A comparison of ARMS and DNA sequencing for mutation analysis in clinical biopsy samples

Highly Sensitive Detection of T790 M with a Three-Level Characteristic Current by Thymine-Hg(II)-Thymine in the α-Hemolysin Nanopore

Sensitive detection of resistance mutation T790 M is of great significance for early diagnosis and prognostic monitoring of non-small-cell lung cancer (NSCLC). In this paper, we showed a highly sensitive detection strategy for T790 M using a three-level characteristic current signal pattern in an α-hemolysin nanopore. A probe was designed that formed a C-T mismatched base pair with wild-type/P and a T-T mismatched with the T790M/P. The T790M/P produced a unique three-level characteristic current signal in the presence of mercury ions(II): first, T790M-Hg2+-P entering the vestibule of α-HL under the transmembrane potential and overhang of probe occupying the β-barrel, then probe unzipping from the T790M/P, T790 M temporally residing inside the nanocavity due to the interaction with Hg(II), and finally T790 M passing through the β-barrel. The blocking current distribution was concentrated with a small relative standard deviation of about 3%, and the signal peaks of T790 M and wild-type can be completely separated with a high separation resolution of more than 2.5, which achieved the highly sensitive detection of T790 M down to 0.001 pM (confidence level P 95%) with a linear range from 0.001 pM to 1 nM in human serum samples. This highly sensitive recognition strategy enables the detection of low abundance T790 M and provides a method for prognostic monitoring in NSCLC patients.

US of thyroid nodules: can AI-assisted diagnostic system compete with fine needle aspiration?

OBJECTIVES

Artificial intelligence (AI) systems can diagnose thyroid nodules with similar or better performance than radiologists. Little is known about how this performance compares with that achieved through fine needle aspiration (FNA). This study aims to compare the diagnostic yields of FNA cytopathology alone and combined with BRAFV600E mutation analysis and an AI diagnostic system.

METHODS

The ultrasound images of 637 thyroid nodules were collected in three hospitals. The diagnostic efficacies of an AI diagnostic system, FNA-based cytopathology, and BRAFV600E mutation analysis were evaluated in terms of sensitivity, specificity, accuracy, and the κ coefficient with respect to the gold standard, defined by postsurgical pathology and consistent benign outcomes from two combined FNA and mutation analysis examinations performed with a half-year interval.

RESULTS

The malignancy threshold for the AI system was selected according to the Youden index from a retrospective cohort of 346 nodules and then applied to a prospective cohort of 291 nodules. The combination of FNA cytopathology according to the Bethesda criteria and BRAFV600E mutation analysis showed no significant difference from the AI system in terms of accuracy for either cohort in our multicenter study. In addition, for 45 included indeterminate Bethesda category III and IV nodules, the accuracy, sensitivity, and specificity of the AI system were 84.44%, 95.45%, and 73.91%, respectively.

CONCLUSIONS

The AI diagnostic system showed similar diagnostic performance to FNA cytopathology combined with BRAFV600E mutation analysis. Given its advantages in terms of operability, time efficiency, non-invasiveness, and the wide availability of ultrasonography, it provides a new alternative for thyroid nodule diagnosis.

CLINICAL RELEVANCE STATEMENT

Thyroid ultrasonic artificial intelligence shows statistically equivalent performance for thyroid nodule diagnosis to FNA cytopathology combined with BRAFV600E mutation analysis. It can be widely applied in hospitals and clinics to assist radiologists in thyroid nodule screening and is expected to reduce the need for relatively invasive FNA biopsies.

KEY POINTS

• In a retrospective cohort of 346 nodules, the evaluated artificial intelligence (AI) system did not significantly differ from fine needle aspiration (FNA) cytopathology alone and combined with gene mutation analysis in accuracy. • In a prospective multicenter cohort of 291 nodules, the accuracy of the AI diagnostic system was not significantly different from that of FNA cytopathology either alone or combined with gene mutation analysis. • For 45 indeterminate Bethesda category III and IV nodules, the AI system did not perform significantly differently from BRAFV600E mutation analysis.

