Molecular cytopathology for thyroid nodules: A review of methodology and test performance

BRAF Detection in FNAC Combined with Semi-Quantitative 99mTc-MIBI Technique and AI Model, an Economic and Efficient Predicting Tool for Malignancy in Thyroid Nodules

BACKGROUND

Technology allows us to predict a histopathological diagnosis, but the high costs prevent the large-scale use of these possibilities. The current liberal indication for surgery in benign thyroid conditions led to a rising frequency of incidental thyroid carcinoma, especially low-risk papillary micro-carcinomas.

METHODS

We selected a cohort of 148 patients with thyroid nodules by ultrasound characteristics and investigated them by fine needle aspiration cytology (FNAC)and prospective BRAF collection for 70 patients. Also, we selected 44 patients with thyroid nodules using semi-quantitative functional imaging with an oncological, 99mTc-methoxy-isobutyl-isonitrile (99mTc-MIBI) radiotracer.

RESULTS

Following a correlation with final histopathological reports in patients who underwent thyroidectomy, we introduced the results in a machine learning program (AI) in order to obtain a pattern. For semi-quantitative functional visual pattern imaging, we found a sensitivity of 33%, a specificity of 66.67%, an accuracy of 60% and a negative predicting value (NPV) of 88.6%. For the wash-out index (WOind), we found a sensitivity of 57.14%, a specificity of 50%, an accuracy of 70% and an NPV of 90.06%.The results of BRAF in FNAC included 87.50% sensitivity, 75.00% specificity, 83.33% accuracy, 75.00% NPV and 87.50% PPV. The prevalence of malignancy in our small cohort was 11.4%.

CONCLUSIONS

We intend to continue combining preoperative investigations such as molecular detection in FNAC, 99mTc-MIBI scanning and AI training with the obtained results on a larger cohort. The combination of these investigations may generate an efficient and cost-effective diagnostic tool, but confirmation of the results on a larger scale is necessary.

Comprehensive evaluation of cytomorphologic, histologic, and molecular features of DICER1-altered thyroid lesions on FNA: A multipractice experience

BACKGROUND

DICER1 mutations, though infrequent, are encountered on preoperative molecular testing of indeterminate adult and pediatric thyroid fine-needle aspiration (FNA) specimens. Yet, published cytomorphologic features of DICER1-altered thyroid lesions are limited. Cytomorphological features of DICER1-altered thyroid lesions were examined in a multipractice FNA cohort with clinical, radiological, and histologic data.

METHODS

The cohort comprised 18 DICER1-altered thyroid FNAs, with 14 having slides available and eight having corresponding surgical resections. Smears, ThinPrep, and formalin-fixed cell block slides were reviewed and correlated with histology, when available. Clinical and radiologic data were obtained from the medical record.

RESULTS

Most DICER1-altered FNAs were classified as atypia of undetermined significance (94.4%). DICER1 mutations occurred in codons 1709 (50%), 1810 (27.8%), and 1813 (22.2%). One patient had an additional DICER1 p.D1822N variant in both of their FNAs. Lesions were often hypoechoic (35.3%) and solid (47.1%) on ultrasound. Notable cytomorphologic features include mixed but prominent microfollicular or crowded component, variable colloid, and insignificant nuclear atypia. On resection (n = 10), histologic diagnoses ranged from benign follicular adenoma and low-risk follicular thyroid carcinoma to high-grade follicular-derived nonanaplastic thyroid carcinoma. Subcapsular infarct-type change was the most common histologic change. There was no evidence of recurrence or metastasis in eight patients on limited follow-up.

CONCLUSION

DICER1-altered thyroid lesions occurred frequently in young females and FNAs show RAS-like cytomorphology including crowded, mixed macro-/microfollicular pattern, and bland nuclear features. On resection, DICER1-altered thyroid lesions include benign (50%), low-risk lesions (30%), or high-risk malignancies (20%).

Utility of Six Ultrasound-Based Risk Stratification Systems in the Diagnosis of AUS/FLUS Thyroid Nodules

RATIONALE AND OBJECTIVES

To estimate the diagnostic performance of the currently used ultrasound (US)-based risk stratification systems (RSSs) (American Thyroid Association, American Association of Clinical Endocrinologists, American College of Endocrinology, and Association Medici Endocrinology Medical Guidelines for Clinical Practice for the Diagnosis and Management of Thyroid Nodules, European Thyroid Association Guidelines for Ultrasound Malignancy Risk Stratification of Thyroid Nodules in Adults [EU-TIRADS], American College of Radiology Thyroid Imaging Reporting and Data System [ACR-TIRADS], Chinese Guidelines for Ultrasound Malignancy Risk Stratification of Thyroid Nodules [C-TIRADS], and Thyroid Imaging Reporting and Data System Developed by Kwak et al [Kwak-TIRADS]) for atypia of undetermined significance or follicular lesion of undetermined significance (AUS/FLUS) thyroid nodules.

MATERIALS AND METHODS

This retrospective study included 514 consecutive AUS/FLUS nodules in 481 patients with final diagnosis. The US characteristics were reviewed and classified using the categories defined by each RSS. The diagnostic performance was evaluated and compared using a generalized estimating equation method.

RESULTS

Of the 514 AUS/FLUS nodules, 148 (28.8%) were malignant and 366 (71.2%) were benign. The calculated malignancy rate increased from the low-risk to high-risk categories for all RSSs (all P < .001). Interobserver correlation for both US features and RSSs showed substantial to almost perfect agreement. The diagnostic efficacy of Kwak-TIRADS (AUC=0.808) and C-TIRADS (AUC=0.804) were similar (P = .721) and higher than those of other RSSs (all P < .05). The EU-TIRADS and Kwak-TIRADS exhibited similar sensitivity (86.5% vs 85.1%, P = .739) and were only higher than that of the C-TIRADS (all P < .05). The specificity of C-TIRADS and ACR-TIRADS were similar (78.1% vs 72.1%, P = .06) and were higher than those of other RSSs (all P < .05).

CONCLUSION

Currently used RSSs can provide risk stratification for AUS/FLUS nodules. Kwak-TIRADS and C-TIRADS have the highest diagnostic efficacy in identifying malignant AUS/FLUS nodules. A detailed knowledge of the benefits and shortcomings of the various RSSs is essential.

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.

How do BRAFV600E and TERT promoter mutations interact with the ATA and TNM staging systems in thyroid cancer?

Context

The American Thyroid Association risk stratification (ATA) and the American Joint Committee on Cancer Tumor Node Metastases (TNM) predict recurrence and mortality of differentiated thyroid cancer (DTC). BRAFV600E and TERT promoter mutations have been shown to correlate with the histopathological features and outcome of DTC. Our objectives were to study the correlation of these molecular markers with these clinicopathological-staging systems.

Patients and methods

We studied 296 unselected patients, 214 females and 82 males with a median age of 36 years (IQR 23.3-49.0). BRAFV600E and TERT promoter mutations were tested by PCR-based Sanger sequencing. Data were extracted from medical records and analysed using Chi-Square and Fisher Exact tests and Kaplan Meier analysis.

Results

Of 296 patients tested, 137 (46.3%) had BRAFV600E-positive tumors and 72 (24.3%) were positive for TERT promoter mutations. The BRAFV600E mutation did not correlate with the ATA and TNM staging, being non-significantly different in various stages of these systems and did not predict the development of persistent disease (PD) (P 0.12). Unlike BRAFV600E, TERT promoter mutations were more frequent in the ATA high-risk than in intermediate- or low-risk tumors (P 0.006) and in TNM stages III and IV than lower stages (P <0.0001). TERT promoter mutations also predicted the outcome, being present in 37.2% of patients with PD compared to only 15.4% in those without evidence of disease (P <0.0001). The same pattern was also seen when BRAFV600E and TERT promoter mutations were combined.

Conclusion

TERT promoter mutations alone or in combination with BRAFV600E mutation, but not BRAFV600E mutation alone, correlated well with the ATA and TNM staging and predicted development of PD, especially in higher stages of these systems.

