Afirma Gene Sequencing Classifier Compared with Gene Expression Classifier in Indeterminate Thyroid Nodules

Performance of Afirma Genomic Sequencing Classifier in Binary Subcategories of Atypia of Undetermined Significance Thyroid Nodules: Single Versus Repeat Diagnosis

Background: Afirma Genomic Sequencing Classifier (GSC) testing has been utilized for further risk stratification of thyroid nodules categorized as atypia of undetermined significance (AUS). The 2023 Bethesda system subcategorizes AUS diagnosis into AUS with nuclear atypia (AUS-N) and other atypia (AUS-O). The current study aims to determine if performance of GSC testing differs between the two AUS subcategories and between single AUS cohort and repeat AUS cohort. Methods: This retrospective study analyzed consecutive thyroid nodule fine-needle aspiration with a single or a repeat AUS diagnosis and a diagnostic GSC testing result (benign vs. suspicious). All AUS nodules were divided into AUS-N or AUS-O subcategory and followed by either surgical intervention or at least 12 months of clinical and/or ultrasound monitoring. We then assessed performance of GSC testing in each subcategory and subsequently compared the individual performance in AUS-N or AUS-O subcategory between single AUS cohort and repeat AUS cohort. Results: The study identified a total of 365 thyroid nodules subcategorized as AUS-N (N = 106) and AUS-O (N = 259). Both cohorts showed a significantly lower GSC benign call rate (BCR) in AUS-N nodules compared with AUS-O nodules (43% vs. 71% in single AUS, p = 0.001; 58% vs. 74% in repeat AUS, p = 0.02). The proportion of histology-proven malignancies associated with a suspicious GSC result tended to be greater in AUS-N nodules than AUS-O nodules (28% vs. 10% in single AUS, p = 0.09; 38% vs. 27% in repeat AUS, p = 0.3). Compared with AUS-N nodules, AUS-O cohorts demonstrated significantly higher specificity in the single AUS group (73% vs. 51%, p = 0.01). In both subcategories, the repeat AUS cohort yielded greater specificity, positive predictive value, and diagnostic accuracy compared with the single AUS group. However, the differences did not reach statistical significance. Conclusions: GSC BCR and diagnostic performance of GSC testing may vary in AUS-N versus AUS-O subcategories. However, there were no statistically significant differences in GSC performance between single and repeat AUS cohorts.

Avoidable biopsies? Validating artificial intelligence-based decision support software in indeterminate thyroid nodules

BACKGROUND

Multiple artificial intelligence (AI) systems have been approved to risk-stratify thyroid nodules through sonographic characterization. We sought to validate the ability of one such AI system, Koios DS (Koios Medical, Chicago, IL), to aid in improving risk stratification of indeterminate thyroid nodules.

METHODS

A retrospective single-institution dataset was compiled of 28 cytologically indeterminate thyroid nodules having undergone molecular testing and surgical resection, with surgical pathology categorized as malignant or benign. Nodules were retrospectively evaluated with Koios DS. After nodule selection, automated and AI-adapter-derived Thyroid Imaging Reporting and Data System (TI-RADS) levels were recorded, and agreement with radiologist-derived levels was assessed using Cohen's κ statistic. The performance of malignancy classification was compared between the radiologist and AI-adapter. Biopsy thresholds were re-evaluated using the AI-adapter.

RESULTS

In this cohort, 7 (25%) nodules were malignant on surgical pathology. The median nodule size was 2.4 cm (interquartile range: 1.8-2.9 cm). Median radiologist and automated TI-RADS levels were both 4, with κ 0.25 ("fair agreement"). Malignancy classification by the radiologist provided sensitivity 100%, specificity 33.3%, positive predictive value (PPV) 33.3%, and negative predictive value (NPV) 100%, compared with the AI-adapter's performance with sensitivity 85.7%, specificity 76.2%, PPV 54.5%, and NPV 94.1%. Using the AI-adapter, 14 of 28 biopsies would have been deferred, 13 of which were surgically benign.

CONCLUSION

Koios automated and radiologist-derived TI-RADS levels were in consistent agreement for indeterminate thyroid nodules. Malignancy reclassification with the AI-adapter improved PPV at minimal cost to NPV. Risk stratification with the addition of the AI-adapter may allow for more accurate patient counseling and the avoidance of biopsies in select cases that would otherwise be cytologically indeterminate.

Outcomes of Cytologically Indeterminate Thyroid Nodules Managed With Genomic Sequencing Classifier

CONTEXT

Molecular testing can refine the risk of malignancy in thyroid nodules with indeterminate cytology to decrease unnecessary diagnostic surgery.

OBJECTIVE

This study was performed to evaluate the outcomes of cytologically indeterminate thyroid nodules managed with Afirma genomic sequencing classifier (GSC) testing.

METHODS

Adult patients who underwent a biopsy at 3 major academic centers between July 2017 and June 2021 with Bethesda III or IV cytology were included. All patients had surgery or minimum follow-up of 1 year ultrasound surveillance. The primary outcomes were the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of GSC in Bethesda III and IV nodules.

RESULTS

The median nodule size of the 834 indeterminate nodules was 2.1 cm and the median follow-up was 23 months. GSC sensitivity, specificity, PPV, and NPV across all institutions were 95%, 81%, 50%, and 99% for Bethesda III nodules and 94%, 82%, 65%, and 98% for Bethesda IV nodules, respectively. The overall false-negative rate was 2%. The NPV of GSC in thyroid nodules with oncocytic predominance was 100% in Bethesda III nodules and 98% in Bethesda IV nodules. However, the PPV of oncocytic nodules was low (17% in Bethesda III nodules and 45% in Bethesda IV nodules). Only 22% of thyroid nodules with benign GSC results grew during surveillance.

CONCLUSION

GSC is a key tool for managing patients with indeterminate cytology, including the higher-risk Bethesda IV category. GSC-benign thyroid nodules can be observed similarly to thyroid nodules with benign cytology.

Diagnostic accuracy of Afirma gene expression classifier, Afirma gene sequencing classifier, ThyroSeq v2 and ThyroSeq v3 for indeterminate (Bethesda III and IV) thyroid nodules: a meta-analysis

Objective

The management of thyroid nodules with indeterminate cytology (ITN) is still a challenge. To evaluate the performance of commercial molecular tests for ITN, we performed this comprehensive meta-analysis.

Methods

We performed an electronic search using PubMed/Medline, Embase, and the Cochrane Library. Studies assessing the diagnostic accuracy of Afirma gene expression classifier (GEC), Afirma gene sequencing classifier (GSC), ThyroSeq v2 (TSv2), or ThyroSeq v3 (TSv3) in patients with ITN (only Bethesda category III or IV) were selected; Statistical analyses were performed by using Stata.

Results

Seventy-one samples (GEC, n = 38; GSC, n = 16; TSv2, n = 9; TSv3, n = 8) in 53 studies, involving 6490 fine needle aspirations (FNAs) with ITN cytology with molecular diagnostics (GEC, GSC, TSv2, or TSv3), were included in the study. The meta-analysis showed the following pooled estimates: sensitivity 0.95 (95% CI: 0.94-0.97), specificity 0.35 (0.28-0.43), positive likelihood ratio (LR+) 1.5 (1.3-1.6), and negative likelihood ratio (LR-) 0.13 (0.09-0.19), with the best performance for TSv3 (area under the ROC curve 0.95 (0.93-0.96), followed by TSv2 (0.90 (0.87-0.92)), GSC (0.86 (0.82-0.88)), and GEC (0.82 (0.78-0.85)); the best rule-out property was observed for GSC (LR-, 0.07 (0.02-0.19)), followed by TSv3 (0.11 (0.05-0.24)) and GEC (0.16 (0.10-0.28), and the best rule-in was observed for TSv2 (LR+, 2,9 (1.4-4.6)), followed by GSC (1.9 (1.6-2.4)). A meta-regression analysis revealed that study design, Bethesda category, and type of molecular test were independent factors.

Conclusion

We showed that in patients with ITN, TSv3 has the best molecular diagnostic performance, followed by TSv2, GSC, and GEC. As regards rule-out malignancy, GSC, and rule-in, TSV2 is superior to other tests.

