Molecular Diagnostic Evaluation of Thyroid Nodules

The value of NGS-based multi-gene testing for differentiation of benign from malignant and risk stratification of thyroid nodules

Background

Fine-needle aspiration (FNA) biopsy is typically used in conjunction with cytopathologic evaluation to differentiate between benign and malignant thyroid nodules. Even so, the cytology results for 20-30% of thyroid nodules are indeterminate. This study sought to evaluate the usefulness of next-generation sequencing (NGS)-based multi-gene panel testing for risk stratification and the differentiation of benign from malignant thyroid nodules.

Methods

Thyroid nodule samples were obtained from a cohort of 359 patients who underwent FNA. An NGS-based multi-gene panel testing was conducted for these samples, in which single-nucleotide variants (SNVs) and small insertion/deletions (InDels) can be detected in 11 genes and fusion events can be identified in 5 genes. Surgical resection was conducted for 113 patients (113/359), and then histopathology results were obtained.

Results

In comparison to cytology alone, the diagnostic sensitivity of NGS combination cytology increased from 0.7245 (95% CI: 0.6289-0.8032) to 0.898 (95% CI: 0.8223-0.9437); the associated AUC was 0.8303 (vs. Cytology AUC: 0.7622, P < 0.001). BRAF V600E was identified in 136 patients, of whom 79 underwent surgery and were diagnosed with papillary thyroid carcinoma (PTC) pathologically. TERT promoter mutations or BRAF/RAS co-mutations with other genes were identified in 5 patients, while 4 patients were diagnosed with malignant thyroid cancer using the pathological method. RAS mutations were identified in 27 patients, while 10 patients underwent surgery, which showed that 3 patients were classified as PTC and 7 cases were benign. In addition, 4 RET fusions, 1 RET activation mutation, and 3 TP53 inactivation mutations were identified in the remaining 8 patients who have not undergone surgery. Negative genetic test results or variants with uncertain significance were identified in 183 patients. Among these patients, 12 malignant thyroid tumors, including 11 PTC and 1 MTC, were diagnosed in 20 patients who received surgery.

Conclusion

Thyroid nodules coupled with BRAF V600E, TERT promoter variants, BRAF/RAS co-mutations with other genes, RET fusions, and RET activating mutations were classified as high-risk. Nodules with RAS mutations (NRAS, KRAS, HRAS) and TP53 inactivating mutations were considered to be in the intermediate-risk group, while those with non-pathogenic mutations (negative and variants of uncertain significance) were placed in the low-risk group. When combined with cytopathology, NGS increases the sensitivity of diagnosing benign and malignant thyroid nodules, and the reference is useful for patient risk stratification.

ThyroSeq overview on indeterminate thyroid nodules: An institutional experience

BACKGROUND

Molecular triage of indeterminate thyroid aspirates offers the opportunity to stratify the risk of malignancy (ROM) more accurately. Here we examine our experience with ThyroSeq v3 testing.

METHODS

We analyzed 276 of 658 (42%) fine needle aspiration samples classified as indeterminate thyroid nodules using ThyroSeq v3 (Sept 2017-Dec 2019). The test provides a ROM and detects specific mutations. Surgical diagnoses were reviewed.

RESULTS

Of 276 ThyroSeq-tested cases, 42% (n = 116) harbored genetic alterations, whereas 64% (n = 74) had surgical follow-up. Notably, 79% cases within intermediate to higher risk mutations were highly associated with surgical intervention, resulting in a 77.5% ROM when including both cancer and noninvasive follicular thyroid neoplasia with papillary-like features (cancer+NIFTP) and 68% malignant diagnosis when excluding NIFTP. RAS-like alterations were most common (66%), exhibiting a 73.4% ROM and a 59% malignant diagnosis. Interestingly, this group included 24 encapsulated follicular variant papillary thyroid carcinomas (EFVPTCs), 1 infiltrative FVPTC, 9 follicular carcinomas, and 7 NIFTP. Additionally, three high-risk mutations and eight BRAF/V600E mutations had a 100% ROM, all diagnosed as classic-type papillary thyroid carcinoma (cPTC). Combined analysis of thyroid nodules from Bethesda III and IV categories revealed a 78.2% positive predictive value (PPV) and a 75.9% negative predictive value (NPV).