Expression of RASSF1A, DIRAS3, and AKAP9 Genes in Thyroid Lesions: Implications for Differential Diagnosis and Prognosis of Thyroid Carcinomas

Thyroid carcinoma is the primary endocrine malignancy worldwide. The preoperative examination of thyroid tissue lesion is often unclear. Approximately 25% of thyroid cancers cannot be diagnosed definitively without post-surgery histopathological examination. The assessment of diagnostic and differential markers of thyroid cancers is needed to improve preoperative diagnosis and reduce unnecessary treatments. Here, we assessed the expression of RASSF1A, DIRAS3, and AKAP9 genes, and the presence of BRAF V600E point mutation in benign and malignant thyroid lesions in a Polish cohort (120 patients). We have also performed a comparative analysis of gene expression using data obtained from the Gene Expression Omnibus (GEO) database (307 samples). The expression of RASSF1A and DIRAS3 was decreased, whereas AKAP9's was increased in pathologically changed thyroid compared with normal thyroid tissue, and significantly correlated with e.g., histopathological type of lesion papillary thyroid cancer (PTC) vs follicular thyroid cancer (FTC), patient's age, tumour stage, or its encapsulation. The receiver operating characteristic (ROC) analysis for the more aggressive FTC subtype differential marker suggests value in estimating RASSF1A and AKAP9 expression, with their area under curve (AUC), specificity, and sensitivity at 0.743 (95% CI: 0.548-0.938), 82.2%, and 66.7%; for RASSF1A, and 0.848 (95% CI: 0.698-0.998), 54.8%, and 100%, for AKAP9. Our research gives new insight into the basis of the aggressiveness and progression of thyroid cancers, and provides information on potential differential markers that may improve preoperative diagnosis.

Tweezer PCR: A Highly Specific Method for Accurate Identification of Low-Abundance Mutations

Somatic mutation is a valuable biomarker for tracking tumor progression and migration due to its distinctive feature in various tumors and its wide distribution throughout body fluids. However, accurately detecting somatic mutations from the abundant DNA of noncancerous origins remains a practical challenge in the clinic. Herein, we developed an ultraspecific method, called tweezer PCR, for detecting low-abundance mutations inspired by the design of DNA origami. The high specificity of tweezer PCR relies on a tweezer-shaped primer containing six basic functional units: a primer, a hairpin, a linker, a blocker, a spacer, and a toehold. After optimizing the structure of the tweezer-shaped primer and enhancing its specificity by adding additional Mg2+ and Na+, tweezer PCR distinguished as low as 20 copies of mutations from 2 million copies of wild-type templates per test. By testing synthesized plasmids and plasma samples gathered from nonsmall-cell lung cancer patients, tweezer PCR showed higher specificity and robustness for detecting low-copy-number mutations in contrast with digital droplet PCR. Additionally, the need for conventional instruments makes tweezer PCR a practically accessible method for testing low-abundance mutations. Because of its numerous advantages, we believe that tweezer PCR offers a precise, robust, and pragmatic tool for cancer screening, prognosis, and genotyping in the clinic.

Successful treatment of lung adenocarcinoma complicated with a rare compound EGFR mutation L833V/H835L using aumolertinib: a case report and literature review

Background: The deletion of exon 19 and the Leu858Arg mutation of exon 21 are the most frequently observed mutations in the epidermal growth factor receptor (EGFR) gene, and patients with these mutations have shown significant benefits from EGFR-tyrosine kinase inhibitors (TKIs). However, there exists a small subgroup of patients with uncommon/rare mutations of EGFR, including compound mutations, which display a high degree of heterogeneity in terms of clinical features and variable sensitivities to EGFR-TKIs. The understanding of these uncommon mutations and their response to targeted therapy is still unclear and requires further investigation. Case presentation: We presented a case of a never-smoking patient with lung adenocarcinoma and brain metastasis. Initially, she received chemotherapy plus immune checkpoint inhibitor as first-line therapy as no EGFR mutations were detected by amplification-refractory mutation system-polymerase chain reaction. However, disease progressed rapidly. Subsequently, next-generation sequencing was carried out and revealed a rare compound mutation, L833V/H835L, in exon 21 of EGFR. As a result, she was switched to second-line therapy with the third-generation TKI aumolertinib, which demonstrated good efficacy. The patient was evaluated for a remarkable progression-free survival of 18 months and an overall survival of 29 months. Conclusion: The present study supports that aumolertinib might be a good treatment option for advanced NSCLC patients with EGFR L833V/H835L mutation, particularly in patients with brain metastasis. Furthermore, conducting a comprehensive screening for gene mutations is crucial in effectively identifying potential oncogenic driver mutations and guiding mutation-targeted therapy decisions in clinical practice.