Diagnostic Performance of Afirma and Interpace Diagnostics Genetic Testing in Indeterminate Thyroid Nodules: A Single Center Study

Indeterminate thyroid nodules (ITN) represent 20–30% of biopsied nodules, with a 10–60% risk of malignancy. Molecular testing can stratify the risk of malignancy among ITNs, and subsequently reduce the need for unnecessary diagnostic surgery. We aimed to assess the performance of these molecular tests at a single institution. Patients with Bethesda III, IV, and V nodules with Afirma and Interpace Diagnostics genetic testing data from November 2013 to November 2021 were included. Three cohorts were formed, including GSC + XA, ThyGeNEXT + ThyraMIR, and GSC + GEC. Statistical analysis determined the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), diagnostic odds ratio (DOR), and accuracy of each type of testing. The PPV of nodules undergoing genetic testing by ThyGeNEXT + ThyraMIR (45.00%, 95%CI: 28.28–62.93%, p = 0.032) and GSC + XA (57.14%, 95%CI: 29.32–81.08%, p < 0.001) were superior to that of GEC + GSC (30.72%, 95%CI: 26.83–34.90%). The NPV was above 85% in all cohorts, suggesting overall suitable rule-out tests. The Afirma platform (GSC + XA) had the highest NPV at 96.97%. The overall accuracy for nodules undergoing ThyGeNEXT + ThyraMIR was 81.42% (95%CI: 73.01–88.11%, p < 0.001). A total of 230 patients underwent thyroidectomy, including less than 60% of each of the ThyGeNEXT + ThyraMIR and GSC + XA cohorts. Specifically, only 25% of patients in the GSC + XA cohort underwent surgery, considerably decreasing the rate of unnecessary surgical intervention. Sub-group analysis, including only patients with surgical pathology, found that PPV tended to be higher in the GSC + XA cohort, at 66.67% (95%CI: 37.28–87.06%), as compared to the ThyGeNEXT + ThyraMIR cohort, at 52.94% (95%CI: 35.25–69.92%). The Afirma genetic testing platform GSC + XA outperformed the other platforms with regards to both PPV and NPV and decreased the rate of surgery in patients with ITNs by 75%, significantly preventing unnecessary surgical intervention.

Core Needle Biopsy Can Early and Precisely Identify Large Thyroid Masses

Background

Large thyroid masses, particularly if rapidly growing, are often characterized by compression and infiltration of the vital structures of the neck. Therefore, an early and precise diagnosis, not only of malignancy but also of histotype, is mandatory to set up the right therapy. The aim of this study was to evaluate the diagnostic performance of fine needle aspiration cytology (FNAC) and core needle biopsy (CNB) in this setting.

Patients and Methods

We prospectively evaluated 95 patients with large and rapidly growing thyroid masses admitted to the University Hospital of Pisa between April 2014 and January 2020. All patients were submitted to FNAC and CNB in the same session. The ability of both procedures to diagnose the malignancy of the lesions, particularly the histotype, and to obtain sufficient material to perform molecular analysis was evaluated.

Results

FNAC obtained adequate tumor sample to reach a diagnosis in 76 of 95 (80%) patients, while a higher percentage was obtained with CNB (92/95, 96.8%). FNAC was able to identify the malignancy of the lesion in 74 of 95 (77.9%) cases, but only in 16 of 74 (21.6%) cases was it able to define the histotype. CNB was able to define the malignancy of the lesion in all but three cases (92/95, 96.8%), and in all specimens, the histotype was identified. Moreover, in all cases, the material extracted from CNB was optimal to perform molecular analysis. No surgery-related complications were experienced with both procedures.

Conclusions

CNB is a rapid and safe procedure with higher performance compared to FNAC in identifying the histotype of large and rapidly growing thyroid masses. Moreover, adequate material can be obtained to characterize the molecular profile for the treatment of potentially lethal cancers. In the era of precision medicine, CNB should be introduced in routine clinical practice as a key procedure for an early diagnosis and therapy of these diseases.

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.

Molecular Markers in the Diagnosis of Thyroid Cancer in Indeterminate Thyroid Nodules

The Bethesda System for the Reporting of Thyroid Cytology recognises six diagnostic categories of thyroid nodule cytology with an incremental risk of malignancy. Although the Bethesda system created a much-needed handhold by standardising the cytological diagnosis and management of thyroid nodules worldwide, the system does not provide a clear answer to the heterogeneous group of nodules with indeterminate cytology. Improvement in the assessment of indeterminate fine-needle aspiration (FNA) results with molecular testing allows better risk stratification and reduces the need for diagnostic thyroid surgery. The molecular markers are classified as a "rule out" test, which has a high negative predictive value and helpful in cases with a low pre-test probability of cancer to rule out thyroid cancer. The "rule in" test has a high positive predictive value and helps in confirming malignancy in those with a high pre-test probability of cancer. This review summarises the commonly used molecular studies in thyroid FNAC aspirates and their current role in clinical practice.

Testing of mutations on thyroid nodules with indeterminate cytology: A prospective study of 112 patients in Argentina

BACKGROUND

The study of genetic mutations in thyroid nodules makes it possible to improve the preoperative diagnosis of and reduce unnecessary surgeries on benign nodules. In this study, we analysed the impact of implementing a 7-gene mutation panel that enables mutations to be detected in BRAF and RAS (H/N/K) and the gene fusions PAX8/PPARG, RET/PTC1 and RET/PTC2, in a population in northern Argentina.

METHODS

We performed a prospective analysis of 112 fine needle aspirations diagnosed as having indeterminate cytology according to the Bethesda classification system. These include the Bethesda III or atypia of unknown significance/follicular lesion of unknown significance and Bethesda IV or follicular neoplasm/suspicious for follicular neoplasm categories. The mutations of the 7-gene panel were analysed and this information was linked to the available histology and ultrasound monitoring.

RESULTS

The BRAF V600E and RET/PTC1 mutations were associated with carcinoma in 100% of cases (n = 8), whereas only 37.5% (n = 3) of the nodules with RAS and 17% (n = 1) with PAX8/PPARG mutations were associated with carcinoma. From the histological diagnosis and ultrasound monitoring of patients, we can estimate that this panel has a sensitivity of 86% in detecting malignant carcinoma, a specificity of 77%, a positive predictive value (PPV) of 54% and a negative predictive value (NPV) of 94%. In this study, it was possible to reduce the number of surgeries by 48% in the patients analysed.

CONCLUSION

The implementation of the mutation panel allowed the appropriate surgical strategy to be selected for each patient, the number of two-step surgeries to be reduced, and active follow-up to be established in low-risk patients.

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.

Combination of ultrasound and molecular testing in malignancy risk estimate of Bethesda category IV thyroid nodules: results from a single-institution prospective study

PURPOSE

Malignancy prediction in indeterminate thyroid nodules is still challenging. We prospectively evaluated whether the combination of ultrasound (US) risk stratification and molecular testing improves the assessment of malignancy risk in Bethesda Category IV thyroid nodules.

METHODS

Ninety-one consecutively diagnosed Bethesda Category IV thyroid nodules were prospectively evaluated before surgery by both ACR- and EU-TIRADS US risk-stratification systems and by a further US-guided fine-needle aspiration cytology (FNAC) for the following molecular testing: BRAFV600E, N-RAS codons 12/13, N-RAS codon 61, H-RAS codons 12/13, H-RAS codon 61, K-RAS codons 12/13, and K-RAS codon 61 point-mutations, as well as PAX8/PPARγ, RET/PC1, and RET/PTC 3 rearrangements.

RESULTS

At histology, 37% of nodules were malignant. No significant association was found between malignancy and either EU- or ACR-TIRADS. In total, 58 somatic mutations were identified, including 3 BRAFV600E (5%), 5 N-RAS 12/13 (9%), 13 N-RAS 61 (22%), 7 H-RAS 12/13 (12%), 11 H-RAS 61 (19%), 6 K-RAS 12/13 (10%), 8 K-RAS 61 (14%) mutations and 2 RET/PTC1 (4%), 0 RET/PTC 3 (0%), 3 PAX8/PPARγ (5%) rearrangements. At least one somatic mutation was found in 28% and 44% of benign and malignant nodules, respectively, although malignancy was not statistically associated with the outcome of the mutational test. However, the combination of ACR-, but not EU-, TIRADS with the presence of at least one somatic mutation, was significantly associated with malignant histology (P = 0.03).