Artificial intelligence assisted diagnosis of early tc markers and its application

Thyroid cancer (TC) is a common endocrine malignancy with an increasing incidence worldwide. Early diagnosis is particularly important for TC patients, because it allows patients to receive treatment as early as possible. Artificial intelligence (AI) provides great advantages for complex healthcare systems by analyzing big data based on machine learning. Nowadays, AI is widely used in the early diagnosis of cancer such as TC. Ultrasound detection and fine needle aspiration biopsy are the main methods for early diagnosis of TC. AI has been widely used in the detection of malignancy in thyroid nodules by ultrasound images, cytopathology images and molecular markers. It shows great potential in auxiliary medical diagnosis. The latest clinical trial has shown that the performance of AI models matches with the diagnostic efficiency of experienced clinicians, and more efficient AI tools will be developed in the future. Therefore, in this review, we summarized the recent advances in the application of AI algorithms in assessing the risk of malignancy in thyroid nodules. The objective of this review was to provide a data base for the clinical use of AI-assisted diagnosis in TC, as well as to provide new ideas for the next generation of AI-assisted diagnosis in TC.

Deciphering the progression of fine-needle aspiration: A bibliometric analysis of thyroid nodule research

This study aims to dissect the evolution and pivotal shifts in Fine-Needle Aspiration (FNA) research for thyroid nodules over the past 2 decades, focusing on delineating key technological advancements and their impact on clinical practice. A comprehensive bibliometric analysis was conducted on 5418 publications from the Web of Science Core Collection database (2000-2023). Publications were rigorously selected based on their contributions to the advancement of FNA techniques and their influence on thyroid nodule management practices. Our analysis uncovered significant breakthroughs, most notably the incorporation of ultrasound and molecular diagnostics in FNA, which have markedly elevated diagnostic accuracy. A pivotal shift was identified towards minimally invasive post-FNA treatments, such as Radiofrequency Ablation, attributable to these diagnostic advancements. Additionally, the emergence of AI-assisted cytology represents a frontier in precision diagnostics, promising enhanced disease identification. The geographical analysis pinpointed the United States, Italy, and China as key contributors, with the United States leading in both publication volume and citation impact. This bibliometric analysis sheds light on the transformative progression in FNA practices for thyroid nodules, characterized by innovative diagnostic technologies and a trend towards patient-centric treatment approaches. The findings underscore the need for further research into AI integration and global practice standardization. Future explorations should focus on the practical application of these advancements in diverse healthcare settings and their implications for global thyroid nodule management.

Cost-Effectiveness Analysis of Molecular Testing for Indeterminate Thyroid Nodules in Nova Scotia

BACKGROUND

The objective of the following retrospective review was to perform a cost-effectiveness analysis of the use of molecular testing of indeterminate thyroid nodules compared to current management practices in Nova Scotia, Canada.

METHODS

All cases of cytologically indeterminate thyroid nodules from January 1st, 2014 to December 31st, 2018 were reviewed. All interventions related to an indeterminate thyroid nodule were recorded. Patients were excluded if less than 18 years old if no further information regarding medical management was electronically available beyond the diagnosis of an indeterminate thyroid nodule, history of radiation, or previous thyroid surgery prior to diagnosis of an indeterminate thyroid nodule in the remaining lobe. Microcosting was performed to determine the cost of all relevant interventions including repeat fine needle aspiration biopsy, ultrasound, thyroid surgery(s), and molecular testing. Institution-specific transition state probabilities were calculated and used to build a cost-effectiveness analysis model. Model output was an incremental cost-effectiveness ratio, defined as the ratio of cost difference to effectiveness difference between routine molecular testing and the current management strategy, yielding cost per surgery avoided.

RESULTS

The mean effectiveness of the current management of indeterminate thyroid nodules in Nova Scotia based on the American Thyroid Association guidelines is 64% at a mean cost of $6431, while the simulated mean effectiveness of routine molecular testing is 89% at a mean cost of $8414. Differences in management strategies generated an incremental cost-effectiveness ratio of $7876 per surgery avoided.

CONCLUSION

Routine molecular testing is the more effective strategy for the appropriate management of indeterminate thyroid nodules; however, it comes at a higher mean cost compared to the current management strategy. As the cost of molecular testing continues to decrease, and the cost of OR resources continues to rise, molecular testing is likely to become the optimal strategy in Nova Scotia.

Performance of Afirma genomic sequencing classifier and histopathological outcome in Bethesda category III thyroid nodules: Initial versus repeat fine-needle aspiration

BACKGROUND

There is limited data comparing the performance of Afirma Genomic Sequencing Classifier (GSC) in thyroid nodules carrying an initial versus a repeat diagnosis of atypia of undetermined significance (AUS). This study reported an institutional experience in this regard.

MATERIALS AND METHODS

This retrospective study included consecutive thyroid nodules that had an initial or a repeat AUS diagnosis and had a subsequent GSC diagnostic result (benign or suspicious) from 2017 to 2021. All nodules were followed by surgical intervention or by clinical and/or ultrasound monitoring. GSC's benign call rate (BCR), rate of histology-proven malignancy associated with a suspicious GSC result, and diagnostic parameters of GSC were calculated and compared between the two cohorts (initial versus repeat AUS). Statistical significance was defined with a p-value of <.05 for all analysis.

RESULTS

A total of 202 cases fulfilled inclusion criteria, including 67 and 135 thyroid nodules with an initial and a repeat AUS diagnosis, respectively. BCR was 67% and 66% in initial and repeat AUS cohorts, respectively. Rate of histology-proven malignancy associated with a suspicious GSC result were 22% and 24% in initial and repeat AUS cohorts, respectively. Compared with the repeat AUS cohort, the initial AUS cohort showed slightly lower sensitivity (83% vs. 100%), specificity (70% vs. 73%), PPV (23% vs. 24%), NPV (98% vs. 100%), and diagnostic accuracy (72% vs. 75%). Nevertheless, these differences did not reach statistical significance.

CONCLUSION

GSC demonstrated comparable performance in thyroid nodules with a repeat AUS diagnosis versus nodules with an initial AUS diagnosis.

ThyroidPrint®: clinical utility for indeterminate thyroid cytology

Molecular testing contributes to improving the diagnosis of indeterminate thyroid nodules (ITNs). ThyroidPrint® is a ten-gene classifier aimed to rule out malignancy in ITN. Post-validation studies are necessary to determine the real-world clinical benefit of ThyroidPrint® in patients with ITN. A single-center, prospective, noninterventional clinical utility study was performed, analyzing the impact of ThyroidPrint® in the physicians' clinical decisions for ITN. Demographics, nodule characteristics, benign call rates (BCRs), and surgical outcomes were measured. Histopathological data were collected from surgical biopsies of resected nodules. Of 1272 fine-needle aspirations, 109 (8.6%) were Bethesda III and 135 (10.6%) were Bethesda IV. Molecular testing was performed in 155 of 244 ITN (63.5%), of which 104 were classified as benign (BCR of 67.1%). After a median follow-up of 15 months, 103 of 104 (99.0%) patients with a benign ThyroidPrint® remained under surveillance and one patient underwent surgery which was a follicular adenoma. Surgery was performed in all 51 patients with a suspicious for malignancy as per ThyroidPrint® result and in 56 patients who did not undergo testing, with a rate of malignancy of 70.6% and 32.1%, respectively. A higher BCR was observed in follicular lesion of undetermined significance (87%) compared to atypia of undetermined significance (58%) (P < 0.05). False-positive cases included four benign follicular nodules and six follicular and four oncocytic adenomas. Our results show that, physicians chose active surveillance instead of diagnostic surgery in all patients with a benign ThyroidPrint® result, reducing the need for diagnostic surgery in 67% of patients with preoperative diagnosis of ITN.

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.

Molecular testing for indeterminate thyroid nodules: past, present, and future

PURPOSE OF REVIEW

To examine the origin, current progress, and future directions of molecular testing in indeterminate Bethesda III and Bethesda IV thyroid nodules.

RECENT FINDINGS

The diagnostic performance of current genomic tests shows improved benign call rates, specificity and positive-predictive values over prior test versions. The choice of test platform for clinical use should consider test performance, institutional rate of malignancy, nodule cytology and the potential for prognostication to help guide decision-making. Current challenges include test reliability, defining the optimal duration of surveillance, and improving test performance in challenging cytology, such as oncocytic nodules and NIFTP. Opportunities also remain to optimize cost-effectiveness across multiple clinical and practice settings and to refine the use of molecular testing for dynamic risk stratification, such as with BRAF V600E mutation testing.