A multiparametric fluorescent visualization approach for detecting drug resistance in living cancer cells

Drug resistance is a worldwide health care crisis which impedes disease treatment and increases financial burden, especially for its multifactorial nature and high complexity. Herein, we developed a multiparametric approach to visualize and detect drug resistance in living cancer cells, through the combination of DNA-templated covalent protein labeling strategy and fluorescent resonance energy transfer technique. Gefitinib resistance in non-small cell lung cancer caused by mesenchymal-epidermal transition factor (Met) overexpression and hyperactivation was investigated as a proof-of-concept. Unlike the traditional single-factor investigation, the proposed approach evaluated the contribution of three important parameters towards the resistance, including the changes of Met expression level, the homodimerization of Met with itself and the heterodimerization of Met with epidermal growth factor receptor (EGFR). A multiple regression model based on these three parameters was tentatively established for evaluation of the resistance level of laboratory-developed resistant cells and evaluation of the resistance level of patient-derived cells. Such an approach facilitates a quick identification of a drug resistance, to evaluate not only the resistance level but also the resistance mechanism.

Diagnostic Efficacy of Ultrasound, Cytology, and BRAFV600E Mutation Analysis and Their Combined Use in Thyroid Nodule Screening for Papillary Thyroid Microcarcinoma

Background

Ultrasound, cytology, and BRAF^V600E mutation analysis were applied as valuable tools in the differential diagnosis of thyroid nodules. The aim of the present study was to evaluate the diagnostic efficiency of the three methods and their combined use in screening for papillary thyroid microcarcinoma (PTMC).

Methods

A total of 1,081 patients with 1,157 thyroid nodules (0.5–1 cm in maximum diameter) classified as thyroid imaging reporting and data system (TIRADS) 4–5 were recruited. All patients underwent ultrasound, fine-needle aspiration (FNA) examination, and an additional BRAF^V600E mutation test. TIRADS and Bethesda System for Reporting Thyroid Cytopathology (BSRTC) were adopted to judge the ultrasound and cytological results. The receiver operating characteristic (ROC) curve was established to assess the diagnostic values of different methods.

Results

Of the 1,157 nodules, 587 were benign and 570 were PTMCs. BRAF^V600E mutation test had highest sensitivity (85.4%), specificity (97.1%), accuracy (91.4%), and area under the ROC curve (Az) value (0.913) among the three methods. The combination of BSRTC and BRAF^V600E mutation analysis yielded a considerably high sensitivity (96.0%), accuracy (94.3%), and negative predictive value (95.9%) than either BSRTC or BRAF^V600E mutation alone (P < 0.0001 for all comparisons). Of all the methods, the combined use of the three methods produced the best diagnostic performance (Az = 0.967), which was significantly higher than that (Az = 0.943) for the combination of BSRTC and BRAF^V600E mutation (P < 0.0001). The diagnostic accuracy of the molecular method in the 121 nodules with indeterminate cytology was 90.1% (109/121), which was significantly higher than that of TIRADS classification, 74.4% (90/121) (P = 0.002).

Conclusion

The combined use of ultrasound, cytology, and BRAF^V600E mutation analysis is the most efficient and objective method for diagnosing PTMC. Both BRAF^V600E mutation and TIRADS classification are potentially useful adjuncts to differentiate thyroid nodules, especially indeterminate samples classified as BSRTC III.