CONCLUSION

ThyroSeq v3 effectively stratifies the ROM in indeterminate thyroid nodules based on specific genetic alterations, guiding appropriate surgical management. Notably, the BRAFV600E/high-risk group and RAS-like groups exhibited ROM of 100% and 77.5%, respectively, with promising predictive accuracy (PPV of 78.2% and NPV of 75.9%).

Preoperative BRAFV600E mutation detection in thyroid carcinoma by immunocytochemistry

The BRAF^V600E (BRAF) mutation is present in 40-50% of papillary thyroid carcinomas (PTC) and has been associated with more aggressive clinicopathological characteristics of PTC. The aim of this study was to evaluate different methods for preoperative identification of the BRAF mutation in PTC using cytological and histological specimens. Prospectively collected preoperative cytological clots from patients with suspected PTC were tested with BRAF immunocytochemistry (ICC) and the Cobas Test (PCR). In addition, histological specimens were tested with BRAF immunohistochemistry (IHC) and the Cobas Test. All nodules were histologically examined. Fifty-three patients were included in the study. Complete mutation testing was available in 32 patients. The main reason for exclusion was insufficient cell content in the cytological specimen. Twenty-seven nodules were histologically diagnosed as PTC, and 41% (n = 11) of PTCs were BRAF ICC positive. All non-PTC nodules were negative by BRAF ICC. In 26 nodules, all four BRAF tests were concordant, while discordant test results were found in six nodules. ICC was in accordance with the consensus BRAF status in five of these nodules, while BRAF status was undetermined in one nodule. BRAF ICC showed high concordance with the Cobas Test and a low rate of false negative stain. These results indicate that BRAF ICC may be a feasible method for preoperative detection of the BRAF^V600E mutation in patients with PTC.

Construction and validation of BRAF mutation diagnostic model based on ultrasound examination and clinical features of patients with thyroid nodules

Introduction: Fine Needle Aspiration (FNA) is currently the most popular method for identifying benign and malignant thyroid nodules. However, its diagnostic sensitivity is sometimes limited, which makes it necessary to apply genetic testing and other modalities as a secondary diagnostic method. The diagnostic accuracy of thyroid nodule can be improved by combining mutations in the B-Raf proto-oncogene serine/threonine kinase (BRAF) with FNA. Thus, this study was conducted to create a nomogram diagnostic model based on the clinical and ultrasonic characteristics of patients with BRAF mutations to aid in the identification of benign and malignant thyroid nodules using FNA.

Methods: From April 2018 to December 2021, 275 patients with thyroid nodules who underwent ultrasonography and BRAF gene testing (137 positive and 138 negative) were included from Xianyang Central Hospital. The clinical and ultrasonic characteristics of the patients were used to develop a nomographic, diagnostic model of BRAF gene mutation, and to validate and evaluate the usefulness of the model.

Results: Independent risk factors for BRAF mutations included: focal strong echogenicity (microcalcifications, OR = 3.04, 95%CI = 1.41–6.58, p = 0.005), hypoechogenicity (OR = 3.8, 95%CI = 1.14–12.61, p = 0.029), lymph node metastases (OR = 3.54, 95%CI = 1.43–8.75, p = 0.006), margin (lobulated, OR = 3.7, 95%CI = 1.66–8.23, p = 0.001; extrathyroidal invasion, OR = 2.81, 95%CI = 1.11–7.06, p = 0.029), and shape (vertical position, OR = 2.7, 95%CI = 1.11–6.59, p = 0.029). The area under the curve (AUC) of the receiver operating characteristic (ROC) curve of the BRAF mutation diagnostic model constructed on these factors was 0.806 (95% CI = 0.754–0.851), and 39.5% was set as the threshold probability of making a clinical decision. The results of the validation and clinical utility evaluation showed that our model had good predictive performance and clinical application value.