SUMMARY

Molecular testing of indeterminate thyroid nodules has helped to reduce the burden of diagnostic surgery, associated healthcare costs, and potential complications. Current-generation tests have demonstrated improvement in diagnostic performance, but challenges remain in improving test performance and refining the scope of testing in care. Decision-making for the management of indeterminate thyroid nodules should consider cytology, clinical and sonographic features, patient values and preferences and molecular testing results, whenever available.

An update on the management of thyroid nodules: rationalising the guidelines

BACKGROUND

Guidance for the management of thyroid nodules has evolved over time, from initial evaluation based predominantly on clinical grounds to now including the established role of ultrasound and fine needle aspiration cytology in their assessment. There is, however, significant variation in the management of thyroid nodules depending on which national guidelines are followed. In addition, there are certain clinical situations such as pregnancy and paediatric thyroid nodules that have differing evaluation priorities.

OBJECTIVES

This review aimed to provide an overview of currently accepted practices for the initial investigation and subsequent management of patients with thyroid nodules for the non-specialist. The review also addresses areas of variance between the systems in common clinical use, as well as newer, evolving technologies, including molecular testing in the evaluation of malignancy in thyroid nodules.

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.

Pilot Study on the Use of Untargeted Metabolomic Fingerprinting of Liquid-Cytology Fluids as a Diagnostic Tool of Malignancy for Thyroid Nodules

Although it is the gold standard for assessing the malignancy of thyroid nodules (TNs) preoperatively, the cytological analysis of fine-needle aspiration cytology (FNAC) samples results in 20-30% of cases in indeterminate lesions (ITNs). As two-thirds of these lesions will appear benign after diagnostic surgery, improved preoperative diagnostic methods need to be developed. In this pilot study, we evaluate if the metabolomic profiles of liquid-based (CytoRich^®) FNAC samples of benign and malignant nodules can allow the molecular diagnosis of TNs. We performed untargeted metabolomic analyses with CytoRich^® FNAC in a monocentric retrospective study. The cohort was composed of cytologically benign TNs, histologically benign or papillary thyroid carcinomas (PTCs) cytologically ITNs, and suspicious/malignant TNs histologically confirmed as PTCs. The diagnostic performance of the identified metabolomic signature was assessed using several supervised classification methods. Seventy-eight patients were enrolled in the study. We identified 7690 peaks, of which 2697 ions were included for further analysis. We selected a metabolomic signature composed of the top 15 metabolites. Among all the supervised classification methods, the supervised autoencoder deep neural network exhibited the best performance, with an accuracy of 0.957 (0.842-1), an AUC of 0.945 (0.833-1), and an F1 score of 0.947 (0.842-1). Here, we report a promising new ancillary molecular technique to differentiate PTCs from benign TNs (including among ITNs) based on the metabolomic signature of FNAC sample fluids. Further studies with larger cohorts are now needed to identify a larger number of biomarkers and obtain more robust signatures.

Advances in Molecular Profiling and Their Potential Influence on the Extent of Surgery in Well-Differentiated Thyroid Carcinoma (WDTC)

Thyroid cancer surgery has evolved dramatically with advances in our understanding of the biological behaviour of WDTC. Molecular profiling is shedding light on the subset that may behave aggressively. In an era when thyroid cancer management is becoming increasingly conservative, decision making regarding the extent of surgery must be objectively guided by molecular markers. The aim of the present article is to summarise the current published literature and provide possible practice recommendations. An online search for relevant published articles was performed using several databases. Title, abstract, and full-text screening, along with data extraction, was performed by two independent reviewers after the inclusion and exclusion criteria were defined. A total of 1241 articles were identified, and 82 relevant articles were extracted and scrutinised. BRAF V600E and TERT promoter mutations were found to be associated with an increased risk of disease recurrence and distant metastases. Several other mutations have been identified that enhance disease aggressiveness (such as RET/PTC, PTEN, and TP53). One of the most important determinants of the outcome in WDTC is the extent of surgical resection. The evolution of molecular testing has reached a stage of personalised incorporation into surgical practice. Guidelines for molecular testing and surgery in WDTC will need to be clearly defined, arguably representing the next chapter in the management of the disease.

Preoperative evaluation of thyroid nodules - Diagnosis and management strategies

Thyroid cancer is the most common endocrine malignancy, with increasing incidence over the past few decades. Fine needle aspiration (FNA) biopsy is the gold standard for preoperative diagnosis of thyroid malignancies. Nevertheless, this method renders indeterminate results in up to 30% of the cases. Therefore, these patients are often referred to unnecessary surgery to establish the diagnosis. To improve the accuracy of preoperative diagnosis, several other ways, such as ultrasonography, elastography, immunohistochemical analysis, genetic testing, and core needle biopsy, have been developed and can be used either in association with or as an alternative to FNA. This review aims to evaluate all these diagnostic tools to determine the most appropriate way of managing thyroid nodules and subsequently improve the selection of cases referred to surgery.

Development and validation of an RNA sequencing-based classifier for medullary thyroid carcinoma on thyroid FNA

This commentary describes the development and validation of the Afirma RNA sequencing–based classifier for medullary thyroid carcinoma (MTC). The importance of the early diagnosis of MTC is discussed along with the limitations of cytomorphology alone.

Risk stratification of cytologically indeterminate thyroid nodules with nondiagnostic or benign cytology on repeat FNA: Implications for molecular testing and surveillance

BACKGROUND

Evidence guiding the management of cytologically indeterminate thyroid nodules with nondiagnostic (ND) or benign cytology on repeat fine-needle aspiration (FNA) is limited. This study evaluates the utility of molecular testing and estimates the risk of noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP) and cancer among such nodules.

METHODS

This was a retrospective single-institution review of thyroid nodules from adults that were classified as atypia of undetermined significance (AUS) or follicular neoplasm (FN) on initial FNA and underwent repeat FNA for cytology and Afirma testing (June 2013-July 2021). The association between repeat FNA cytology and RNA yield for Afirma was determined. Histologic outcomes were integrated with Afirma results to define end points for each nodule.

RESULTS

A total of 691 AUS and FN nodules underwent repeat FNA and Afirma testing. Diagnostic Afirma results were obtained in 98% of cases overall and in 91% of nodules with ND cytology on repeat FNA. Using combined molecular and histologic end points, the NIFTP and/or cancer prevalence for nodules with ND cytology on repeat FNA was 9% (95% confidence interval [CI], 0.042-0.182), falling between those nodules classified as benign (5%; 95% CI, 0.029-0.094) and those classified as AUS or FN (18%; 95% CI, 0.140-0.218) on repeat FNA, although not reaching statistical significance from either subgroup (p = .38 and .10, respectively).

CONCLUSIONS

AUS and FN nodules that are ND on repeat FNA have low but nonnegligible risk of NIFTP and/or cancer and may benefit from molecular testing, given the low test failure rate in this subgroup. Conversely, AUS and FN nodules reclassified as benign on repeat FNA have a very low risk of NIFTP and/or cancer and are unlikely to benefit from molecular testing.

Molecular testing in fine-needle aspiration of thyroid nodules

BACKGROUND

Thyroid nodules are commonly faced by clinicians as palpable nodules or incidentally identified on imaging. Nodules that are found to be suspicious by imaging can be biopsied by fine needle aspiration, which can yield material for molecular testing to refine the diagnosis.

METHODS

The current literature concerning molecular testing in thyroid nodules including available commercial assays was reviewed and summarized.

RESULTS/CONCLUSIONS

Commonly encountered alterations include mutations in RAS, BRAF, TERT promoter, PTEN, and DICER1 as well as fusions of RET, ALK, PAX8-PPARγ, and NTRK. This article provides a summary of these molecular alterations, commercially available molecular assays, and general considerations for thyroid epithelial malignancies and benign thyroid nodules.

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.

Real World Performance of The Afirma Genomic Sequencing Classifier (GSC) - A Meta-analysis

CONTEXT

The Afirma® GSC aids in risk stratifying indeterminate thyroid nodule cytology (ITN). The 2018 GSC validation study (VS) reported a sensitivity (SN) of 91%, specificity (SP) of 68%, positive predictive value (PPV) of 47%, and negative predictive value (NPV) of 96%. Since then, 13 independent real world (RW) post-validation studies have been published.