Sensitive detection of T790M mutations in lung cancer biopsies using a PCR-based lateral flow assay

T790 M point mutations in EGFR exon 20 are regarded as the most common cause of resistance to epidermal growth factor receptor tyrosine kinase inhibitor treatment. In this study, a PCR-based lateral flow assay (PCR-LFA) was developed to detect T790 M mutations in human genomic DNA. Detection sensitivity was determined using DNA at different mutant to wild-type ratios. The limit of detection of mutant alleles was 15 copies per reaction. The sensitivity of detection of these mutations in 40 formalin-fixed paraffin-embedded tissue biopsies from non-small cell lung cancer patients was analyzed using PCR-LFA and amplification refractory mutation system (ARMS) PCR. Our assay provided the same information as ARMS PCR for 95% (38/40) of the samples. T790 M mutations were detected in 15 (37.5%) and 13 samples using our assay and ARMS PCR, respectively. Droplet digital PCR confirmed the presence of T790 M mutations in the two discordant samples. These results indicate that PCR-LFA is more sensitive than ARMS PCR for clinical screening of these mutations.

The Prognostic Implication of the BRAF V600E Mutation in Papillary Thyroid Cancer in a Chinese Population

BACKGROUND

The BRAF V600E mutation is an important genetic event in papillary thyroid cancer (PTC). This study aimed to provide additional information regarding the association of the BRAF V600E mutation with PTC prognosis.

METHODS

A retrospective single-center study based on a Chinese population was performed to analyze the association of the BRAF V600E mutation with several clinicopathological features. Kaplan-Meier survival curves and Cox proportional hazards regression analysis were applied to implement the survival analysis.

RESULTS

The BRAF V600E mutation was present in 1102 (87.7%) of the 1257 patients and was significantly associated with older age, conventional subtype, multifocality, advanced TNM stage, and a reduced prevalence of Hashimoto's thyroiditis. The Kaplan-Meier survival curves demonstrated that the difference between the BRAF V600E-positive and BRAF V600E-negative groups was significant with a log-rank P-value of 0.048. The Cox proportional hazards regression analysis adjusted HR was 3.731 (95% CI, 1.457 to 9.554). We further demonstrated that larger tumor size (>1 cm), extrathyroidal extension (ETE), and lateral lymph node metastasis (LNM) were associated with a higher probability of PTC recurrence in patients harboring the BRAF V600E mutation.

CONCLUSIONS

The BRAF V600E mutation remains an independent risk factor for PTC recurrence and may be useful for clinical decisions when it combines with some pathological factors.

Recent advances in lung cancer genomics: Application in targeted therapy

Genomic characterization of lung cancer has not only improved our understanding of disease biology and carcinogenesis but also revealed several therapeutic opportunities. Targeting tumor dependencies on specific genomic alterations (oncogene addiction) has accelerated the therapeutic developments and significantly improved the outcomes even in advanced stage of disease. Identification of genomic alterations predicting response to specific targeted treatment is the key to success for this "personalized treatment" approach. Availability of multiple choices of therapeutic options for specific genomic alterations highlight the importance of optimum sequencing of drugs. Multiplex gene testing has become mandatory in view of constantly increasing number of therapeutic targets and effective treatment options. Influence of genomic characteristics on response to immunotherapy further makes comprehensive genomic profiling necessary before therapeutic decision making. A comprehensive elucidation of resistance mechanisms and directed treatments have made the continuum of care possible and transformed this deadly disease into a chronic condition. Liquid biopsy-based approach has made the dynamic monitoring of disease possible and enabled treatment optimizations accordingly. Current lung cancer management is the perfect example of "precision-medicine" in clinical oncology.

The expanding capability and clinical relevance of molecular diagnostic technology to identify and evaluate EGFR mutations in advanced/metastatic NSCLC

Epidermal growth factor receptor (EGFR) mutation testing in advanced non-small-cell lung cancer (NSCLC) has evolved rapidly over the past decade, largely triggered by the introduction of the targeted EGFR tyrosine kinase inhibitors (TKIs). Initially used to detect common EGFR mutations and determine the most appropriate first-line therapy at diagnosis, testing methodologies have expanded to test for multiple mutations at multiple time points throughout the disease course. Here we review the current mutation testing approaches, including types of biopsies, and the available assays commonly used in the clinic. Specific application of these approaches in advanced NSCLC, including current guideline recommendations, and potential future developments are discussed.