Conclusion: Our nomogram diagnostic model based on clinical and ultrasound features of patients accurately predicted the possibility of BRAF gene mutations in patients with thyroid nodules.

Clinicopathologic features of thyroid nodules with PTEN mutations on preoperative testing

The incidence of cancer in thyroid nodules carrying germline or somatic phosphatase and tensin homolog (PTEN) mutations is not well-defined. This study characterizes the clinical and histopathologic features of thyroid nodules with preoperatively detected PTEN mutations and their impact on management. Thyroid nodules with PTEN mutations on molecular testing of fine-needle aspiration (FNA) specimens from November 2017 to July 2020 at our institution were included. Demographic and clinicopathologic data were obtained through retrospective chart review. We identified 49 PTEN mutation-positive nodules from 48 patients. Surveillance was pursued for 28 patients and surgery for 20 patients. There were 14 follicular adenomas (FA), 4 oncocytic adenomas, 1 oncocytic hyperplastic nodule, and 1 encapsulated follicular variant papillary thyroid carcinoma (EFVPTC). The EFVPTC had two somatic PTEN mutations, an NRAS mutation, and was a low-risk tumor with capsular but no angiolymphatic invasion. Four patients, all with multiple nodules, had PTEN hamartoma syndrome (PHTS) with germline mutations or a clinical diagnosis of Cowden syndrome (CS); two had surgery finding FAs, and one previously had follicular carcinoma removed. Among surveillance patients, 1/20 had a significant increase in the size of the thyroid nodule and underwent repeat FNA, and no thyroid malignancy was found with a mean of 1.77 years of follow-up (range 1.00-2.78). Thyroid nodules with isolated somatic PTEN mutations are primarily benign and unlikely to grow at a high rate, at least on short-term follow-up. About 8% of patients with PTEN mutations may have PHTS or CS, which should be suspected in younger patients with multiple thyroid nodules.

Molecular Testing for Thyroid Nodules: The Experience at McGill University Teaching Hospitals in Canada

In the past few decades, molecular characterization of thyroid cancer has made significant progress and is able to identify thyroid-cancer-related molecular markers that can then be applied clinically for improved decision making. The aim of this review is to provide a general overview about the molecular markers (mutations and alterations) of thyroid cancers, present several molecular tests, and discuss the clinical applications of identifying these markers supported by the clinical experience of several high-volume thyroid cancer specialists at the McGill university hospitals in Montreal, Canada. Our group experience showed that molecular testing can reclassify more than half of the patients with indeterminate thyroid nodules (Bethesda III and IV) into benign and spare these patients from unnecessary diagnostic surgery. Furthermore, it can help optimize the initial management in thyroid cancers with no evidence of high risk of recurrence of disease preoperatively. While routine molecular testing is not firmly established for thyroid FNA specimens that are suspicious or positive for malignancy (Bethesda V and VI), knowledge of a thyroid nodule’s molecular risk group profile in such cases, together with its clinical and radiologic features, can help select the optimal surgical options (lobectomy versus upfront total thyroidectomy and central neck dissection), as demonstrated by our studies.

The application value of CDFI and SMI combined with serological markers in distinguishing benign and malignant thyroid nodules

PURPOSE

The purpose of this study is to explore the application value of CDFI and SMI combined with serological markers in distinguishing benign and malignant thyroid nodules.

METHOD

A total of 192 patients with thyroid nodules admitted to our hospital from July 2019 to December 2020 were selected as subjects. Color Doppler blood flow imaging (CDFI) and supermicro blood flow imaging (SMI) methods are used to detect the blood flow of patients and the levels of serum thyroglobulin antibody (TgAb), thyroid peroxidase antibody (TPOAb), and thyroid stimulating hormone (TSH). The receiver operating characteristic curve (ROC curve) was used to observe the sensitivity and specificity of serological markers for distinguishing benign and malignant thyroid nodules, and combined with CDFI and SMI to observe the sensitivity and specificity for distinguishing benign and malignant thyroid nodules.