OBJECTIVE

This study's objective is to compare the RW GSC performance to the VS metrics.

METHODS

Rules and assumptions applying to this analysis include: 1. At least one patient with molecular benign results must have surgery for that study to be included in SN, SP and NPV analyses. 2. Molecular benign results without surgical histology are considered true negatives (TN) (as are the molecular benign results with benign surgical histology) 3. Unoperated patients with suspicious results are either excluded from the analysis (observed PPV (oPPV) and observed SP (oSP)) or assumed as histology negatives (false positives - conservative PPV (cPPV) and conservative SP (cSP)) 4. NIFTP is considered malignant.

RESULTS

In RW studies, the GSC demonstrates a SN, oSP, oPPV and NPV of 97%, 88%, 65%, 99% respectively, and conservative RW performance showed cSP of 80% and cPPV of 49%, all significantly higher than the VS save for SN and cPPV. There was also a higher benign call rate (BCR) of 67% in RW studies compared to 54% in the VS (p < 0.05).

CONCLUSION

RW data for the Afirma GSC demonstrates significantly better oSP and oPPV performance compared to the VS, indicating an increased yield of cancers for resected GSC suspicious nodules. The higher BCR likely increases the overall rate of clinical observation in lieu of surgery.

SFE-AFCE-SFMN 2022 Consensus on the management of thyroid nodules : Role of molecular tests for cytologically indeterminate thyroid nodules

The SFE-AFCE-SFMN 2022 consensus deals with the management of thyroid nodules, a condition that is a frequent reason for consultation in endocrinology. In more than 90% of cases, patients are euthyroid, with benign non-progressive nodules that do not warrant specific treatment. The clinician's objective is to detect malignant thyroid nodules at risk of recurrence and death, toxic nodules responsible for hyperthyroidism or compressive nodules warranting treatment. The diagnosis and treatment of thyroid nodules requires close collaboration between endocrinologists, nuclear medicine physicians and surgeons, but also involves other specialists. Therefore, this consensus statement was established jointly by 3 societies: the French Society of Endocrinology (SFE), French Association of Endocrine Surgery (AFCE) and French Society of Nuclear Medicine (SFMN); the various working groups included experts from other specialties (pathologists, radiologists, pediatricians, biologists, etc.). Because of the emerging role of molecular fine-needle cytology diagnostics, the French Endocrine Society convened a panel of experts to review the evidence for the diagnostic value of molecular tests performed on cytologically indeterminate thyroid nodules.

Performance of Afirma genomic sequencing classifier and histopathological outcome are associated with patterns of atypia in Bethesda category III thyroid nodules

BACKGROUND

Data on Afirma's genomic sequencing classifier (GSC) performance in atypia of undetermined significance (AUS) subcategories is limited. This study investigated GSC performance in AUS nodules with architectural atypia (AUS-A), cytological atypia (AUS-C), architectural and cytological atypia (AUS-AC), and predominantly Hürthle cells (AUS-HC).

METHODS

This study retrieved consecutive thyroid nodules having a recurrent cytologic diagnosis of AUS with qualifiers and a concurrent GSC diagnostic result. All nodules were followed by either surgical intervention or clinical and/or ultrasound monitoring (≥6 months). GSC benign call rate (BCR), rate of histology-proven malignancy, and diagnostic parameters of GSC were calculated for individual AUS subcategories. Statistical analysis was performed using the Fisher exact test.

RESULTS

A total of 135 AUS nodules fulfilled inclusion criteria, including 79 AUS-A, 9 AUS-C, 29 AUS-AC, and 18 AUS-HC. BCR was 72.2%, 66.7%, 44.8%, and 77.8% in AUS-A, AUS-C, AUS-AC, and AUS-HC, respectively. AUS-A showed a greater BCR than AUS-AC (p &lt; .05). All GSC-benign nodules were considered benign on clinical or surgical follow-up. Among GSC-suspicious nodules, histology-proven malignancies represented 4.5% of AUS-A, 0% of AUS-C, 56.3% of AUS-AC, and 25.0% of AUS-HC cases. AUS-AC demonstrated a higher malignant rate compared with AUS-A (p &lt; .05). GSC offers 100% NPV and a wide range (5%-56%) of PPV across all AUS subcategories. AUS-AC demonstrated a greater PPV compared with AUS-A (p &lt; .05).

CONCLUSION

BCR of GSC and malignant rates associated with suspicious GSC may differ in various AUS subcategories. GSC-suspicious nodules with both architectural and cytologic atypia are more likely to be malignant. These findings may improve clinical triage and/or management of patients with AUS thyroid nodules.

MEG3 Expression Indicates Lymph Node Metastasis and Presence of Cancer-Associated Fibroblasts in Papillary Thyroid Cancer

Papillary thyroid cancer is the most common endocrine malignancy, occurring at an incidence rate of 12.9 per 100,000 in the US adult population. While the overall 10-year survival of PTC nears 95%, the presence of lymph node metastasis (LNM) or capsular invasion indicates the need for extensive neck dissection with possible adjuvant radioactive iodine therapy. While imaging modalities such as ultrasound and CT are currently in use for the detection of suspicious cervical lymph nodes, their sensitivities for tumor-positive nodes are low. Therefore, advancements in preoperative detection of LNM may optimize the surgical and medical management of patients with thyroid cancer. To this end, we analyzed bulk RNA-sequencing datasets to identify candidate markers highly predictive of LNM. We identified MEG3, a long-noncoding RNA previously described as a tumor suppressor when expressed in malignant cells, as highly associated with LNM tissue. Furthermore, the expression of MEG3 was highly predictive of tumor infiltration with cancer-associated fibroblasts, and single-cell RNA-sequencing data revealed the expression of MEG3 was isolated to cancer-associated fibroblasts (CAFs) in the most aggressive form of thyroid cancers. Our findings suggest that MEG3 expression, specifically in CAFs, is highly associated with LNM and may be a driver of aggressive disease.

Assessing Bias and Limitations of Clinical Validation Studies of Molecular Diagnostic Tests for Indeterminate Thyroid Nodules: Systematic Review and Meta-Analysis

Background: Molecular tests for thyroid nodules with indeterminate fine needle aspiration results are increasingly used in clinical practice; however, true diagnostic summaries of these tests are unknown. A systematic review and meta-analysis were completed to (1) evaluate the accuracy of commercially available molecular tests for malignancy in indeterminate thyroid nodules and (2) quantify biases and limitations in studies that validate those tests. Summary: PubMed, EMBASE, and Web of Science were systematically searched through July 2021. English language articles that reported original clinical validation attempts of molecular tests for indeterminate thyroid nodules were included if they reported counts of true-negative, true-positive, false-negative, and false-positive results. We performed screening and full-text review, followed by assessment of eight common biases and limitations, extraction of diagnostic and histopathological information, and meta-analysis of clinical validity using a bivariate linear mixed-effects model. Forty-nine studies were included. Meta-analysis of Afirma Gene expression classifiers (GEC; n = 38 studies) revealed a sensitivity of 0.92 (confidence interval: 0.90-0.94), specificity of 0.26 (0.20-0.32), negative likelihood ratio (LR-) of 0.32 (0.23-0.44), positive LR+ of 1.24 (1.15-1.35), and area under the curve (AUC) of 0.83 (0.74-0.89). Afirma Genomic Sequencing Classifier (GSC; n = 10) had a sensitivity of 0.94 (0.89-0.96), specificity of 0.38 (0.27-0.50), LR- of 0.18 (0.10-0.30), LR+ of 1.52 (1.28-1.87), and AUC of 0.91 (0.62-0.92). ThyroSeq v1 and v2 (n = 10) had a sensitivity of 0.86 (0.82-0.90), specificity of 0.74 (0.59-0.85), LR- of 0.19 (0.13-0.26), LR+ of 3.52 (2.08-5.92), and AUC of 0.86 (0.81-0.90). ThyroSeq v3 (n = 6) had a sensitivity of 0.92 (0.86-0.95), specificity of 0.41 (0.18-0.69), LR- of 0.24 (0.09-0.62), LR+ of 1.67 (1.09-2.98), and AUC of 0.90 (0.63-0.92). Fourteen percent of studies conducted a blinded histopathologic review of excised thyroid nodules, and 8% made the decision to go to surgery blind to molecular test results. Conclusions: Meta-analyses reveal a high diagnostic accuracy of molecular tests for thyroid nodule assessment of malignancy risk; however, these studies are subject to several limitations. Limitations and their potential clinical impacts must be addressed and, when feasible, adjusted for using valid statistical methodologies.

