologic diagnoses. The MTR sensitivity for malignant disease was 89% and the negative predictive value was 91%.

CONCLUSIONS

MTR analysis reveals the importance of cytologic atypia as a determinant of malignancy risk in AUS cases. Periodic analysis of MTR data alongside individual pathologist AUS rates can help refine diagnostic criteria and potentially reduce AUS overuse.

Clinical use of Molecular Data in Thyroid Nodules and Cancer

Over the past 3 decades, advances in the molecular genetics of thyroid cancer (TC) have been translated into diagnostic tests, prognostic markers, and therapeutic agents. The main drivers in differentiated TC pathogenesis are single-point mutations and gene fusions in components of the Mitogen-activated protein kinase (MAPK) and phosphoinositide-3-kinase-protein kinase B/Akt (PI3K/Akt) pathways. Other important genetic alterations in the more advanced types of TC include TERT promoter, TP53, EIF1AX, and epigenetic alterations. Using this knowledge, several molecular tests have been developed for cytologically indeterminate thyroid nodules. Currently, 3 commercially available tests are in use including a DNA/RNA-based test (ThyroSeq v.3), an RNA-based test (Afirma Gene Sequencing Classifier), and a hybrid DNA/miRNA test, ThyGeNEXT/ThyraMIR. These tests are mostly used to rule out malignancy in Bethesda III and IV thyroid nodules because they all have high sensitivities and negative predictive values. Their common use, predominantly in the United States, has resulted in a significant reduction in unnecessary thyroid surgeries for benign nodules. Some of these tests also provide information on the underlying molecular drivers of TC; this may support decision making in initial TC management planning, although this practice has not yet been widely adopted. More importantly, molecular testing is essential in patients with advanced disease before using specific mono-kinase inhibitors (eg, selpercatinib for RET-altered TC) because these drugs are ineffective in the absence of a specific molecular target. This mini-review discusses the utilization of molecular data in the clinical management of patients with thyroid nodules and TC in these different clinical situations.

Indeterminate Thyroid Nodules and Advances in Molecular Pathology

Thyroid cytology has in recent years been augmented by molecular testing for indeterminate lesions. Three commercial molecular tests are available which provide variable amounts of detail regarding the genetic alterations identified in a sample. This paper will describe these tests, as well as the common molecular drivers associated with papillary thyroid carcinoma (PTC) and follicular patterned lesions, in order to help the practicing pathologist and clinician better interpret the results of these tests and incorporate this information into their management of cytologically indeterminate thyroid lesions.

Molecular testing in indeterminate thyroid nodules: an additional tool for clinical decision-making

Thyroid nodules are commonly encountered in clinical practice, affecting up to 50% of the population. The large majority of thyroid lumps are benign incidental findings detected by imaging, while approximately 5-15% harbor malignancy. For a target patient's care, it is of paramount importance to identify and treat thyroid malignancy, while preventing unnecessary invasive surgery in patients with benign lesions. Although fine needle aspiration (FNA) associated with cytological examination provides malignant risk information, 20-30% of diagnoses fall into the "indeterminate thyroid nodule" (ITN) category. ITN clinical management remains a challenging issue for physicians since the ITN risk of malignancy varies from 5% to 40% and most thyroid nodules undergo overtreatment with surgery procedures. ITN molecular testing may better define malignant risk in the single nodule and is able to discriminate with accuracy benign from malignant nodules. Nowadays there are different technologies and different molecular panels, each with its own specificity, sensitivity and predictive values. In view of widespread introduction of molecular testing , some outstanding questions remain and are addressed in the present review such as the presence of molecular panels acting as "rule in" or "rule out" tools, the effective impact of testing results in the clinical decision-making process, and the prohibitive cost of commercial assays associated with the lack of test reimbursement in national health systems.