RESULTS

The levels of TgAb, TPOAb and TSH in benign thyroid nodules were lower than those of the malignant group, and the difference was statistically significant (P < 0.01). There was no statistically significant difference between benign and malignant thyroid nodules in the presence or absence of the capsule and the presence or absence of vocal halo (P > 0.05), while the differences in the nodule morphology, boundary, internal echo and internal calcification were statistically significant (P < 0.01).

CONCLUSION

CDFI and SMI combined with serological index detection have higher value in the differential diagnosis of thyroid cancer, which can significantly improve the sensitivity and specificity of differential diagnosis.

The Autoantibodies against Tumor-Associated Antigens as Potential Blood-Based Biomarkers in Thyroid Neoplasia: Rationales, Opportunities and Challenges

The Autoantibodies targeting Tumor-Associated Antigens (TAA-AAbs) emerge as a result of a variety of tumor-related immunogenic stimuli and may be regarded as the eyewitnesses to the anti-tumor immune response. TAA-AAbs may be readily detected in peripheral blood to unveil the presence of a particular TAA-expressing tumor, and a fair number of TAAs eliciting the tumor-associated autoantibody response have been identified. The potential of TAA-AAbs as tumor biomarkers has been extensively studied in many human malignancies with a major influence on public health; however, tumors of the endocrine system, and, in particular, the well-differentiated follicular cell-derived thyroid neoplasms, remain understudied in this context. This review provides a detailed perspective on and legitimate rationales for the potential use of TAA-AAbs in thyroid neoplasia, with particular reference to the already established diagnostic implications of the TAA-AAbs in human cancer, to the windows for improvement and diagnostic niches in the current workup strategies in nodular thyroid disease and differentiated thyroid cancer that TAA-AAbs may successfully occupy, as well as to the proof-of-concept studies demonstrating the usefulness of TAA-AAbs in thyroid oncology, particularly for the pre-surgical discrimination between tumors of different malignant potential in the context of the indeterminate results of the fine-needle aspiration cytology.

Gene expression profile in functioning and non-functioning nodules of autonomous multinodular goiter from an area of iodine deficiency: unexpected common characteristics between the two entities

PURPOSE

Toxic multinodular goiter is a heterogeneous disease associated with hyperthyroidism frequently detected in areas with deficient iodine intake, and functioning and non-functioning nodules, characterized by increased proliferation but opposite functional activity, may coexist in the same gland. To understand the distinct molecular pathology of each entity present in the same gland, the gene expression profile was evaluated by using the Affymetrix technology.

METHODS

Total RNA was extracted from nodular and healthy tissues of two patients and double-strand cDNA was synthesized. Biotinylated cRNA was obtained and, after chemical fragmentation, was hybridized on U133A and B arrays. Each array was stained and the acquired images were analyzed to obtain the expression levels of the transcripts. Both functioning and non-functioning nodules were compared versus healthy tissue of the corresponding patient.

RESULTS

About 16% of genes were modulated in functioning nodules, while in non-functioning nodules only 9% of genes were modulated with respect to the healthy tissue. In functioning nodules of both patients and up-regulation of cyclin D1 and cyclin-dependent kinase inhibitor 1 was observed, suggesting the presence of a possible feedback control of proliferation. Complement components C1s, C7 and C3 were down-regulated in both types of nodules, suggesting a silencing of the innate immune response. Cellular fibronectin precursor was up-regulated in both functioning nodules suggesting a possible increase of endothelial cells. Finally, Frizzled-1 was down-regulated only in functioning nodules, suggesting a role of Wnt signaling pathway in the proliferation and differentiation of these tumors. None of the thyroid-specific gene was deregulated in microarray analysis.