Multigene Combined Detection by RT-qPCR Using Cytological Specimens

OBJECTIVE

The aim of the study was to investigate the mutation status of multiple driver genes by RT-qPCR and their significance in advanced lung adenocarcinoma using cytological specimens.

MATERIALS AND METHODS

155 cytological specimens that had been diagnosed with lung adenocarcinoma in the Fourth Hospital of Hebei Medical University were selected from April to November 2019. The cytological specimens included serous cavity effusion and fine-needle aspiration biopsies. Among cytological specimens, 108 cases were processed by using the cell block method (CBM), and 47 cases were processed by the disposable membrane cell collector method (MCM) before DNA/RNA extraction. Ten drive genes of EGFR, ALK, ROS1, BRAF, KRAS, NRAS, HER2, RET, PIK3CA, and MET were combined detected at one step by the amplification refractory mutation system and ABI 7500 RT-qPCR.

RESULTS

The purity of RNA (p = 0.005) and DNA (p = 0.001) extracted by using the MCM was both significantly higher than that extracted by using the CBM. Forty-seven cases of fresh cell specimens processed by the MCM all succeeded in multigene detections, while of 108 specimens processed by the CBM, 6 cases failed in multigene detections. Among 149 specimens, single-gene mutation rates of EGFR, ALK, ROS1, RET, HER2, MET, KRAS, NRAS, BRAF, and PIK3CA mutations were 57.71%, 6.04%, 3.36%, 2.68%, 2.01%, 2.01%, 1.34%, 0.67%, 0% and 0% respectively, and 6 cases including 2 coexistence mutations. We found that mutation status was correlated with gender (p = 0.047), but not correlated with age (p = 0.141) and smoking status (p = 0.083). We found that the EGFR mutation status was correlated with gender (p = 0.003), age (p = 0.015) and smoking habits (p = 0.007), and ALK mutation status was correlated with age (p = 0.002).

CONCLUSION

Compared with the CBM, the MCM can improve the efficiency of DNA/RNA extraction and PCR amplification by removing impurities and enriching tumor cells. And we speculate that the successful detection rate of fresh cytological specimens was higher than that of paraffin-embedded specimens. EGFR, ALK, and ROS1 mutations were the main driver mutations in patients with advanced lung adenocarcinoma. We speculate that EGFR and ALK are more prone to concomitant mutations, respectively. Targeted therapies for patients with coexisting mutations need further study.

Clinical evaluation of RB1 genetic testing reveals novel mutations in Vietnamese patients with retinoblastoma

Clinical evaluation of the genetic testing strategy is essential for ensuring the correct determination of mutation carriers. The current study retrospectively analyzed genetic and clinicopathological data from 62 Vietnamese patients with retinoblastoma (RB) referred to the Vinmec Hi-Tech Center for RB transcriptional corepressor 1 (RB1) genetic testing between 2017 and 2019. The present study aimed to evaluate the sensitivity of the Next Generation Sequencing (NGS) method to identify novel RB1 mutations, and to consider using age at diagnosis as a risk factor. Genomic DNA was analyzed with custom panel based targeted NGS. NGS was performed on the Beijing Genomics Institute (BGI) sequencing platform, and pathogenic or likely pathogenic variants were confirmed by Sanger sequencing, quantitative PCR (qPCR) or Multiplex Ligation-dependent Probe Amplification assay (MLPA). Constitutional RB1 variants were identified in 100% (25/25) of the bilateral cases, while several common previously reported RB1 mutations were also recorded. In addition, in Vietnamese patients with RB, nine novel RB1 mutations were identified. Children aged between 0-36 months were more likely to be RB1 carriers compared with those aged >36 months. The current findings indicated that the NGS method implemented in the Vinmec Hi-Tech Center was highly accurate, and age at diagnosis may be used to assess the risk of hereditary RB. Furthermore, the newly identified RB1 mutations may provide additional data to improve the current understanding of the mechanisms underlying RB1 inactivation and the development of rapid assays for detecting RB1 mutations. Overall, the present study suggested that NGS may be applied for detecting germline RB1 mutations in routine clinical practice.