Preoperative Identification of Medullary Thyroid Carcinoma (MTC): Clinical Validation of the Afirma MTC RNA-Sequencing Classifier

Background: Cytopathological evaluation of thyroid fine-needle aspiration biopsy (FNAB) specimens can fail to raise preoperative suspicion of medullary thyroid carcinoma (MTC). The Afirma RNA-sequencing MTC classifier identifies MTC among FNA samples that are cytologically indeterminate, suspicious, or malignant (Bethesda categories III-VI). In this study we report the development and clinical performance of this MTC classifier. Methods: Algorithm training was performed with a set of 483 FNAB specimens (21 MTC and 462 non-MTC). A support vector machine classifier was developed using 108 differentially expressed genes, which includes the 5 genes in the prior Afirma microarray-based MTC cassette. Results: The final MTC classifier was blindly tested on 211 preoperative FNAB specimens with subsequent surgical pathology, including 21 MTC and 190 non-MTC specimens from benign and malignant thyroid nodules independent from those used in training. The classifier had 100% sensitivity (21/21 MTC FNAB specimens correctly called positive; 95% confidence interval [CI] = 83.9-100%) and 100% specificity (190/190 non-MTC FNAs correctly called negative; CI = 98.1-100%). All positive samples had pathological confirmation of MTC, while all negative samples were negative for MTC on surgical pathology. Conclusions: The RNA-sequencing MTC classifier accurately identified MTC from preoperative thyroid nodule FNAB specimens in an independent validation cohort. This identification may facilitate an MTC-specific preoperative evaluation and resulting treatment.

The Effect Modification of Ultrasound Risk Classification on Molecular Testing in Predicting the Risk of Malignancy in Cytologically Indeterminate Thyroid Nodules

Background: Thyroid nodules with indeterminate cytology are increasingly subjected to molecular testing. We evaluated the diagnostic performances of Afirma Genomic Sequencing Classifier (GSC) and ThyroSeq v3 in thyroid nodules with high versus low/intermediate suspicion ultrasound classification. Methods: In this prospective cohort study, we analyzed all Bethesda III and IV thyroid nodules that underwent fine-needle aspiration biopsies in the University of California Los Angeles Health System from July 2017 to April 2020. All patients underwent molecular testing with Afirma GSC or ThyroSeq v3 as part of an institutional randomized trial (NCT02681328). Nodules were categorized according to the American Thyroid Association (ATA) ultrasound risk classification. The benign call rate and the positive predictive value of molecular testing were compared between ATA high suspicion versus all other categories. Results: A total of 343 patients with 375 indeterminate thyroid nodules were included. The malignancy rate in ATA high suspicion nodules was not significantly increased by a suspicious Afirma GSC result (77.8% for all ATA high suspicion nodules vs. 87.5% for nodules with ATA high suspicion and suspicious Afirma GSC results, positive likelihood ratio [LR] = 2.0, 95% confidence interval [CI 0.5-8.0], p = 1.0) or by a positive ThyroSeq v3 result (80.0% vs. 80.0%, positive LR = 1.0 [CI 1.0-1.0], p = 1.0). The rate of malignancy in ATA low/intermediate suspicion nodules increased from 21.0% to 56.3% with a suspicious Afirma GSC result (positive LR = 4.8 [CI 3.4-6.9], p < 0.0001) and decreased to 3.8% with a benign Afirma GSC result (negative LR = 0.1 [CI 0.07-0.3], p < 0.0001). Similarly, the rate of malignancy in ATA low/intermediate suspicion nodules increased from 24.3% to 66.7% with a positive ThyroSeq v3 result (positive LR = 6.2 [CI 4.0-9.7], p < 0.0001) and decreased to 2.1% with a negative ThyroSeq v3 result (negative LR = 0.07 [CI 0.02-0.3], p < 0.0001). Conclusions: Afirma GSC and ThyroSeq v3 performed well in ruling out malignancy in sonographically low/intermediate suspicion thyroid nodules but has limited diagnostic value in sonographically high suspicion nodules. Molecular testing can prognosticate more aggressive thyroid cancers, which can inform treatment decisions.

Thyroid nodules of indeterminate cytology in Hispanic/Latinx patients

BACKGROUND

Behavior of differentiated thyroid cancer (DTC) varies among ethnic groups. Recommended management of thyroid nodules with indeterminate cytology (TN-IC) is based on molecular analysis from predominantly non-Hispanic white patients. We hypothesized that TN-IC in Hispanic/Latinx patients would have different features, management, and outcomes and that molecular testing might perform differently in Hispanic/Latinx patients.

METHODS

Retrospective chart review was performed on 127 TN-IC analyzed with Afirma. Patient characteristics were compared using linear model ANOVA and Fisher's exact test.

RESULTS

Out of 127 TN-IC, 71 (56%) were Hispanic/Latinx. Hispanic/Latinx had a greater prevalence of diabetes, but Afirma results (benign or suspicious) were similar between ethnic groups. Fourteen patients had malignant pathology. Their management and outcomes were similar across groups. The negative predictive value for our cohort (97.9%) was similar to published data.

CONCLUSIONS

Data from our predominantly-Hispanic/Latinx cohort suggest that Afirma performs similarly in Hispanic/Latinx and non-Hispanic white patients with TN-IC.

A Bibliometric Analysis of 8271 Publications on Thyroid Nodules From 2000 to 2021

Introduction

Thyroid nodules (TNs) are a common clinical condition. The probability of thyroid nodules being malignant is 7-15%. However, in recent decades, a number of publications on TNs have not been well summarized and discussed. The aim of this study was to summarize and sort out medical publications on TNs over the past 2 decades using a bibliometric method.

Materials and Methods

Medical publications from January 1st, 2000, to November 1st, 2021, were searched in the Web of Science Core Collection database using the Medical Subject Heading (MeSH) term "thyroid nodule". Full associated data were downloaded, and detailed information was extracted using the bibliometric analysis platform VOSviewer.

Results

A total of 8271 publications related to TNs from the last 2 decades were found and included in this study. An increasing trend was presented in the annual number of publications. The United States, China and Italy contributed the most publications. Carcinoma, management, ultrasound, and fine-needle aspiration were the most popular subjects in the field of TNs. The topics of the studies could be stratified into four clusters. The first cluster was using ultrasound to evaluate the nodules, including the thyroid imaging reporting and data system (TI-RADS), elastography and benign features. The second cluster was the fine-needle aspiration method, including the Bethesda system, cytology and BRAF mutations. The third cluster was the management of nodules, including radiofrequency and thermal ablation, surgery, and consensus statements. The last cluster was carcinoma, which is correlated with all three clusters described above. The preoperative diagnosis of cytologically indeterminate nodules was particularly highlighted in the top 10 most cited publications in recent years.

Conclusion

How to diagnose thyroid nodules as malignant or benign, especially in cytologically indeterminate nodules, is still the most concerning topic in TN research. Although the fine-needle aspiration method and gene-expression classifiers show promising results, there is still a crucial need for translations from fundamental studies to clinical applications.

Risk stratification of indeterminate thyroid nodules using ultrasound and machine learning algorithms

BACKGROUND

Indeterminate thyroid nodules (Bethesda III) are challenging to characterize without diagnostic surgery. Auxiliary strategies including molecular analysis, machine learning models, and ultrasound grading with Thyroid Imaging, Reporting and Data System (TI-RADS) can help to triage accordingly, but further refinement is needed to prevent unnecessary surgeries and increase positive predictive values.

DESIGN

Retrospective review of 88 patients with Bethesda III nodules who had diagnostic surgery with final pathological diagnosis.

MEASUREMENTS

Each nodule was retrospectively scored through TI-RADS. Two deep learning models were tested, one previously developed and trained on another data set, mainly containing determinate cases and then validated on our data set while the other one trained and tested on our data set (indeterminate cases).