CONCLUSION

In conclusion, the main finding from our data is a similar modulation for both kinds of nodules in genes possibly implicated in thyroid growth.

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.

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.

Prediction of thyroid nodule histopathology by expert ultrasound evaluation

OBJECTIVE

The basis of thyroid nodule diagnostics is ultrasound-guided fine needle biopsy with cytological evaluation (FNC) if ultrasound appearance is not clearly benign. The aim of this study was to investigate the predictive potential of dedicated, expert high-resolution ultrasound, to see if histopathological entities of thyroid nodules can be diagnosed without invasive FNC biopsies.

DESIGN

Prospective case-cohort study.

METHODS

187 patients with 221 thyroid nodules were examined with ultrasound and prospectively assigned to the expected histopathological diagnosis: colloid nodule, adenomatoid colloid nodule, follicular adenoma, follicular carcinoma, follicular variant of papillary thyroid carcinoma, papillary thyroid carcinoma, or other thyroid cancer. In 101 of these, we later obtained histopathological reports for comparison.

RESULTS

Overall accuracy for classification into discrete histopathological categories by expert ultrasound was 71.3% and Cohen's Kappa was 0.62. The sensitivity and specificity for detecting malignancy were 97.3% and 78.1%. The diagnostic accuracy for malignancy was 85.1%. ACR-TIRADS scores for the same nodules had a sensitivity of 97.3%, specificity of 26.6%, and accuracy of 52.5%.

CONCLUSION

Dedicated expert high-resolution ultrasound without FNC can reliably distinguish benign vs malignant nodules, but also differentiate between several histopathological entities in thyroid nodules. There is potential for a reduction in the number of invasive FNC biopsies and diagnostic operations.

Atypical de Quervain's thyroiditis diagnosed as atypia of undetermined significance by cytology and suspicious for cancer by Afirma Genomic Sequencing Classifier

We report a case of atypical de Quervain's thyroiditis diagnosed as atypia of undetermined significance by cytology and suspicious for cancer by Afirma Genomic Sequencing Classifier. A 71-year-old male underwent thyroid ultrasound for goiter and was found to have two American Thyroid Association (ATA) 2015 high-suspicion nodules. The larger, 2.2-cm nodule was biopsied and the cytology showed atypical follicular cells and histiocytes. The Afirma Genomic Sequencing Classifier (detecting mRNA expression profile) result was ''suspicious'' (risk of malignancy ~50%) but Afirma Xpression Atlas (detecting specific mutations) did not find mutations in BRAF V600E, RET/PTC1, or RET/PTC3. The patient saw two endocrine surgeons and two endocrinologists who each recommended hemithyroidectomy. The patient chose to monitor the nodules. A new diagnostic ultrasound performed 3 months after the first one showed that the thyroid was significantly smaller and the previously seen nodules were no longer found. Re-examination of the cellular smears confirmed that the cytological findings were also compatible with de Quervain's thyroiditis. This case illustrates that atypical de Quervain's thyroiditis should be in the differential diagnosis of thyroid nodules for cytologists, radiologists, and clinicians. Furthermore, this case demonstrates that atypical de Quervain's thyroiditis can generate false positive results of molecular tests for indeterminate thyroid nodules.

Machine Learning by Ultrasonography for Genetic Risk Stratification of Thyroid Nodules

Importance

Thyroid nodules are common incidental findings. Ultrasonography and molecular testing can be used to assess risk of malignant neoplasm.

Objective

To examine whether a model developed through automated machine learning can stratify thyroid nodules as high or low genetic risk by ultrasonography imaging alone compared with stratification by molecular testing for high- and low-risk mutations.