CONCLUSION

US risk stratification and FNAC molecular testing may synergistically contribute to improve malignancy risk estimate of Bethesda category IV thyroid nodules.

Molecular Testing of Thyroid Fine-Needle Aspiration: Local Issues and Solutions. An Interventional Cytopathologist Perspective

Molecular testing has acquired a relevant role for diagnostic and prognostic stratification of indeterminate thyroid nodules. Besides the available commercial solutions marketed in the United States, various local testing strategies have been developed in the last decade. In this setting, the modern interventional cytopathologist, the physician who performs the both aspirate and the morphologic interpretation plays a key role in the correct handling of fine-needle aspiration (FNA) samples not only for microscopy but also for molecular techniques. This review summarizes experiences with local approaches to the molecular testing of thyroid FNA, highlighting the role of the modern interventional cytopathologist.

Testing of mutations on thyroid nodules with indeterminate cytology: A prospective study of 112 patients in Argentina

BACKGROUND

The study of genetic mutations in thyroid nodules makes it possible to improve the preoperative diagnosis of and reduce unnecessary surgeries on benign nodules. In this study, we analysed the impact of implementing a 7-gene mutation panel that enables mutations to be detected in BRAF and RAS (H/N/K) and the gene fusions PAX8/PPARG, RET/PTC1 and RET/PTC2, in a population in northern Argentina.

METHOD

We performed a prospective analysis of 112 fine needle aspirations diagnosed as having indeterminate cytology according to the Bethesda classification system. These include the Bethesda III or atypia of unknown significance/follicular lesion of unknown significance and Bethesda IV or follicular neoplasm/suspicious for follicular neoplasm categories. The mutations of the 7-gene panel were analysed and this information was linked to the available histology and ultrasound monitoring.

RESULTS

The BRAF V600E and RET/PTC1 mutations were associated with carcinoma in 100% of cases (n=8), whereas only 37.5% (n=3) of the nodules with RAS and 17% (n=1) with PAX8/PPARG mutations were associated with carcinoma. From the histological diagnosis and ultrasound monitoring of patients, we can estimate that this panel has a sensitivity of 86% in detecting malignant carcinoma, a specificity of 77%, a positive predictive value (PPV) of 54% and a negative predictive value (NPV) of 94%. In this study, it was possible to reduce the number of surgeries by 48% in the patients analysed.

CONCLUSION

The implementation of the mutation panel allowed the appropriate surgical strategy to be selected for each patient, the number of two-step surgeries to be reduced, and active follow-up to be established in low-risk patients.

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.

Thyroid and Molecular Testing. Advances in Thyroid Molecular Cytopathology

Thyroid nodules are a common finding in the adult population including the fact that more than 50% of individuals, over the age of 60, have thyroid nodules. The majority have been mostly detected with ultrasonography and 10% by palpation. The majority of these nodules are benign, whereas 5–15% of them are malignant. The pre-operative diagnosis of cancer is a critical challenge in order to ensure that each patient can be treated with the best tailored management with a reduction of unnecessary surgery for benign lesions. Fine needle aspiration cytology (FNAC) represents the first and most important diagnostic tool for the evaluation of thyroid lesions. According to the literature, FNAC is able to render a conclusive diagnosis in up to 70–80% of all cases. For the remaining 20–30% of nodules, cytological diagnoses fall into the category of indeterminate lesions mostly due to the lack of specific morphological features. According to the Bethesda system for reporting thyroid cytopathology (TBSRTC), indeterminate lesions can be sub-stratified into three different subcategories including “atypia of undetermined significance/follicular lesion of undetermined significance-AUS/FLUS”; “follicular or Hürthle cell neoplasm/suspicious for follicular or Hürthle cell neoplasm-FN/SFN”; and “suspicious for malignancy-SFM”. Many of these indeterminate lesions undergo repetition or diagnostic lobectomy. Nonetheless, the majority of these cases will have a benign diagnosis due to the fact that the rate of cancer ranges between 6 and 30%. It stands to reason that the application of ancillary technique, mostly molecular testing, emerged as a critical additional tool for those thyroid indeterminate lesions. Since the early 1990s, material collected from cytological samples yields sufficient and adequate cells for the detection of point mutation or gene fusions. Nonetheless, the further availability of new sequencing technologies such as next-generation sequencing (NGS) has led to more comprehensive molecular applications adopted now in clinical use. The current review investigates the multiple advances in the field of molecular testing applied in thyroid cytology.

Moving towards a local testing solution for undetermined thyroid fine-needle aspirates: validation of a novel custom DNA-based NGS panel

AIMS

In thyroid cytopathology, the undetermined diagnostic categories still pose diagnostic challenges. Although next-generation sequencing (NGS) is a promising technique for the molecular testing of thyroid fine-needle aspiration (FNA) specimens, access to such technology can be difficult because of its prohibitive cost and lack of reimbursement in countries with universal health coverage. To overcome these issues, we developed and validated a novel custom NGS panel, Nexthyro, specifically designed to target 264 clinically relevant mutations involved in thyroid tumourigenesis. Moreover, in this study, we compared its analytical performance with that of our previous molecular testing strategy.

METHODS

The panel, which includes 15 genes (BRAF, EIF1AX, GNAS, HRAS, IDH1, KRAS, NF2, NRAS, PIK3CA, PPM1D, PTEN, RET, DICER1, CHEK2, TERT promoter), was validated with a cell-line derived reference standard and 72 FNA archival samples previously tested with the 7-gene test.

RESULTS

Nexthyro yielded 100% specificity and detected mutant alleles at levels as low as 2%. Moreover, in 5/72 (7%) FNAs, it detected more clinically relevant mutations in BRAF and RAS genes compared with the 7-gene test. Nexthyro also revealed better postsequencing metrics than the previously adopted commercial 'generic' NGS panel.

CONCLUSION

Our comparative analysis indicates that Nexthyro is a reliable NGS panel. The study also implies that a custom-based solution for routine thyroid FNA is sustainable at the local level, allowing patients with undetermined thyroid nodules affordable access to NGS.

Application of ultrasonic shear wave elastography and contrast-enhanced ultrasound in the differential diagnosis of patients with benign and malignant thyroid lesions

Background

Thyroid nodules are a common thyroid disorder. The aim of the present study was to observe the application value of ultrasonic shear wave elastography (SWE) and contrast-enhanced ultrasound (CEUS) in the differential diagnosis of patients with benign and malignant thyroid lesions.

Methods

Eighty-two patients with thyroid nodules (96 thyroid nodules) at our hospital were enrolled. All patients underwent ultrasonic SWE and CEUS examination. With surgical pathology as the gold standard, the Young's modulus, CEUS imaging features, and quantitative parameters were compared between the benign and malignant groups. The diagnostic efficiency of SWE, CEUS, and their combination was analyzed by receiver-operating characteristic curve (ROC).

Results

The average of the Young's modulus in the malignant group was significantly higher than that of the benign group (P<0.05). There were significant differences in the CEUS images of nodules between the benign and malignant groups in terms of boundary conditions, morphology, perfusion intensity, homogeneous enhancement, and perfusion defects (P<0.05), while there were no significant difference in initial increase time, peak intensity, time to peak, and area under the curve (P>0.05). The curve sharpness in the benign group was significantly lower than that of the malignant group (P<0.05). ROC analysis found that the diagnostic sensitivity and specificity of SWE, CEUS, and their combination were 90.1% and 81.6%, 67.8% and 75.4%, and 97.3% and 71.5%, respectively.

Conclusions

Compared with CEUS, the sensitivity and specificity of SWE were relatively higher in the differential diagnosis of benign and malignant thyroid lesions, and a combination of both can improve the diagnostic sensitivity of SWE alone to a certain extent.

Incorporation of a Machine Learning Algorithm With Object Detection Within the Thyroid Imaging Reporting and Data System Improves the Diagnosis of Genetic Risk

Background

The role of next generation sequencing (NGS) for identifying high risk mutations in thyroid nodules following fine needle aspiration (FNA) biopsy continues to grow. However, ultrasound diagnosis even using the American College of Radiology's Thyroid Imaging Reporting and Data System (TI-RADS) has limited ability to stratify genetic risk. The purpose of this study was to incorporate an artificial intelligence (AI) algorithm of thyroid ultrasound with object detection within the TI-RADS scoring system to improve prediction of genetic risk in these nodules.