Analysis of Multigene Mutations in Lung Adenocarcinoma in Zunyi

OBJECTIVE

Driver gene mutation in lung adenocarcinoma patients in Zunyi and its relationship with clinical features were probed in this investigation.

METHODS

In total, with 244 patients with lung adenocarcinoma as study subjects, including 141 males and 103 females, amplification-refractory mutation system-polymerase chain reaction (ARMS-PCR) was utilized for detecting multigene mutations. Subsequently, the relationship between gene mutation and clinical characteristics was analyzed.

RESULTS

The total mutation rate of driver genes was 65.17%, including 48.36% EGFR, 6.15% KRAS, 5.74% ALK, 2.05% HER-2, 1.23% ROS1, 0.82% RET, 0.41% NRAS, and 0.41% BRAF. Among EGFR mutations, 47.46% were EGFR-19-deletion, 42.37% EGFR-21-L858R mutation, 4.24% EGFR-20-T790M mutation, 2.54% EGFR-21-L861Q mutation, 2.54% EGFR-20-insertion, and 0.85% EGFR-18-G719X mutation. Both female patients and nonsmoking patients with lung adenocarcinoma had a higher rate of EGFR mutation. Additionally, 15 patients with multiple mutations in EGFR, including 13 patients with 2 mutations in EGFR and 2 patients with 3 mutations in EGFR, were found.

CONCLUSION

Among driver gene mutations in patients with lung adenocarcinoma in Zunyi, EGFR mutation has the highest incidence, followed by ALK fusion and KRAS mutation. Although both mutations and multisite mutations in the other driver genes account for a low proportion, they still have great clinical significance. Multigene mutation detection contributes to the rapid screening of patients with lung adenocarcinoma who respond to targeted therapy.

Improving the diagnosis of AUS/FLUS thyroid nodules using an algorithm with combination of BRAFV600E mutation analysis and ultrasound pattern-based risk stratification

PURPOSE

To propose a diagnostic algorithm for improving the diagnosis of atypia of undetermined significance or follicular lesion of undetermined significance (AUS/FLUS) thyroid nodules.

METHODS

This study retrospectively enrolled 77 consecutive patients with 81 AUS/FLUS nodules who underwent preoperative BRAFV600E mutation analysis. A new diagnostic algorithm was proposed that BRAFV600E mutation analysis for the Fine-needle aspiration cytology specimen was firstly carried out, in which positive BRAFV600E mutation indicated malignancy and classification of the nodules with negative BRAFV600E mutation was further performed based on ultrasound pattern-based risk stratification of American Thyroid Association Guidelines. The diagnostic performance of the new diagnostic algorithm was evaluated.

RESULTS

The sensitivity, specificity, positive predictive value, negative predictive value, accuracy, and area under the receiver operating characteristic curve (AUROC) of new diagnostic algorithm were 94.6%, 84.0%, 91.4%, 86.9%, 90.1%, and 0.893, respectively. The proposed diagnostic algorithm significantly increased the diagnostic performances (AUROC: 0.893 vs. 0.837 and 0.795), sensitivity (94.6% vs. 71.4% and 75.0%), and accuracy (90.1% vs. 79.0% and 77.8%) compared with BRAFV600E mutation analysis alone and ultrasound pattern-based risk stratification alone (all P < 0.05).

CONCLUSION

The proposed diagnostic algorithm is helpful for improving the diagnosis of AUS/FLUS nodules, which might be as a routine approach.