Paving the path toward multi-omics approaches in the diagnostic challenges faced in thyroid pathology

INTRODUCTION

Despite advancements in diagnostic methods, the classification of indeterminate thyroid nodules still poses diagnostic challenges not only in pre-surgical evaluation but even after histological evaluation of surgical specimens. Proteomics, aided by mass spectrometry and integrated with artificial intelligence and machine learning algorithms, shows great promise in identifying diagnostic markers for thyroid lesions.

AREAS COVERED

This review provides in-depth exploration of how proteomics has contributed to the understanding of thyroid pathology. It discusses the technical advancements related to immunohistochemistry, genetic and proteomic techniques, such as mass spectrometry, which have greatly improved sensitivity and spatial resolution up to single-cell level. These improvements allowed the identification of specific protein signatures associated with different types of thyroid lesions.

EXPERT COMMENTARY

Among all the proteomics approaches, spatial proteomics stands out due to its unique ability to capture the spatial context of proteins in both cytological and tissue thyroid samples. The integration of multi-layers of molecular information combining spatial proteomics, genomics, immunohistochemistry or metabolomics and the implementation of artificial intelligence and machine learning approaches, represent hugely promising steps forward toward the possibility to uncover intricate relationships and interactions among various molecular components, providing a complete picture of the biological landscape whilst fostering thyroid nodule diagnosis.

Molecular testing in thyroid cancer diagnosis and management

Molecular diagnostic testing has had a profound impact on the diagnosis and management of thyroid nodules and thyroid cancer. Based on the tremendous expansion of knowledge of the genomic landscape of thyroid cancer over the past few decades, tests have been developed, analyzed, modified, and implemented into clinical practice. Genomic testing of thyroid nodules to improve preoperative diagnosis has become an important component supporting decision-making in clinical care, reducing the need for diagnostic surgeries and improving accuracy of cancer risk assessment. In addition, a role for molecular testing of established thyroid cancers to assist in selection of therapeutic options for patients with advanced and/or progressive disease has been established. Research is ongoing to determine if molecular results should affect management of less aggressive forms of thyroid cancer earlier in clinical management. This review will outline the various commercial platforms for molecular diagnostics for nodules emphasizing their performance parameters and indications for use, as well as discuss the use of genomic analysis for progressive thyroid cancer and highlight opportunities for further research.

Molecular diagnostics in the evaluation of thyroid nodules: Current use and prospective opportunities

Thyroid cancer is the most common endocrine malignancy with an estimated 43,800 new cases to be diagnosed in 2022 and representing the 7th most common cancer in women. While thyroid nodules are very common, being identified in over 60% of randomly selected adults, only 5-15% of thyroid nodules harbor thyroid malignancy. Therefore, it is incumbent upon physicians to detect and treat thyroid malignancies as is clinically appropriate and avoid unnecessary invasive procedures in patients with benign asymptomatic lesions. Over the last 15-20 years, rapid advances have been made in cytomolecular testing to aid in thyroid nodule management. Initially, indeterminate thyroid nodules, those with Bethesda III or IV cytology and approximately a 10-40% risk of malignancy, were studied to assess benignity or malignancy. More recently, next generation sequencing and micro-RNA technology platforms have refined the diagnostic capacity of thyroid nodule molecular testing and have introduced opportunities to glean prognostic information from both cytologically indeterminate and malignant thyroid nodules. Therefore, clinicians can move beyond determination of malignancy, and utilize contemporary molecular information to aid in decisions such as extent of surgery and post-therapy monitoring plans. Future opportunities include molecularly derived information about tumor behavior, neo-adjuvant treatment opportunities and response to thyroid cancer therapies.

Clinicoradiological Characteristics in the Differential Diagnosis of Follicular-Patterned Lesions of the Thyroid: A Multicenter Cohort Study

OBJECTIVE

Preoperative differential diagnosis of follicular-patterned lesions is challenging. This multicenter cohort study investigated the clinicoradiological characteristics relevant to the differential diagnosis of such lesions.