Methods

Two hundred fifty-two nodules from 249 patients that underwent ultrasound imaging and ultrasound-guided FNA with NGS with or without resection were retrospectively selected for this study. A machine learning program (Google AutoML) was employed for both automated nodule identification and risk stratification. Two hundred one nodules were used for model training and 51 reserved for testing. Three blinded radiologists scored the images of the test set nodules using TI-RADS and assigned each nodule as high or low risk based on the presence of highly suspicious imaging features on TI-RADS (very hypoechoic, taller-than-wide, extra-thyroidal extension, punctate echogenic foci). Subsequently, the TI-RADS classification was modified to incorporate AI for T4 nodules while treating T1-3 as low risk and T5 as high risk. All diagnostic predictions were compared to the presence of a high-risk mutation and pathology when available.

Results

The AI algorithm correctly located all nodules in the test dataset (100% object detection). The model predicted the malignancy risk with a sensitivity of 73.9%, specificity of 70.8%, positive predictive value (PPV) of 70.8%, negative predictive value (NPV) of 73.9% and accuracy of 72.4% during the testing. The radiologists performed with a sensitivity of 52.1 ± 4.4%, specificity of 65.2 ± 6.4%, PPV of 59.1 ± 3.5%, NPV of 58.7 ± 1.8%, and accuracy of 58.8 ± 2.5% when using TI-RADS and sensitivity of 53.6 ± 17.6% (p=0.87), specificity of 83.3 ± 7.2% (p=0.06), PPV of 75.7 ± 8.5% (p=0.13), NPV of 66.0 ± 8.8% (p=0.31), and accuracy of 68.7 ± 7.4% (p=0.21) when using AI-modified TI-RADS.

Conclusions

Incorporation of AI into TI-RADS improved radiologist performance and showed better malignancy risk prediction than AI alone when classifying thyroid nodules. Employing AI in existing thyroid nodule classification systems may help more accurately identifying high-risk nodules.

miR‑592 acts as an oncogene and promotes medullary thyroid cancer tumorigenesis by targeting cyclin‑dependent kinase 8

Medullary thyroid carcinoma (MTC) is a relatively rare subtype of thyroid cancer, accounting for 5‑10% of all cases of thyroid cancer worldwide. Due to the current lack of knowledge regarding the tumorigenesis of MTC, the clinical treatment of MTC remains a challenge. It has been reported that microRNAs (miRNAs) regulate the progression of MTC; however, the regulatory network of miRNAs and the exact underlying mechanisms are not completely understood. In the present study, an miRNA expression profile (GSE40807), consisting of 80 samples, was downloaded and analyzed using Gene Expression Omnibus‑2R to identify differentially expressed miRNAs between MTC and normal samples. miR‑592 expression levels were significantly increased in MTC tissues and cell lines compared with normal tissues and cell lines. Patients with high miR‑592 expression levels exhibited a less favorable prognosis compared with patients with low miR‑592 expression. The results suggested that miR‑592 overexpression promoted TT and MZ‑CRC‑1 cell proliferation in vitro. In addition, miR‑592 negatively regulated cyclin‑dependent kinase 8 (CDK8) via targeted binding in MTC cells. Moreover, co‑transfection of CDK8 overexpression plasmid and miR‑592 mimic reversed miR‑592‑mediated MTC cell proliferation. In conclusion, miR‑592 may serve as an oncogene in MTC by decreasing the expression of CDK8, indicating that the miR‑592/CDK8 axis might serve as a promising therapeutic target for MTC.

European perspective on the use of molecular tests in the diagnosis and therapy of thyroid neoplasms

Thyroid nodules are frequently observed, particularly in individuals of over 60 years of age. On the other hand, most of the detected changes are benign and they do not require surgery. Therefore, differentiation between benign and malignant lesions in preoperative diagnosis is of crucial importance. Currently, the use of fine-needle aspiration biopsy (FNAB) and cytological assessment are the gold standard in the diagnosis of thyroid nodules. This procedure significantly reduces the need for diagnostic surgical intervention. However, approximately 15-30% of cytological results are classified as indeterminate. This is mainly due to the lack of specific cytomorphologic features that would facilitate the diagnosis based on cell evaluation under microscopic assessment. For the diagnoses of atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS), the assessment of invasion is crucial. Such an evaluation is not possible in cytology. Recently, molecular tests have been developed. They improve cytological diagnosis, particularly in the case of indeterminate results. Commercially available tests are developed based on the North American population. It is important to assess whether such tests can be used in the evaluation of e.g., European population.

Thyroid nodules: diagnostic evaluation based on thyroid cancer risk assessment

Thyroid nodules are extremely common and can be detected by sensitive imaging in more than 60% of the general population. They are often identified in patients without symptoms who are undergoing evaluation for other medical complaints. Indiscriminate evaluation of thyroid nodules with thyroid biopsy could cause a harmful epidemic of diagnoses of thyroid cancer, but inadequate selection of thyroid nodules for biopsy can lead to missed diagnoses of clinically relevant thyroid cancer. Recent clinical guidelines advocate a more conservative approach in the evaluation of thyroid nodules based on risk assessment for thyroid cancer, as determined by clinical and ultrasound features to guide the need for biopsy. Moreover, newer evidence suggests that for patients with indeterminate thyroid biopsy results, a combined assessment including the initial ultrasound risk stratification or other ancillary testing (molecular markers, second opinion on thyroid cytology) can further clarify the risk of thyroid cancer and the management strategies. This review summarizes the clinical importance of adequate evaluation of thyroid nodules, focuses on the clinical evidence for diagnostic tests that can clarify the risk of thyroid cancer, and highlights the importance of considering the patient's values and preferences when deciding on management strategies in the setting of uncertainty about the risk of thyroid cancer.

Impact of the Italian Society of Anatomic Pathology and Diagnostic Cytology Classification of Thyroid Nodules in the Treatment of Indeterminate Follicular Lesions: Five-Year Results at a Single Center

PURPOSE

Aim of the study was to assess the impact of the Italian Society of Anatomic Pathology and Diagnostic Cytology (SIAPEC) classification of 2014, on the treatment of indeterminate thyroid lesions (TIR3).

METHODS

We retrospectively analyzed patients undergoing thyroid surgery for TIR3 lesions between 2013 and 2018, at the General Surgery Department of Trieste University Hospital. According to the SIAPEC classification, patients were divided into TIR3A and TIR3B groups. All patients treated before 2014 underwent surgical treatment, and surgical specimens were retrospectively classified after revision of fine-needle aspiration cytology. Starting 2014, TIR3A patients were treated only when symptomatic (i.e., coexistent bilateral thyroid goiter or growing TIR3A nodules), whereas TIR3B patients always received surgical treatment. Hemithyroidectomy (HT) was the procedure of choice. Total thyroidectomy (TT) was performed in case of concurrent bilateral goiter, autoimmune thyroid disease, and/or presence of BRAF and/or RAS mutation. Lastly, we analyzed the malignancy rate in the two groups.

RESULTS

29 TIR3A and 90 TIR3B patients were included in the study. HT was performed in 10 TIR3A patients and 37 TIR3B patients, respectively, with need for reoperation in 4 TIR3B (10.8%) patients due to histological findings of follicular thyroid carcinoma >1  cm. The malignancy rates were 17.2% in TIR3A and 31.1% in TIR3B, (p = 0.16). Predictability of malignancy was almost 89% in BRAF mutation and just 47% in RAS mutation.

CONCLUSIONS

The new SIAPEC classification in association with biomolecular markers has improved diagnostic accuracy, patient selection, and clinical management of TIR3 lesions.

Classification of Thyroid Nodules with Stacked Denoising Sparse Autoencoder

PURPOSE

Several commercial tests have been used for the classification of indeterminate thyroid nodules in cytology. However, the geographic inconvenience and high cost confine their widespread use. This study aims to develop a classifier for conveniently clinical utility.