Design, Setting, and Participants

This diagnostic study was conducted at a single tertiary care urban academic institution and included patients (n = 121) who underwent ultrasonography and molecular testing for thyroid nodules from January 1, 2017, through August 1, 2018. Nodules were classified as high risk or low risk on the basis of results of an institutional molecular testing panel for thyroid risk genes. All thyroid nodules that underwent genetic sequencing for cytological results with Bethesda System categories III and IV were reviewed. Patients without diagnostic ultrasonographic images within 6 months of fine-needle aspiration or who received definitive treatment at an outside medical center were excluded.

Main Outcomes and Measures

Thyroid nodules were categorized by the model as high risk or low risk using ultrasonographic images. Results were compared using genetic testing.

Results

Among the 134 lesions identified in 121 patients (mean [SD] age, 55.7 [14.2] years; 102 women [84.3%]), 683 diagnostic ultrasonographic images were selected. Of the 683 images, 556 (81.4%) were used for training the model, 74 (10.8%) for validation, and 53 (7.8%) for testing. Most nodules had no mutation (75 [56.0%]), whereas 43 nodules (32.1%) had a high-risk mutation and 16 (11.9%) had an unknown or a low-risk mutation (χ2 = 39.060; P < .001). In total, 228 images (33.4%) were of nodules classified as genetically high risk (n = 43), and 455 (66.6%) were of low-risk nodules (n = 91). The model performed with a sensitivity of 45% (95% CI, 23.1%-68.5%), a specificity of 97% (95% CI, 84.2%-99.9%), a positive predictive value of 90% (95% CI, 55.2%-98.5%), a negative predictive value of 74.4% (95% CI, 66.1%-81.3%), and an overall accuracy of 77.4% (95% CI, 63.8%-97.7%).

Conclusions and Relevance

The study found that the model developed through automated machine learning could produce high specificity for identifying nodules with high-risk mutations on molecular testing. This finding shows promise for the diagnostic applications of machine learning interpretation of sonographic imaging of indeterminate thyroid nodules.

ThyroSeq v3 for Bethesda III and IV: An institutional experience

BACKGROUND

The ThyroSeq v3 genomic classifier is a commercial molecular test that examines a wide spectrum of genomic alterations in a thyroid fine-needle aspiration (FNA) sample and reports test results as either negative or positive. The authors report their institutional experience with ThyroSeq v3.

METHODS

Thyroid FNA specimens diagnosed as either atypia of undetermined significance or follicular lesion of undetermined significance (AUS/FLUS) (Bethesda category III [Bethesda III] according to The Bethesda System for Reporting Thyroid Cytopathology) or follicular neoplasm/suspicious for follicular neoplasm (FN/SFN) (Bethesda IV) that had ThyroSeq v3 results available from December 2017 through October 2019 were retrieved for analysis. FNA diagnoses were correlated with ThyroSeq v3 results and follow-up histopathology.

RESULTS

In total, 415 cases (AUS/FLUS, n = 251; FN/SFN, n = 164) were retrieved: 294 (71%) were reported as ThyroSeq v3-negative, and 121 (29%) were reported as ThyroSeq v3-positive. The benign call rate (BCR) of ThyroSeq v3 for AUS/FLUS (82%; 206 of 251 cases) was significantly higher (P < .001) than that for FN/SFN (BCR, 54%; 88 of 164 cases). Histopathologic follow-up was available for 127 cases (ThyroSeq v3-positive, 96; ThyroSeq v3-negative, 31), of which 57 were benign and 70 were malignant (including noninvasive follicular thyroid neoplasm with papillary-like nuclear features). The negative predictive value of ThyroSeq v3 was significantly higher for AUS/FLUS (99.5%) than for FN/SFN (95.4%; P < .0294), given malignancy rates of 10% for AUS/FLUS and 30% for FN/SFN. Forty-five unique combinations of genetic alterations were detected in the operated ThyroSeq-positive cases, and there were only 5 false-negative cases, comprised of 4 low-risk neoplasms.

CONCLUSIONS

The high BCR of ThyroSeq v3 for AUS/FLUS prevents surgery in a majority of patients. The ThyroSeq v3 genomic classifier reveals the complexity of the genetic signature of indeterminate nodules.