MATERIALS AND METHODS

From June to September 2015, 4787 thyroid nodules (≥ 1.0 cm) with a final diagnosis of benign follicular nodule (BN, n = 4461), follicular adenoma (FA, n = 136), follicular carcinoma (FC, n = 62), or follicular variant of papillary thyroid carcinoma (FVPTC, n = 128) collected from 26 institutions were analyzed. The clinicoradiological characteristics of the lesions were compared among the different histological types using multivariable logistic regression analyses. The relative importance of the characteristics that distinguished histological types was determined using a random forest algorithm.

RESULTS

Compared to BN (as the control group), the distinguishing features of follicular-patterned neoplasms (FA, FC, and FVPTC) were patient's age (odds ratio [OR], 0.969 per 1-year increase), lesion diameter (OR, 1.054 per 1-mm increase), presence of solid composition (OR, 2.255), presence of hypoechogenicity (OR, 2.181), and presence of halo (OR, 1.761) (all p < 0.05). Compared to FA (as the control), FC differed with respect to lesion diameter (OR, 1.040 per 1-mm increase) and rim calcifications (OR, 17.054), while FVPTC differed with respect to patient age (OR, 0.966 per 1-year increase), lesion diameter (OR, 0.975 per 1-mm increase), macrocalcifications (OR, 3.647), and non-smooth margins (OR, 2.538) (all p < 0.05). The five important features for the differential diagnosis of follicular-patterned neoplasms (FA, FC, and FVPTC) from BN are maximal lesion diameter, composition, echogenicity, orientation, and patient's age. The most important features distinguishing FC and FVPTC from FA are rim calcifications and macrocalcifications, respectively.

CONCLUSION

Although follicular-patterned lesions have overlapping clinical and radiological features, the distinguishing features identified in our large clinical cohort may provide valuable information for preoperative distinction between them and decision-making regarding their management.

Performance of repeat cytology with reflex ThyroSeq genomic classifier for indeterminant thyroid cytology

BACKGROUND

The American Thyroid Association recommends either repeat fine-needle aspiration biopsy (FNAB) or molecular testing (eg, ThyroSeq) of Bethesda category III (atypia of undetermined significance/follicular lesion of undetermined significance [AUS/FLUS]) nodules to provide further risk stratification. How a testing algorithm that uses ancillary molecular tests performs as a reflex test for repeat sampling of indeterminant nodules remains unclear.

METHODS

Thyroid FNABs performed over a 24-month period that received a diagnosis of AUS/FLUS and underwent subsequent FNAB were analyzed.

RESULTS

In total, 187 patients were identified who received an FNAB diagnosis of AUS/FLUS and had repeat sampling. Of these patients, 64% received a subsequent indeterminant diagnosis on repeat biopsy: 7 (3.7%) repeat biopsies were diagnosed as nondiagnostic/unsatisfactory, 104 (55.6%) were diagnosed as AUS/FLUS, and 8 (4.3%) were diagnosed as follicular neoplasm/suspicious for follicular neoplasm. Of the repeat biopsied nodules, 63% underwent subsequent testing with ThyroSeq version 3. The diagnostic performance was calculated using only surgically confirmed nodules (sensitivity, 100%; specificity, 30%; positive predictive value, 41%; negative predictive value, 100%) and by assigning nonresected nodules with negative ThyroSeq or benign cytology results as benign (sensitivity, 100%; specificity, 88%; positive predictive value, 41%; negative predictive value, 100%).

CONCLUSIONS

In the majority of patients, repeat FNAB for AUS/FLUS did not preclude subsequent molecular ancillary testing because of the high rate of indeterminant results on repeat biopsy. The diagnostic performance of the testing algorithm reported here was very similar to other reports using either repeat biopsy or molecular testing alone. Ultimately, the algorithm of performing molecular testing on repeat indeterminant nodules increased the number of biopsies performed and lengthened the time to definitive risk stratification without a disproportionate decrease in the use of molecular testing or an appreciable improvement in diagnostic performance.