METHODS

Gene expression data of thyroid nodule tissues were collected from three public databases. Immune-related genes were used to construct the classifier with stacked denoising sparse autoencoder.

RESULTS

The classifier performed well in discriminating malignant and benign thyroid nodules, with an area under the curve of 0.785 [0.638-0.931], accuracy of 92.9% [92.7-93.0%], sensitivity of 98.6% [95.9-101.3%], specificity of 58.3% [30.4-86.2%], positive likelihood ratio of 2.367 [1.211-4.625], and negative likelihood ratio of 0.024 [0.003-0.177]. In the cancer prevalence range of 20-40% for indeterminate thyroid nodules in cytology, the range of negative predictive value of this classifier was 37-61%, and the range of positive predictive value was 98-99%.

CONCLUSION

The classifier developed in this study has the superb discriminative ability for thyroid nodules. However, it needs validation in cytologically indeterminate thyroid nodules before clinical use.

Microfluidic Droplet Digital PCR Is a Powerful Tool for Detection of BRAF and TERT Mutations in Papillary Thyroid Carcinomas

We examined the utility of microfluidic digital PCR (dPCR) for detection of BRAF and TERT mutations in thyroid tumors. DNA extracted from 100 thyroid tumors (10 follicular adenomas, 10 follicular cancers, 5 medullary cancers, and 75 papillary thyroid cancer (PTC) were used for detection of BRAF and TERT mutations. Digital PCRs were performed using rare mutation SNP genotyping assays on QuantStudio 3D platform. In PTCs, BRAFV600E was detected by dPCR and Sanger sequencing in 42/75 (56%) and in 37/75 (49%), respectively. BRAFV600E was not detected in other tumors. The ratio of mutant/total BRAF alleles varied from 4.7% to 47.5%. These ratios were higher in classical PTCs (27.1%) as compared to follicular variant PTCs (9.4%) p = 0.001. In PTCs with and without metastases, the ratios of mutant/total BRAF alleles were 27.6% and 18.4%, respectively, (p = 0.03). In metastatic lesions percentages of mutant/total BRAF alleles were similar to those detected in primary tumors. TERTC228T and TERTC250T were found in two and one cases, respectively, and these tumors concomitantly harbored BRAFV600E. These tumors exhibited gross extra-thyroidal extension, metastases to lymph nodes, and pulmonary metastases (one case). Our results showed that dPCR allows quantitative assessment of druggable targets in PTCs and could be helpful in a molecular-based stratification of prognosis in patients with thyroid cancer.

BRAF mutation analysis by ARMS-PCR refines thyroid nodule management

BACKGROUND

Fine-needle aspiration (FNA) of thyroid nodules leads to nearly 25% indeterminate nodules, while BRAF^V600E mutation helps to predicting papillary thyroid carcinoma (PTC). However, the clinical validity and utility of the BRAF^V600E mutation detected using preoperative FNA samples in a large cohort were rarely reported.

AIM

To explore the clinical significance of the BRAF^V600E mutation on preoperative diagnosis and decision-making in a large FNA cohort in China.

DESIGN

This was a prospective study of BRAF^V600E mutation analysis using an amplification refractory mutation system-polymerase chain reaction (ARMS-PCR) in FNA samples.

PATIENTS

The study involved 2640 samples from 2307 patients undergoing FNA procedures in a Chinese medical centre.

RESULTS

A high mutation rate of 86.7% was found in the PTC population. For indeterminate thyroid nodules, the malignant rate of BRAF^V600E+ and BRAF^V600E- was 87.8% and 39.5% in the Bethesda System for Reporting Thyroid Cytopathology (BSRTC) III, and 88.2% and 31.8% in the BSRTC IV, respectively. A cost-effective diagnostic model combining both BSRTC grading and BRAF^V600E mutation status showed the highest sensitivity of 82.9% and specificity of 85.4%. Central lymph node metastasis (CLNM) was independent of the BRAF mutation status and accounted for 34.2% of the patients with PTC. C_T values of BRAF^V600E of patients with PTMC were significantly lower in young patients and patients with CLNM.

CONCLUSIONS

The combined analysis of cytological results and BRAF^V600E mutation is highly recommended in BRAF^V600E high-prevalence regions, including China. Prophylactic central neck dissection should be performed in selected patients without regard to the BRAF mutation status.

Thyroid imaging reporting and data system combined with Bethesda classification in qualitative thyroid nodule diagnosis

OBJECTIVE

We aimed to investigate the value of the combined use of high-resolution ultrasound thyroid imaging reporting and data system (TI-RADS) classification and thyroid fine needle aspiration cytology (Bethesda classification) for the qualitative diagnosis of benign and malignant thyroid nodules.

METHODS

We enrolled 295 patients with 327 thyroid nodules who were scheduled to undergo thyroid nodule surgery. Before surgery, all the patients underwent ultrasound and scoring with the TI-RADS classification, along with thyroid fine needle biopsy cytology under ultrasound guidance (US-FNAC) and scoring with the Bethesda classification. After surgery, the TI-RADS and Bethesda classification scores, separately and in combination, were compared with the postoperative pathological results in terms of the differential diagnosis of thyroid nodules.

RESULTS

TI-RADS classification score 4 exhibited the highest diagnostic value for thyroid cancer; the sensitivity, specificity, and accuracy were 92.7%, 70.7%, and 87.1%, respectively, whereas the Kappa and receiver-operating characteristics (ROC) values were 0.651 and 0.817, respectively. Moreover, Bethesda classification score 3 exhibited the highest diagnostic value for thyroid cancer; the sensitivity, specificity, and accuracy were 90.0%, 94.3%, and 91.1%, respectively, whereas the Kappa and ROC values were 0.78 and 0.914, respectively. With regard to the combined diagnostic method, a score of 7 exhibited the highest diagnostic value for thyroid cancer; the sensitivity, specificity, and accuracy were 97.3%, 92.0%, and 95.9%, respectively, whereas the Kappa and ROC values were 0.893 and 0.946, respectively.

CONCLUSION

The combination of high-resolution ultrasonography TI-RADS classification and US-FNAC (Bethesda classification) can improve the accuracy of malignant thyroid nodules diagnosis.

Digital Gene Expression Analysis on Cytology Smears Can Rule Out Malignancy in Follicular-Patterned Thyroid Tumors

Patients with indeterminate thyroid nodules (Bethesda III and IV) are often treated with diagnostic lobectomy, which in most cases represents an overtreatment. A reliable rule-out molecular test could spare patients unnecessary surgery. Stained smears of 88 indeterminate thyroid nodules with histologic diagnosis of follicular-patterned tumors were selected: 34 follicular adenomas (FAs), 34 follicular variant papillary thyroid carcinomas (FVPTCs), and 20 noninvasive follicular neoplasms with papillary-like nuclear features (NIFTPs). The expression level of 126 genes was measured by digital counting. Mutation testing was performed for the main gene mutations and fusions. Performance of gene expression and mutation tests was calculated by receiver operating characteristic analysis. The gene expression model showed an area under the curve (AUC) of 88%, with 91% negative predictive value in FAs and FVPTCs only. Part of NIFTPs was labeled as benign, and part was labeled as malignant; thus, the classifier performance worsened. Two FAs (5.9%), eight NIFTPs (40%), and 22 FVPTCs (64.7%) were mutation positive. Mutation testing AUC was 79% in FAs and FVPTCs, and decreased by including NIFTPs. This gene expression-based test was feasible in thyroid-stained smears, showed higher AUC than mutation test, and had a high negative predictive value-making it a good candidate as a rule-out test for indeterminate thyroid cytology. NIFTPs have a heterogeneous phenotype, and their preoperative diagnosis requires further investigation.

Molecular mutations as a possible factor for determining extent of thyroid surgery

Background

Molecular testing of thyroid nodules is a diagnostic tool used to better understand the nature of thyroid nodules. The aim of this study is to better comprehend the relationship between specific mutations and aggressive behavior of the tumour as demonstrated on postoperative pathological analysis.