RESULTS

The mean TI-RADS score was 3 for benign and 4 for malignant nodules (p = .0022). Radiological high risk (TI-RADS 4,5) and low risk (TI-RADS 2,3) categories were established. The PPV for the high radiological risk category in those with >10 mm nodules was 85% (CI: 70%-93%). The NPV for low radiological risk in patients >60 years (mean age was 100% (CI: 83%-100%). The area under the curve (AUC) value of our novel classifier was 0.75 (CI: 0.62-0.84) and differed significantly from the chance-level (p < .00001).

CONCLUSIONS

Novel radiomic and radiologic strategies can be employed to assist with preoperative diagnosis of indeterminate thyroid nodules.

Long-term Follow-up of Cytologically Indeterminate Thyroid Nodules Found Benign on Molecular Testing: A Validation Study

Objective

Molecular testing has revolutionized management of indeterminate thyroid nodules (Bethesda categories III and IV). Few studies have attempted to validate the negative predictive value of molecular tests. Using long-term observation as a surrogate for surgical resection, we sought to examine the false-negative rate of “benign” indeterminate thyroid nodules on molecular testing.

Study Design

Case series with retrospective data collection and chart review.

Setting

Large community-based practice with multiple satellite offices.

Methods

All patients with thyroid nodules that underwent ultrasound-guided fine-needle aspiration biopsy between 2013 and 2019 were evaluated through retrospective analysis. Cytologically indeterminate nodules reflexively underwent molecular testing to guide clinical management. Observation was recommended for lesions with benign molecular testing, and these nodules were followed clinically and by ultrasound.

Results

A total of 2011 nodules underwent fine-needle aspiration, of which 280 (14%) were indeterminate thyroid nodules. Of those 280 nodules, 100 (36%) were benign on molecular testing. Three samples were excluded from analysis due to patient deaths from unrelated causes. Surgical resection was recommended in 16 of the 97 nodules (17%), with the majority due to size and compressive symptoms. Histopathology was available in 14 nodules that underwent surgery, with 1 demonstrating minimally invasive follicular carcinoma.

Conclusion

While molecular testing is safe to use in guiding management of indeterminate thyroid nodules, consideration of individualized clinical factors and close long-term follow-up remains paramount.

Performance of Afirma Gene Sequencing Classifier versus Gene Expression Classifier in thyroid nodules with indeterminate cytology

INTRODUCTION

About 15% to 30% of thyroid fine-needle aspiration (FNA) nodules have indeterminate cytology. The Afirma (Veracyte Inc, South San Francisco, CA) Gene Expression Classifier (GEC)/Gene Sequencing Classifier (GSC) tests were designed to improve risk stratification of the indeterminate thyroid nodules. This study aimed to evaluate and compare the performance of the Afirma GEC and GSC tests in the indeterminate thyroid lesions.

METHODS

Thyroid FNA cases with indeterminate cytology were searched in the pathology database and only those with available Afirma results were selected for this study. Each patient's demographic, sonographic, cytologic, molecular, and subsequent surgical follow-up results were collected and analyzed.

RESULTS

There were 100 cases with indeterminate thyroid FNA results, including 49 cases tested by GEC and 51 cases by GSC. In the GEC group, benign call rate (BCR) was 53% (26 of 49) and the calculated negative predictive value (NPV) and positive predictive value (PPV) were 88% and 47% respectively. In the GSC group, the BCR was 63% (32 of 51) and the calculated NPV and PPV were 100% and 64%, respectively. Whereas only 17% (1 of 6) of benign oncocytic lesions were tested benign by the GEC, 60% (3 of 5) of benign oncocytic nodules were tested benign by the GSC.

CONCLUSION

We demonstrated in this study that a little more than half of the indeterminate thyroid nodules had negative Afirma GEC/GSC results and the BCR using the Afirma GSC test was higher than GEC. The Afirma GSC showed higher NPV and PPV than GEC. In addition, the Afirma GSC appeared to be superior for differentiating benign and malignant oncocytic thyroid lesions.

Molecular Characterization of Thyroid Follicular Lesions in the Era of "Next-Generation" Techniques

It is unequivocally recognized that thyroid nodules are frequently detected in the adult population and mostly characterized by benign lesions (up to 70% of them), with only 5%-15% malignant lesions. The evaluation of thyroid lesions with fine-needle aspiration cytology (FNAC) represents one of the first and most useful diagnostic tools in the definition of their nature. Despite the fact that the majority of thyroid lesions are correctly diagnosed as either benign (70%-75%) or malignant (5%-10%) entities, the remaining nodules (20%-25%) represent the "gray zone" of follicular lesions, which belong to indeterminate categories, according to the different classification systems. This indeterminate group of lesions includes both benign and malignant entities, which cannot be easily discriminate with morphology alone. In these last decades, the increasing role of molecular testings, feasibly performed on cytological material combined with the discoveries of specific genetic alterations in the field of thyroid pathology, has opened the pace to their more accurate and specific contribution on cytology. In fact, in 2015, in the revised management guidelines for patients with thyroid nodules and well-differentiated thyroid cancers (WDTCs), the American Thyroid Association (ATA) confirmed the performance of molecular testing in thyroid indeterminate cytology, and the same performance was addressed in recent update of the management of thyroid nodules in the second edition of the Bethesda system for reporting thyroid cytopathology (TBSRTC). In the current review, we discuss the role of molecular tests for the different thyroid diagnostic categories of the Bethesda system for reporting thyroid cytopathology, mostly focusing our attention on the follicular and indeterminate lesions.

Diagnostic Value of TI-RADS Classification System and Next Generation Genetic Sequencing in Indeterminate Thyroid Nodules

RATIONALE AND OBJECTIVES

This study aims to evaluate the diagnostic accuracy, inter-reader, and intra-reader variability of the ACR Thyroid Imaging Reporting and Data System (TI-RADS) for risk-stratification of indeterminate thyroid nodules using next generation genetic sequencing and tissue histology as a reference standard.

MATERIALS AND METHODS

Retrospective chart review was performed on all patients who underwent thyroid ultrasound for a nodule with subsequent fine-needle aspiration ± surgical resection from January 2017 to August 2018. Four radiologists with expertise in thyroid ultrasound assessed imaging twice, ≥1 month apart. Results of cytology and next generation genetic sequencing were used as a reference standard for high versus low risk of malignancy in each nodule. Inter-reader reliability between readers and intra-reader reliability between replicate self-reads for TI-RADS categorization were assessed. Univariate analysis, kappa statistics, and receiver operating characteristic curve were calculated.

RESULTS

One hundred and thirty six nodules across 121 patients met inclusion criteria. 84.6% of patients were female and average age was 55.8 ± 14.1 years. One hundred and eighteen of 135 nodules (87%) had indeterminate cytology (Bethesda III or IV). One of 23 high-risk mutations was identified in 30.1% (42) of the nodules. Of the 52 patients who had surgery, 24 (47.1%) had confirmed malignant disease on surgical pathology. Inter-reader reliability between the four radiologists was marginal, κ = 0.293. Intra-reader reliability ranged from marginal to good, κ = 0.337 to κ = 0.560, respectively. The area under the receiver operating characteristic curve was 0.509, and no optimal TI-RADS Level for identifying high-risk nodules existed.

CONCLUSION

The ACR TI-RADS classification system performs with low inter-reader and intra-reader reliability when assessing the genetic risk of nodules with indeterminate cytology.

Comparison of Afirma GEC and GSC to Nodules Without Molecular Testing in Cytologically Indeterminate Thyroid Nodules

Background

Analysis of cytologically indeterminate thyroid nodules with Afirma Gene Expression Classifier (GEC) and Genomic Sequencing Classifier (GSC) can reduce surgical rate and increase malignancy rate of surgically resected indeterminate nodules.

Methods

Retrospective cohort analysis of all adults with cytologically indeterminate thyroid nodules from January 2013 through December 2019. We compared surgical and malignancy rates of those without molecular testing to those with GEC or GSC, analyzed test performance between GEC and GSC, and identified variables associated with molecular testing.