Utility of a multigene testing for preoperative evaluation of indeterminate thyroid nodules: A prospective blinded single center study in China

Background

Thyroid nodules are highly prevalent, with fine‐needle aspiration (FNA) commonly used as the standard preoperative tool for their diagnosis. However, the method classifies some of the samples as indeterminate, leading to unnecessary surgery. In this study, we evaluated the value of next‐generation sequencing (NGS) for cancer diagnosis in indeterminate thyroid nodules.

Materials and methods

We performed a prospective, blinded cohort study on 189 patients, with 196 Bethesda III/IV nodules. Specifically, we analyzed DNA mutations and RNA fusions across the FNA samples using NGS, then reviewed follow‐up reports from 84 nodules following definitive surgery, to determine the assay performance.

Results

Enough DNA and RNA were obtained in 188 nodules, revealing mutations or fusions in 34.6% of them. The most frequently mutated genes were RAS, followed by BRAF V600E. Based on surgical pathology, 39% (33/84) and 4.8% (4/84) of the nodules were malignant and intermediate, respectively. According to the risk stratification criteria, 28 cases were categorized High‐Risk group, all of the resected nodules (n = 20) were malignant. Twenty‐four thyroid nodules were in the Low‐Risk group, 28.6% (4/14) surgically removed nodules were malignant. In the Benign‐Like category, 18.0% (9/50) were malignant. Five out of 13 nodules with benign mutations were resected, including SPOP, EZH1, and ZNF148, all of them were benign. If genetic alterations annotated with High‐Risk or Low‐Risk was considered as positive, and negative if Benign‐Like. Multigene testing revealed sensitivity, specificity, positive predictive values (PPV), and negative predictive value (NPV) of 73%, 80%, 71%, and 82%, respectively. In addition, if four intermediate nodules were counted as malignant, the PPV and NPV were 71% and 74%.

Conclusion

Our results allow for further stratification of Bethesda III/IV thyroid nodules based on the risk of their malignancy. SPOP, EZH1, and ZNF148 mutations may be used as benign markers.

EIF1AX c.338-2A>T splice site mutation in a patient with trabecular adenoma and cytological indeterminate lesion

The EIF1AX gene mutations have been recently associated with papillary thyroid carcinoma and anaplastic thyroid cancer. According with these reports, the gene as been considered as a drive gene for thyroid cancer development. However, the occurrence of these alterations in benign thyroid lesions is not known and is still under investigation. Some authors have already reported the presence of EIF1AX variants in follicular adenomas and hyperplastic nodules. Here, we describe for the first time a case of a man with the EIF1AX c.338-2A>T splice site mutation in an indeterminate FNA lesion with trabecular adenoma at final histology in the absence of other pathogenetic mutations, demonstrating that further studies are required to better understand EIF1AX role in the tumorigenesis of thyroid carcinoma.

Real-world Comparison of Afirma GEC and GSC for the Assessment of Cytologically Indeterminate Thyroid Nodules

CONTEXT

Molecular tests have improved the accuracy of preoperative diagnosis of indeterminate thyroid nodules. The Afirma Gene Sequencing Classifier (GSC) was developed to improve the specificity of the Gene Expression Classifier (GEC). Independent studies are needed to assess the performance of GSC.

OBJECTIVE

The aim was to compare the performance of GEC and GSC in the assessment of indeterminate nodules.

DESIGN, SETTINGS, AND PARTICIPANTS

Retrospective analysis of Bethesda III and IV nodules tested with GEC or GSC in an academic center between December 2011 and September 2018. Benign call rates (BCRs) and surgical outcomes were compared. Histopathologic data were collected on nodules that were surgically resected to calculate measures of test performance.