Methods

A retrospective chart review of 103 cases was performed. Included were patients who had undergone molecular testing using a panel that tests for 9 mutations (ThyGenX®) and were found to have malignant tumours. The following gene alterations were found pre-operatively in the nodules: BRAF V600E (n = 32), BRAF K601E (n = 4), NRAS (n = 11), HRAS (n = 4), KRAS (n = 3), RET/PTC1 rearrangement (n = 1), TERT promoter (n = 2), PAX8-PPARγ rearrangement (n = 1), and 45 cases where no mutation was detected. Aggressive behavior was defined by extra-thyroidal extension (ETE), lymph node metastasis (LN+), and the following variants of papillary thyroid carcinoma: tall cell, solid, diffuse sclerosing, columnar cell and hobnail. Chi-squared testing was performed to compare groups.

Results

The group with BRAF V600E, RET/PTC1 rearrangement, and TERT promoter mutations was associated with ETE 37.1%, and LN+ 45.7% of the time compared to 4.3 and 13.0% in the group with other mutations, and 4.4 and 4.4% in the group with no mutations (p-value 0.02, p-value < 0.001, p-value 0.006). In addition, the BRAF V600E, RET/PTC1 rearrangement, and TERT mutations group demonstrated tall cell variants (17.1%), columnar cell variants (5.7%), and hobnail variants (3%). The other mutations group demonstrated columnar cell variants (4.3%), and the no mutations group demonstrated solid variants (2.2%).

Conclusions

In this study, BRAF V600E, RET/PTC1 rearrangement, and TERT mutations were associated with aggressive behaving thyroid malignancies as defined above. Molecular testing may be a useful method to anticipate aggressive tumour types and therefore assist in planning the extent and timing of surgery.

Preoperative metabolic classification of thyroid nodules using mass spectrometry imaging of fine-needle aspiration biopsies

Thyroid neoplasia is common and requires appropriate clinical workup with imaging and fine-needle aspiration (FNA) biopsy to evaluate for cancer. Yet, up to 20% of thyroid nodule FNA biopsies will be indeterminate in diagnosis based on cytological evaluation. Genomic approaches to characterize the malignant potential of nodules showed initial promise but have provided only modest improvement in diagnosis. Here, we describe a method using metabolic analysis by desorption electrospray ionization mass spectrometry (DESI-MS) imaging for direct analysis and diagnosis of follicular cell-derived neoplasia tissues and FNA biopsies. DESI-MS was used to analyze 178 tissue samples to determine the molecular signatures of normal, benign follicular adenoma (FTA), and malignant follicular carcinoma (FTC) and papillary carcinoma (PTC) thyroid tissues. Statistical classifiers, including benign thyroid versus PTC and benign thyroid versus FTC, were built and validated with 114,125 mass spectra, with accuracy assessed in correlation with clinical pathology. Clinical FNA smears were prospectively collected and analyzed using DESI-MS imaging, and the performance of the statistical classifiers was tested with 69 prospectively collected clinical FNA smears. High performance was achieved for both models when predicting on the FNA test set, which included 24 nodules with indeterminate preoperative cytology, with accuracies of 93% and 89%. Our results strongly suggest that DESI-MS imaging is a valuable technology for identification of malignant potential of thyroid nodules.

Ancillary molecular testing of indeterminate thyroid nodules

Cytological specimens from thyroid nodules are increasingly being adopted as the first available material for cost effectively managing patients in the era of personalized medicine. Cytology aspirates not only play a central role in providing accurate diagnoses, but are also being collected for ancillary molecular testing. Molecular analysis, including the evaluation of somatic mutations and other genomic alterations, has accordingly become well integrated in the cytological workup of thyroid lesions. Appropriately handled thyroid cytology preparations provide well-preserved and adequately cellular material with improved DNA/RNA quantity. The recent publication of the 2nd edition of The Bethesda System for Reporting Thyroid Cytopathology and the American Thyroid Association guidelines confirm the relevant role of molecular testing in the management of the different subcategories of indeterminate thyroid lesions. This review discusses the role of molecular testing for indeterminate thyroid nodules, including the recent introduction of the noninvasive, encapsulated follicular variant of papillary thyroid carcinoma (FVPTC), known also as noninvasive follicular neoplasm with papillary-like nuclear features (NIFTP).

The Role of Molecular Testing for the Indeterminate Thyroid FNA

Thyroid nodules are common in the adult population where a majority are benign and only 4.0% to 6.5% are malignant. Fine needle aspiration (FNA) is a key method used in the early stages to evaluate and triage patients with thyroid nodules. While a definitive cytological diagnosis is provided in more than 70–75% of all thyroid FNA cases, the group of indeterminate lesions offers a challenge in terms of interpretation and clinical management. Molecular testing platforms have been developed, are recognized as an option by the 2015 American Thyroid Association Guidelines, and are frequently used in conjunction with FNA as an integral part of the cytologic evaluation. In this review, the utility of molecular testing options for nodules assigned to the group of indeterminate thyroid FNAs is described.

Comparison of Postmarketing Findings vs the Initial Clinical Validation Findings of a Thyroid Nodule Gene Expression Classifier: A Systematic Review and Meta-analysis

Importance

In the United States, the most used molecular test for the evaluation of cytologically indeterminate thyroid nodules is the Afirma gene expression classifier (GEC).

Objective

To evaluate the GEC's diagnostic performance through a novel approach to assess whether the findings of the initial validation study are consistent with the results of postmarketing studies.

Data Sources

PubMed was systematically searched from inception through October 26, 2017, using the terms gene expression classifier or Afirma or GEC and thyroid.

Study Selection

Studies included were those in which the GEC diagnostic performance could be calculated on consecutively resected cytologically indeterminate thyroid nodules.

Data Extraction and Synthesis

Two observers independently assessed study eligibility and risk of bias using the quality assessment tool for observational cohort and cross-sectional studies of the National Heart, Lung, and Blood Institute. Summary data were extracted by a reviewer and reviewed independently by another. Study authors were contacted if missing data were needed. Data were pooled using a random-effects model. PRISMA and MOOSE guidelines were followed.

Main Outcomes and Measures

Evaluation of the linear correlation between the benign call rate (BCR) and the positive predictive value (PPV).

Results

Of the 137 retrieved titles, 19 (13.9%) were included, comprising a total of 2568 thyroid nodules. Based on a simulation using the sensitivity and specificity reported in the initial validation study, the observed BCR and PPV values in postmarketing studies would have to be explained by different underlying prevalence rates of cancer (15% vs 30%), which is an impossible event. Furthermore, the overall correlation between BCR and PPV for independent studies fell outside the PPV 95% CI of the initial validation study (95% CI, 0.17-0.32) at the BCR of pooled independent studies (0.45) and was just at the limit of the BCR 95% CI of the initial validation study (95% CI, 0.32-0.45) at the PPV of pooled independent studies (0.45). The diagnostic performance was statistically significantly better for atypia or follicular lesions of undetermined significance (diagnostic odds ratio [DOR], 5.67; 95% CI, 4.23-7.60) compared with follicular neoplasms (DOR, 2.24; 95% CI, 1.45-3.47).

Conclusions and Relevance

The findings suggest that the initial validation study cohort was not representative of the populations in whom the GEC has been used, calling into question its reported diagnostic performance, including its negative predictive value.

Noninvasive Follicular Thyroid Neoplasm with Papillary-Like Nuclear Features (NIFTP): Update and Diagnostic Considerations-a Review

Advances in our understanding of thyroid lesions, especially those entities with an indolent behavior, has led clinicians to question the most appropriate surgical management of such thyroid nodules. Several studies have shown that the non-invasive encapsulated follicular variant of papillary thyroid carcinomas (NI-EFVPC) exhibits poor histopathologic diagnostic reproducibility and have been over-treated as conventional thyroid cancer. In 2015, an international thyroid working group re-evaluated NI-EFVPC and its diagnostic criteria. The new terminology of "noninvasive follicular thyroid neoplasm with papillary-like nuclear features" (NIFTP) was accordingly introduced to replace NI-EFVPC. The literature has emphasized that NIFTPs are biologically similar to follicular adenomas lacking lymph node metastases and/or recurrence. While the definition of NIFTP is based on specific morphological parameters, recent studies have questioned whether the criterion allowing less than 1% of true papillae should be revised to a total absence of papillae. The motivation for this revision is the rare finding, in some studies, of lymph nodes with metastatic NIFTP. This review evaluates the existing published series of NIFTP cases, clinical consequences of NIFTP, and emerging changes in the diagnostic criteria for NIFTP. The introduction of NIFTP has resulted in significant impact on the clinical management of thyroid nodules. Recent revisions in the morphological criteria for NIFTP emphasize the need to adhere to very stringent histomorphologic criteria when making a diagnosis of NIFTP. The adoption of NIFTP terminology instead of NI-EFVPC is associated with conservative lobectomy without radioactive iodine treatment in the majority of cases.