Results

468 indeterminate thyroid nodules were included. No molecular testing was performed in 273, 71 had GEC, and 124 had GSC testing. Surgical rate was 68% in the group without molecular testing, 59% in GEC, and 40% in GSC. Malignancy rate was 20% with no molecular testing, 22% in GEC, and 39% in GSC (P = 0.022). GEC benign call rate (BCR) was 46%; sensitivity, 100%; specificity, 61%; and positive predictive value (PPV), 28%. GSC BCR was 60%; sensitivity, 94%; specificity, 76%; and PPV, 41%. Those with no molecular testing had larger nodule size, preoperative growth of nodules, and constrictive symptoms and those who underwent surgery in the no molecular testing group had higher body mass index, constrictive symptoms, higher Thyroid Imaging Reporting and Data System and Bethesda classifications. Type of provider was also associated with the decision to undergo surgery.

Conclusion

Implementation of GEC showed no effect on surgical or malignancy rate, but GSC resulted in significantly lower surgical and higher malignancy rates. This study provides insight into the factors that affect the real-world use of these molecular markers preoperatively in indeterminate thyroid nodules.

Precision diagnostics: Integration of tissue pathology and genomics in cancer

Traditionally, cancer diagnosis and management has been reactionary in that symptoms lead to investigations, then a diagnosis is followed by clinical management. This process is heavily dependent on tissue diagnosis mainly by histopathology and to a lesser extent, cytopathology. However, in recent times there has been a shift towards precision medicine to enable prevention, prediction and personalisation in healthcare. The core of precision medicine is optimising therapeutic benefit for patients, by using genomic and molecular profiling, analogously termed precision pathology. This review explores (1) the evolution of pathology from a para-clinical discipline to a mainstream medical field integral to oncology tumour boards; (2) its critical role in preventative, diagnostic, therapeutic and follow-up cancer care; (3) the future of tissue pathology in the era of precision oncology; and (4) how pathologists may evolve to future-proof their profession.

Thyroid diagnostic modalities (fine needle aspiration and core needle biopsy) with histology correlation: a tertiary centre experience

AIMS

To determine the proportion of thyroid fine needle aspiration (FNA) and core needle biopsy (CNB) cases reported at a single institute into each UK Royal College of Pathologists (RCPath) Thy1-5 and local T category, respectively. Where subsequent histology was available, malignancy rates, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and diagnostic accuracy were compared for both procedures.

METHODS

1591 FNAs (2010-2018) and 514 CNBs (2013-2018) cases were identified, together with paired histology excision specimens.

RESULTS

The FNA samples were classified as: Thy1: 45.3%, Thy2/Thy2c: 22.1%, Thy3a/Thy3f: 28%, Thy4: 1.6% and Thy5: 3%; while the CNB were classified as: T1: 7.2%, T2: 22.4%, T3 59.3%, T4: 1% and T5: 10.1%. Comparison of FNA and CNB classified as Thy5/T5 showed a 100% risk of malignancy (ROM), sensitivity (98% vs 100%), specificity (14.1% vs 12.1%), PPV (29.4% vs 29.4%), NPV (94.9% vs 100%) and accuracy (36.5% vs 35.6%), respectively, for a diagnosis of malignancy. ROMs for other categories were: Thy1/T1 (9% vs 6.7%), Thy2/T2 (5.1% vs 0%), Thy3/T3 (17.5% vs 18.4%) and Thy4/T4 (73.3% vs 100%).

CONCLUSIONS

The proportion of cases in each RCPath Thy category has remained relatively stable during the 9-year study period, with the exception of the Thy3a category, which has increased over time. This finding is in line with other more recent reports in the literature and the proportion of T3 cases in the CNB group. The proportion of Thy2/Thy2c cases has also reduced over time, reflecting a local change in the triaging protocol for probable benign lesions. Both FNA and CNB showed comparable performance in our study.

Single Institution Experience with Afirma and Thyroseq Testing in Indeterminate Thyroid Nodules

Background: Thyroid nodules are a very common often incidental finding on physical examination or imaging. Of those who undergo fine needle aspiration, cytology is indeterminate in up to 15%. Molecular testing is increasingly being used to help identify which nodules may be high risk for malignancy and guide management with regard to clinical follow-up or surgical intervention. Recently there has been an increase in publication of independent studies assessing the performance of these molecular tests and comparing "real-world" data with the validation studies. Methods: This retrospective study identified all thyroid nodules at our institution that had Afirma gene expression classifier (GEC), genomic sequencing classifier (GSC), or Thyroseq v3 molecular testing from January 2014 to January 2020 and compared measurements of test performance between them at our institution, and then with the original validation studies and other published institutional data. Results: Overall, the benign call rate was highest in the Afirma GSC group (78%) compared with the GEC group (60%) and Thyroseq group (66%). Surgical histopathology revealed malignancy in 6 of 31of biopsied nodules in the GEC group, 8 of 13 in the GSC group, and 3 of 16 in the Thyroseq v3 group. Based on our data, the GSC specificity (73.7%) and positive predictive value (PPV) (61.5%) were higher than the GEC specificity (60.4%) and PPV (22.2%) as well as Thyroseq v3 specificity (55.2%) and PPV (18.8%). Conclusions: From our short-term institutional experience, we found that the GSC classified more cytologically indeterminate nodules as benign compared with the Afirma GEC, and had improved specificity and PPV, which is similar to the validation study and other institutions' reported experiences. We also found that the Thyroseq v3 was similar to the Afirma GEC in terms of specificity and PPV, both of which are much lower than the validation studies.

Molecular Testing for Thyroid Nodules Including Its Interpretation and Use in Clinical Practice

Despite advances in imaging and biopsy techniques, the management of thyroid nodules often remains a diagnostic and clinical challenge. In particular, patients with cytologically indeterminate nodules often undergo diagnostic thyroidectomy although only a minority of patients are found to have thyroid malignancy on final pathology. More recently, several molecular testing platforms have been developed to improve the stratification of cancer risk for patients with cytologically indeterminate thyroid nodules. Based on numerous studies demonstrating its accuracy, molecular testing has been incorporated as an important diagnostic adjunct in the management of indeterminate thyroid nodules in the National Comprehensive Cancer Network Guidelines as well as in the American Thyroid Association (ATA) and American Association of Endocrine Surgeons (AAES) guidelines. This overview describes the currently available molecular testing platforms and highlights the published data to date on the clinical validity and utility of molecular testing in the contemporary management of thyroid nodules.

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

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

Clinical Laboratory Improvement Amendments laboratory performing Afirma Genomic Sequencing Classifier (GSC) and Xpression Atlas (XA) testing.

PARTICIPANTS

A total of 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 noninvasive follicular thyroid neoplasm with papillary-like nuclear features was >95%, whereas for BRAF and ALK fusions it was 81% and 67%, respectively. At least 1 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 one-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.

Tumor invasive ability of papillary thyroid carcinomas is not conferred by acquired gene mutations

Papillary thyroid carcinoma (PTC) is the most common type of thyroid cancer. The ability to predict whether a carcinoma would exhibit invasive ability in patients with PTC is important and has clinical implications for the selection of therapeutic strategies. Although several studies have focused on the genetic characterization of invasive cancer cells, the factors critical to the origination of invasive cancer cells are still unclear. This study aimed to determine whether genomic mutations contribute to the acquisition of the tumor invasion phenotype and to investigate the genetic features of invasive cancer cells in patients with PTC. We performed customized 48-gene deep exon sequencing in samples obtained from 88 patients with PTC via fine needle aspiration; the results revealed that no genetic changes were specifically associated with the tumor aggressiveness phenotype. Our results indicate that genetic mutations do not cause indolent PTCs to become invasive.

Retrospective analysis of cancer-specific gene expression panel for thyroid fine needle aspiration specimens

BACKGROUND

While molecular testing is a promising strategy for preoperative assessment of cytologically indeterminate thyroid nodules, thyroid fine needle aspiration biopsy (FNA) presents unique challenges for molecular assays, including contaminating peripheral blood mononuclear cells (PBMC) and variable numbers of evaluable epithelial thyroid cells. Moreover, the newly recognized entity, noninvasive follicular thyroid neoplasm with papillary-like nuclear features (NIFTP), has added an additional challenge to the currently available molecular diagnostic platforms. New diagnostic tools are still needed to correctly distinguish benign and malignant thyroid nodules preoperatively.