RESULTS

The BCR was 41% (73/178) for GEC and 67.8% (82/121) for GSC (P < .001). Among specimens with dominant Hürthle cell cytology, the BCR was 22% (6/27) for GEC and 63.2% (12/19) for GSC (P = .005). The overall surgery rate decreased from 47.8% in the GEC group to 34.7% in the GSC group (P = .025). One GEC-benign and 3 GSC-benign nodules proved to be malignant on surgical excision. GSC had a statistically significant higher specificity (94% vs 60%, P < .001) and positive predictive value (PPV) (85.3% vs 40%, P < .001) than GEC. While sensitivity and negative predictive value (NPV) dropped with GSC (97.0% vs 90.6% and 98.6% vs 96.3%, respectively), these differences were not significant.

CONCLUSIONS

GSC reclassified more indeterminate nodules as benign and improved the specificity and PPV of the test. These enhancements appear to be resulting in fewer diagnostic surgeries.

Diagnostic accuracy of molecular testing with three molecular markers on thyroid fine-needle aspiration cytology with abnormal category

BACKGROUND

Cases with abnormal category, determined by thyroid fine-needle aspiration (FNA), frequently undergo surgical resection, despite the majority of cases being identified as benign after resection. Additional diagnostic markers are needed to guide the management of patients with abnormal thyroid nodules.

MATERIALS AND METHODS

The retrospective study enrolled 150 cases diagnosed abnormal by FNA cytology that had undergone molecular testing with three markers (BRAF V600E, NRAS, and KRAS) on the cell block. Seventy-one cases had a surgical follow-up.

RESULTS

When NIFTP is not considered as malignant, positive predictive values (PPVs) of cytology and combined cytology and molecular testing (CC-MT) were 67.6% (95% CI: 0.555-0.782) and 89.2% (95% CI: 0.746-0.970) (P = .004), respectively. The sensitivity of the CC-MT was 68.8%, specificity was 82.5%, and the false-positive rate was 17.4%. When NIFTP is considered as malignant, PPVs of cytology and CC-MT were 83.1% (95% CI: 0.743-0.918) and 94.6% (95% CI: 0.873-1.018) (P = .047), respectively. The sensitivity of the CC-MT was 59.3%, specificity was 83.3%, and the false-positive rate was 16.7%.

CONCLUSION

The addition of molecular testing with a small panel to FNA cytology may increase the PPV of cytology in abnormal categories. Small panel (BRAF V600E, KRAS, and NRAS) with high specificity and high PPVs may be used particularly for the detection of thyroid malignancy. Cell blocks can be an especially useful and straightforward method for molecular diagnostic studies.

Thyroid Nodule Molecular Testing: Is It Ready for Prime Time?

Cytologically indeterminate thyroid nodules remain a diagnostic and clinical challenge, and molecular testing has been advocated and advanced as a diagnostic modality to help guide treatment. While studies have expounded on the improved diagnostic certainty with these tests, data demonstrating meaningful clinical impact and supporting their routine use is still limited at best. In this review, we discuss the limitations regarding diagnostic accuracy, impact on surgical decision-making and outcomes, and cost-effectiveness of molecular testing. By highlighting the limitations of these tests, we aim to promote more thoughtful utilization of these tools in the management of thyroid nodules going forward.

MALDI-MSI as a Complementary Diagnostic Tool in Cytopathology: A Pilot Study for the Characterization of Thyroid Nodules

The present study applies for the first time as Matrix-Assisted Laser Desorption/Ionization (MALDI) Mass Spectrometry Imaging (MSI) on real thyroid Fine Needle Aspirations (FNAs) to test its possible complementary role in routine cytology in the diagnosis of thyroid nodules. The primary aim is to evaluate the potential employment of MALDI-MSI in cytopathology, using challenging samples such as needle washes. Firstly, we designed a statistical model based on the analysis of Regions of Interest (ROIs), according to the morphological triage performed by the pathologist. Successively, the capability of the model to predict the classification of the FNAs was validated in a different group of patients on ROI and pixel-by-pixel approach. Results are very promising and highlight the possibility to introduce MALDI-MSI as a complementary tool for the diagnostic characterization of thyroid nodules.