Case report of a neuroendocrine tumor of the thyroid gland with limited calcitonin expression: a diagnostic challenge

Medullary thyroid carcinoma (MTC) is a malignant tumor of the parafollicular cells, which produce calcitonin. As a result, calcitonin is an important tool for diagnosing MTC. When there is focal or no calcitonin staining, diagnosis of MTC can be challenging as this may suggest differences in cell origin and in prognosis and recurrence of the disease. The prognosis and guidelines for management and follow up for MTC remain inconclusive. Here, we present a case of primary neuroendocrine tumor of the thyroid gland with only focal calcitonin staining on immunohistochemistry and low serum calcitonin level despite a tumor size of almost 4 cm. The assumption of C-cell origin was made from positive staining for carcinoembryonic agent (CEA), thyroid transcription factor 1 (TTF-1) and paired box 8 (PAX8) without expression of thyroglobulin (Tg). The patient underwent thyroid lobectomy and follow-up monitoring with ultrasound and measurements of calcitonin and CEA levels, without any further surgical intervention. Few cases of neuroendocrine tumors with limited calcitonin expression have been published and the etiology and prognosis are still unknown. Our case suggests that limited calcitonin expression cannot completely exclude the diagnosis of MTC. This rare type of MTC should be differentiated from the typical presentation of MTC. Treatment and post-operative surveillance should be tailored based on the individual.

Rethinking Malignancy Risk in Indeterminate Thyroid Nodules with Positive Molecular Studies: Southern California Permanente Experience

Objectives

To recognize that thyroid nodules with atypia of undetermined significance/follicular lesion of undetermined significance (AUS/FLUS; Bethesda III) have different risks of malignancy based on genetic mutation and to consider molecular testing of nodules with AUS/FLUS to help avoid unnecessary morbidity or cost.

Study Design

Retrospective cohort study.

Setting

Multiple locations within Southern California Permanente Medical Group.

Subjects and Methods

Patients included those with indeterminate thyroid nodules and AUS/FLUS on 2 separate fine-needle aspirations with positive ThyGenX testing from 2014 to 2017 who underwent thyroid surgery. Patients were classified as having benign or malignant disease. Noninvasive follicular thyroid neoplasm with papillary-like nuclear features was considered benign.

Results

A total of 231 patients had repeat AUS/FLUS with positive molecular testing and surgery. The most frequent type of malignancy was papillary carcinoma, followed by follicular carcinoma. The overall prevalence of malignancy in nodules with mutations was 74.0%, although there was considerable variation: BRAF = 100%, RET = 100%, PAX8-PPARγ = 84.6%, HRAS = 70.7%, NRAS = 63.4%, and KRAS = 33%—a statistically significant finding ( P < .001).

Conclusions

Not all molecular mutations in thyroid nodules with AUS/FLUS have a high risk of malignancy. Of note, patients with BRAF and RET mutations in our population had a 100% risk of malignancy. Patients with PAX, HRAS, or NRAS mutations had a high risk of malignancy, while patients with KRAS mutations had a lower risk of malignancy. Further studies are needed to determine if the presence of certain molecular mutations can help personalize care and aid in the decision for thyroid surgery.

Update on Molecular Testing for Cytologically Indeterminate Thyroid Nodules

Fine needle aspiration biopsy (FNAB) and ultrasonography are the most common modalities for the diagnosis and follow up of thyroid nodules. FNAB is able to distinguish benign from malignant nodules with high sensitivity and specificity; however, 20% to 30% of nodules are diagnosed as indeterminate with a risk of malignancy varying from 10% to 75% based on the 2017 revision of the Bethesda System for Reporting Thyroid Cytopathology. Molecular tests are being increasingly used to triage this group of nodules. Several molecular tests are commercially available and newer upgrades are being developed to either "rule in" or "rule out" malignancy with greater accuracy. The Afirma gene expression classifier and its recent upgrade (the Afirma gene sequencing classifier), Thryoseq v2, a next generation sequencing test and its recent upgrade (the v3), RosettaGX Reveal based on microRNA alterations, and ThyGenX/ThyraMIR, a combination test, are currently on the market. Familiarity with these tests, their performance, and postvalidation publications will enable appropriate test selection and improve triage of patients for appropriate therapy. The underlying rate of malignancy at different institutions and the interobserver variability in cytologic and histologic diagnosis of thyroid lesions are important factors that impact the performance of the various molecular tests.

The mutational analysis in the diagnostic work-up of thyroid nodules: the real impact in a center with large experience in thyroid cytopathology

PURPOSE

Fine-needle aspiration (FNA) cytology is a mainstay in the evaluation of thyroid nodules, but fails to reach reliable results in 25-30% of cases. The role of molecular markers in helping clinical decisions has been investigated for the last years, but their clinical usefulness is still unsettled.

METHODS

Mutation analysis of BRAF, RAS genes and TERT promoter was performed in a series of 617 consecutive cytological specimens undergoing FNA.

RESULTS

The 617 nodules had the following cytological diagnosis: non diagnostic 22 (3.6%), benign 425 (68.9%), indeterminate 114 (18.5%), suspicious 11 (1.8%) and malignant 45 (7.3%). BRAF mutations were found in 31 cases (5.0%), all but two in suspicious and malignant nodules. RAS mutations were detected in 47 samples (7.6%): 25 benign (5.9%) and 19 indeterminate nodules (16.7%). TERT promoter mutation alone was detected in three samples. Histological outcome was available for 167 nodules, 81 of which proved malignant: all the 48 with suspicious or malignant cytology; 25 out of 56 (44.6%) with indeterminate and 8 out of 57 (14%) with benign cytology. BRAF mutations were associated with worse tumors pathological features. The presence of RAS mutations was indicative of follicular-patterned malignancies in 5 out of 8 benign nodules and 9 out of 11 indeterminate nodules.

CONCLUSIONS

Our study established mutational rates for BRAF and RAS genes in a large series of FNA specimens. BRAF mutations were confirmed as highly specific but not able to improve cytological diagnosis, while RAS testing proved effective in assessing malignancy in nodules with indeterminate and benign cytology.

Centrifuged supernatants from FNA provide a liquid biopsy option for clinical next-generation sequencing of thyroid nodules

BACKGROUND

Molecular testing is recommended as an adjunct to improve the preoperative diagnosis of fine-needle aspiration (FNA) of thyroid nodules. Centrifuged supernatants from FNA samples, which are typically discarded, have recently emerged as a novel liquid-based biopsy for molecular testing. This study evaluates the use of thyroid FNA supernatants for detecting clinically relevant mutations.

METHODS

Supernatants from thyroid FNA samples (n = 156) were evaluated. A 50-gene next-generation sequencing (NGS) assay was used, and mutation analysis results from a subset of samples were further compared with those of paired FNA smears and/or cell blocks.

RESULTS

All 156 samples yielded adequate DNA (median, 135 ng; range, 11-3180 ng), and 129 of these samples (83%) were successfully sequenced by NGS. The most frequently detected somatic mutations included BRAF and RAS mutations, which were followed by RET, TP53, PTEN, CDKN2A, and PIK3CA mutations. Eleven of 31 cases with an indeterminate cytologic diagnosis and 9 of 12 cases that were suspicious for malignancy had somatic mutations, including the BRAF V600E mutation, which is highly definitive for papillary thyroid carcinoma (PTC). Seven of the 9 indeterminate and suspicious cases with the BRAF V600E mutation had surgical follow-up, and they were all confirmed to be PTC. A comparison of the mutation profiles derived from supernatants with those of paired smears and/or cell blocks in a small subset of cases (n = 8) showed 100% concordance.