METHODS

Twenty-two transcript splice variants from 12 genes we previously identified as discriminating benign from malignant thyroid nodules were characterized in 80 frozen thyroid tumors from 8 histological subtypes. Isoforms detectable in PBMC were excluded, and the 5 most discriminating isoforms were further validated by real-time quantitative PCR (qPCR) on intraoperative FNA samples from 59 malignant tumors, 55 benign nodules, and 23 NIFTP samples. The qPCR threshold cycle values for each transcript were normalized to the thyrocyte-specific thyroid peroxidase isoform 1 (TPO1) and z-transformed. Receiver operating characteristic (ROC) analyses of the composite transcript scores were used to evaluate classification of thyroid FNAs by the 5-gene isoform expression panel.

RESULTS

A molecular signature was developed by combining expression levels of specific isoforms of CDH3, FNDC4, HMGA2, KLK7, and PLAG1. FNAs containing at least 12-36 thyrocytes were sufficient for this assay. The 5-gene composite score achieved an area under the ROC curve (AUC) of 0.86 for distinguishing malignant from benign nodules, with a specificity of 91%, sensitivity of 75%, negative predictive value of 91%, and positive predictive value of 74%.

CONCLUSION

Our newly developed 5-gene isoform expression panel distinguishes benign from malignant thyroid tumors and, may help distinguish benign from malignant thyroid nodules in the context of the new NIFTP subtype.

Impact of Molecular Testing on the Management of Indeterminate Thyroid Nodules Among Western and Asian Countries: a Systematic Review and Meta-analysis

Molecular testing has a potential to improve the management of patients with indeterminate thyroid nodules considered for surgery. This study examined the influence of molecular tests on the treatment of indeterminate nodules, particularly the differences between Western and Asian countries. Electronic databases including PubMed and Web of Science were searched for relevant articles from 2010 to March 2019. We computed meta-analysis of proportion and their 95% confidence intervals (CIs) utilizing the random-effect model. We used independent samples t test to compare the resection rate (RR), rate of malignancy (ROM), rate of preoperative molecular testing (RMT), and rate of positive test (RP) between subgroups. We included a total of 34 studies with 7976 indeterminate nodules. The multigene panel testing methods were exclusively used in the USA. Compared with the non-molecular era, molecular testing was associated with a significantly increased ROM (47.9% versus 32.1%; p = 0.001). The ROM of indeterminate nodules in Asian institutes was significantly higher than that in Western countries (75.3% versus 36.6%; p < 0.001, respectively). Institutes employing single-gene tests achieved a higher ROM (59.8% versus 37.9%; p = 0.013). Molecular testing is a promising method to tailor the clinical management for indeterminate thyroid FNA. Certain differences in routine thyroid cytopathology practice among the West and the East are still present. The combination of molecular testing and active surveillance enhances the accuracy of case selection for surgery in Asian countries.

Performance of Afirma genomic sequencing classifier vs gene expression classifier in Bethesda category III thyroid nodules: An institutional experience

BACKGROUND

Afirma gene expression classifier (GEC) is an adjunct to thyroid fine needle aspiration shown to improve pre-operative risk assessment and reduce unnecessary surgery of indeterminate thyroid nodules. Genomic sequencing classifier (GSC) is a newer version aiming to improve specificity and positive predictive value (PPV) of Afirma testing. There are limited studies comparing GSC vs GEC. This study was undertaken to compare these classifiers in terms of diagnostic performance and effect on clinical management of indeterminate thyroid nodules.

METHODS

The study cohort consisted of patients with thyroid nodules that had a recurrent cytologic diagnosis of atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS) and were tested by either GEC or GSC. Patient demographics, nodule size, and clinical follow-up were recorded. Benign call rate (BCR) of Afirma testing, rate of subsequent surgery (RSS), rate of histology-confirmed malignancy (RHM), as well as diagnostic sensitivity, specificity, PPV, negative predicative value (NPV), and accuracy were calculated and compared between GSC and GEC cohorts.

RESULTS

Among 264 AUS/FLUS thyroid nodules, 127 and 137 were tested with GEC and GSC, respectively. Compared to GEC, GSC demonstrated increased BCR (77.3% vs 52%), decreased RSS (31.4% vs 51.2%), greater RHM (29% vs 9.8%) associated with a suspicious Afirma result, as well as improved specificity (82.8% vs 54.5%), PPV (29% vs 9.8%), and diagnostic accuracy (83.9% vs 56.7%), while maintaining high sensitivity and NPV.

CONCLUSION

Afirma GSC substantially improved BCR, RSS, RHM, and diagnostic performance, enhancing appropriate triage and thereby helped avoid unnecessary surgery in AUS/FLUS thyroid nodules.

Adherence to Active Surveillance and Clinical Outcomes in Patients with Indeterminate Thyroid Nodules Not Referred for Thyroidectomy

OBJECTIVE

Outcomes of patients with cytologically indeterminate thyroid nodules not referred for thyroidectomy have hardly been investigated. We previously reported outcomes of 322 patients with thyroid nodules classified according to the Bethesda System of Reporting Thyroid Cytology (BSRTC) as indeterminate (B3/B4), of whom 123 (38.2%) underwent thyroidectomy. In the present extension study, we investigated adherence and outcomes in the remaining unoperated 199 patients.

METHODS

We conducted a file review of 189/199 patients with thyroid nodules cytologically diagnosed as B3 (n = 174) or B4 (n = 15) in 2011-2012 who were conservatively followed at our institution until 2019.

RESULTS

Among 174 patients with B3 nodules, 140 (80.4%) underwent repeated ultrasound. Nodular growth was detected in 23 (16.4%), and findings remained stable in 105 (75%). Fine-needle aspiration was repeated in 88/174 patients (50.6%), with B2 results in 62 (70.4%) and B3/B4/B5 in 20 (22.7%). Thyroidectomy was performed in 14/174 patients (8%) in the B3 and 5/15 patients (33%) in the B4 group at a median of 5 years' follow-up; thyroid cancer was diagnosed in 4/14 patients (28.5%) and 3/5 patients (60%), respectively. For B3 patients who remained unoperated, none had evidence of thyroid cancer at last follow-up. A reason for avoiding surgery was documented in 6/10 unoperated B4 patients (1 thyroid lymphoma, 3 died of unrelated causes, 2 were considered inoperable due to advanced age).

CONCLUSIONS

Most patients with initially unoperated B3/B4 nodules adhere, at least partially, to active surveillance. For B3 nodules, subsequent thyroidectomy and thyroid cancer detection are rare events, and patients may be safely managed without using molecular markers. Thyroid cancer is diagnosed in most B4 patients who undergo thyroidectomy in our institution.

National differences in cost analysis of Afirma Genomic sequencing classifier

CONTEXT

Thyroid nodules of indeterminate cytology can be subjected to molecular testing such as the Afirma Genomic Sequencing Classifier (GSC), thereby minimizing the number of unnecessary diagnostic surgeries.

OBJECTIVE

This work aimed to evaluate and compare the cost of routine GSC testing of indeterminate thyroid nodules in different countries.

DESIGN, PATIENTS AND MAIN OUTCOME MEASURES

The cost of diagnostic hemithyroidectomy of indeterminate thyroid nodules was calculated by performing a Monte Carlo simulation cost analysis on a Markov decision-analytic model and then compared to that of GSC testing in the UK, Australia, USA, and Israel.

RESULTS

Assuming that patients are treated by surgical resection and routine GSC testing is performed for all nodules of indeterminate significance, we found the GSC test to be more cost effective compared with diagnostic hemithyroidectomy when malignancy rates of thyroid nodules are less than 22.6%-37.1%, depending on the country where the test is performed. Given the cost of a thyroidectomy in the UK, Australia and Israel, performing routine GSC tests on all Bethesda IV nodules is more expensive than routine diagnostic hemithyroidectomy and becomes cost effective for Bethesda III when the GSC cost is below 3,031-3,087 USD. In comparison, in the USA, higher cost of thyroidectomy makes the GSC test cost effective for Bethesda III nodules at its current cost, but not for Bethesda IV nodules where it becomes cost effective under the price of 3,031 USD.

CONCLUSIONS

Different molecular testing and surgical costs in different countries should be considered when performing cost analysis. In addition, since different medical centres have different malignancy rates, personalized in-house assessment of cost-effectiveness is warranted.