CONCLUSIONS

This study provides evidence that FNA supernatants can be used as a surrogate for thyroid molecular testing to improve diagnostic accuracy in indeterminate nodules, provide prognostic/predictive information, and improve overall patient management.

Determining the molecular test for indeterminate thyroid nodules best suited for our practice: A quality assurance study

INTRODUCTION

Currently, molecular studies are widely used as a guiding tool in further management of cytologically indeterminate thyroid nodules. At our institution, clinicians have recently expressed concern over receiving "less positive molecular results" upon switching from an extended 14 gene mutation panel (EGMP) to a 7 gene mutation panel (GMP). Our goal is to compare outcomes of these two tests in regards to the performance characteristics and clinical impact.

MATERIALS AND METHODS

All thyroid fine-needle aspiration (FNA) biopsy specimens sent for molecular studies from 2016 to 2017 were retrospectively studied. Cytopathology diagnosis, pertinent clinical findings, molecular results, and follow-up (F/U) surgical and cytology diagnoses were recorded.

RESULTS

Of the total 165 cases sent for molecular tests 86 (52%) were GMP and 79 (47%) EGMP. There were 21 (24%) and 40 (50%) cases with positive GMP and EGMP results, respectively. Within these positive cases (n = 61), there were a total of 33 (54%) patients who underwent surgical resection and 28 (45%) patients had no follow-up. The molecular findings and surgical pathologic diagnoses obtained are illustrated in Figures 1 through 4 for GMP and EGMP, respectively.

CONCLUSIONS

The selection of molecular testing should be directed toward optimizing patient care and facilitate clinical management. This quality assurance study helped in understanding the complexities associated with test selection best suited for our institution and in educating clinicians.

Standardized terminology systems in cytopathology

There has been increasing pressure for systemization in cytopathology. Lack of uniformity in categorization, variation in opinion based regional practice, and technologic advancement have created an environment disposed toward creation of more consistent evidence-based approaches to diagnostic problems. This review provides an overview of the major standardized terminology systems in cytology, with historical perspectives and commentary on current uses of these systems. These systems now include gynecologic, thyroid, pancreaticobiliary, urinary, salivary gland, and breast cytology. We summarize major classification systems supported by national and international professional organizations, outlining the structure and goals of each system. Specific benefits and potential pitfalls in the implementation of each system are given. Finally, we address potential criticisms of standardized terminology systems and proposed future directions to continue the evolution of standardized terminology to improve clinical practice.

A retrospective analysis of the performance of the RosettaGX® Reveal™ thyroid miRNA and the Afirma Gene Expression Classifiers in a cohort of cytologically indeterminate thyroid nodules

BACKGROUND

Molecular tests are increasingly used to triage cytologically indeterminate thyroid nodules for surgery and/or follow-up. We retrospectively compared the performance of the Afirma Gene Expression Classifier (AGEC) with that of the more recently developed RosettaGX^® Reveal™ miRNA Classifier (Reveal) in a cohort of Bethesda III-V thyroid FNAs with surgical follow-up.

DESIGN

Eighty-one samples (54 Bethesda III, 26 Bethesda IV, 1 Bethesda V) with available AGEC (74 AGEC-SUSP and 7 AGEC-BENIGN) and surgical pathology results were studied from three academic centers. Reveal was performed in a blinded fashion.

RESULTS

The final diagnoses were benign/NIFTP (n = 63) and malignant (n = 18). The overall "correct" rate was 64.2% for Reveal and 28.4% for AGEC (P = 1.4e-6). The specificity of Reveal was 60.3%, compared with 9.5% for AGEC (P = 2.1e-9). Among the 18 malignant cases, 77.8% and 94.4% were correctly classified as suspicious by Reveal and AGEC, respectively (P = 0.2). In the FLUS and the FN group, the specificity of AGEC was lower than the specificity of Reveal. Whether the 7 NIFTP in our study were considered benign or malignant, specificity and PPV of Reveal were higher than those of AGEC. Reveal also outperformed AGEC in correctly classifying the 26 benign Hürthle lesions studied (P = 7.6e-5).

CONCLUSION

Reveal outperformed AGEC in this cohort, whether NIFTP is considered benign or malignant, and in Hürthle lesions. Reveal has the potential to reduce the number of unnecessary resections in patients with indeterminate thyroid cytology. Based on our findings and the practical advantages offered by Reveal methodology, large prospective studies are warranted. Diagn. Cytopathol.

Current controversies and future directions in the diagnosis and management of differentiated thyroid cancers

Despite the development of novel diagnostic, surgical, and chemotherapeutic approaches to differentiated thyroid cancers (DTCs), the diagnosis and management of these tumors remains controversial. The most recent American Thyroid Association (ATA) guidelines, released in 2015, reflect a recent shift towards less aggressive management for patients with DTCs. However, many clinicians have expressed concern that more conservative management will put patients at risk for disease recurrence and metastasis. In particular, the management of indeterminate nodules on fine needle aspiration (with special attention to genetic and epigenetic markers of malignancy), the extent of surgery for known differentiated cancers, the role of adjuvant radioactive iodine (RAI) therapy, and novel targeted treatments with tyrosine kinase inhibitors (TKIs) represent current areas of uncertainty and opportunities for future research. In this review, we examine the current state of the art in these areas, and address some of the questions that remain.

ThyroSeq®V2.0 Molecular Testing: A Cost-Effective Approach for the Evaluation of Indeterminate Thyroid Nodules

OBJECTIVE

Approximately 15 to 30% of thyroid nodules have indeterminate cytology. Many of these nodules are treated surgically, but only 5 to 30% are malignant. Molecular testing can further narrow the risk of malignancy of these nodules. Our objective was to assess the cost effectiveness of ThyroSeq^®V2.0 compared to diagnostic thyroidectomy for the evaluation of indeterminate nodules.

METHODS

Cytology and histopathology slides of Bethesda category III and IV (suspicious for follicular neoplasia [SFN]) nodules obtained between January 1, 2014 and November 30, 2016 were re-reviewed by 2 endocrine cytopathologists. Costs for a diagnostic approach using ThyroSeq^® were calculated and compared to those of diagnostic thyroidectomy.

RESULTS

We included 8 Bethesda category III nodules that underwent ThyroSeq^® and 8 that underwent diagnostic surgery. Of those submitted for ThyroSeq^®, 4 were positive for mutations and underwent thyroid surgery. The average cost per nodule evaluated was $14,669 using ThyroSeq^®, compared to $23,338 for diagnostic thyroid surgery. The cost per thyroid cancer case detected was $58,674 using ThyroSeq^® compared to $62,233 for diagnostic thyroid surgery. We included 13 nodules Bethesda category IV that underwent ThyroSeq^® and 11 that underwent diagnostic surgery. Of those submitted for ThyroSeq^®, 6 were positive for mutation and underwent thyroid surgery. The average costs per nodule evaluated were $14,641 using ThyroSeq^® and $24,345 using diagnostic thyroidectomy. The cost per thyroid cancer case detected was $31,721 when using ThyroSeq^® compared to $53,560 for diagnostic thyroidectomy.

CONCLUSION

The use of ThyroSeq® in our institution is cost effective compared to diagnostic thyroid surgery for the evaluation of Bethesda categories III and IV (SFN) nodules.

ABBREVIATIONS

FNA = fine-needle aspiration; GEC = gene expression classifier; NIFTP = noninvasive follicular thyroid neoplasm with papillary-like nuclear features; PTC = papillary thyroid cancer; SFN = suspicious for follicular neoplasia.

Current methodologies for molecular screening of thyroid nodules

Several molecular tests have been developed for thyroid cytology with the main purpose to define the nature of indeterminate nodules in presurgical phase thus overcoming the limitations of cytological analysis. Molecular tests currently available for thyroid nodules are based on a variety of methodologies and display peculiar strengths and limitations: in this review of the literature they are summarized and critically discussed. The use of molecular diagnostics for thyroid cytology is increasingly widespread and accepted, however large, prospective validation studies are still needed to ultimately demonstrate the clinical efficacy of a wide incorporation of molecular tests into clinical practice.