Programmable One-Pot Enzymatic Reaction for Direct Fluorescence Detection of Ultralow-Abundance Mutations in the DNA Duplex

Sensitive detection of low-abundance driver mutations may provide valuable information for precise clinical treatment. Compared to next-generation sequencing and droplet digital PCR methods, fluorescent probes show great flexibility in rapid detection of specific mutations with high sensitivity and easily accessible instruments. However, existing approaches with fluorescent probes need an additional step to convert duplex DNA to single-stranded DNA (ssDNA) before the detection step, which increases the time, cost, and risk of loss of low-input target strands. In this work, we attempt to integrate the ssDNA-generation step with the subsequent detection into a programable one-pot reaction by employing lambda exonuclease (λ exo), a versatile nanopore nuclease which exercises different functions on different substrates. The capability of λ exo in discrimination of mismatched bases in 5'- FAM-ended 2 nt-unpaired DNA duplexes was first demonstrated. Specific fluorescent probes were developed for EGFR exon 19 E746-A750del and PIK3CA E545K mutations with discrimination factors as high as 8470 and 884, respectively. By mixing the probes and λ exo with the PCR products of cell-free circulating DNA extracted from plasma samples, the reaction was immediately initiated, which allowed sensitive detection of the two types of mutations at an abundance as low as 0.01% within less than 2 h. Compared to existing approaches, the new method has distinct advantages in simplicity, low cost, and rapidity. It provides a convenient tool for companion diagnostic tests and other routine analysis targeting genetic mutations in clinical samples.

Arms-qPCR Improves Detection Sensitivity of Earlier Diagnosis of Papillary Thyroid Cancers With Worse Prognosis Determined by Coexisting BRAF V600E and Tert Promoter Mutations

OBJECTIVE

The coexistence of BRAF V600E and the telomerase reverse transcriptase (TERT) promoter mutation C228T/C250T is extensively associated with thyroid cancer prognosis. Our study aimed to establish a sensitive method for mutation detection and explore the correlation in detail.

METHODS

The BRAF and TERT promoter mutation status of 250 papillary thyroid cancers was determined using amplification-refractory mutation system quantitative polymerase chain reaction (ARMS-qPCR) and Sanger sequencing to compare the sensitivity of the 2 methods. Associations between the mutation status and clinicopathological features were then analyzed.

RESULTS

ARMS-qPCR was more sensitive than Sanger sequencing (BRAF V600E: 75.2% [188 of 250] vs 52.4% [131 of 250], P < .001; TERT promoter C228T/C250T mutation: 12.0% [30 of 250] vs 3.6% [9 of 250], P = .001; comutation: 9.6% [24 of 250] vs 3.2% [8 of 250], P = .005). Both ARMS-qPCR and Sanger sequencing indicated that patients with coexisting BRAF V600E and TERT promoter mutations had an older diagnosis age, higher recurrence rate, and were associated with a more advanced TNM stage and higher metastasis, age, completeness of resection, invasion, and size score. Moreover, ARMS-qPCR helped identify an earlier group stage, which was younger and had smaller tumors and a lower recurrence rate, compared with the group with coexisting BRAF V600E and TERT promoter mutations identified by Sanger sequencing. The newly identified group had a lower metastasis, age, completeness of resection, invasion, and size score and TNM stage.

CONCLUSION

Patients with coexisting BRAF V600E and TERT promoter mutations had a worse prognosis. ARMS-qPCR, the more sensitive method, can be used to identify patients who have a potentially worse prognosis earlier.

BRAF as a positive predictive biomarker: Focus on lung cancer and melanoma patients

In the era of personalized medicine, BRAF mutational assessment is mandatory in advanced-stage melanoma and non-small cell lung cancer (NSCLC) patients. The identification of actionable mutations is crucial for the adequate management of these patients. To date various drugs have been implemented in clinical practice. Similarly, various methods may be adopted for the identification of BRAF mutations. Here, we briefly review the current literature on BRAF in melanoma and NSCLC, focusing attention in particular on the different methods and drugs adopted in these patients. In addition, an overview of the real-world practice in different Italian laboratories with high expertise in molecular predictive pathology testing is provided.

Detection of epidermal growth factor receptor mutations in peripheral blood circulating tumor DNA in patients with advanced non-small cell lung cancer: A PRISMA-compliant meta-analysis and systematic review

BACKGROUND

The epidermal growth factor receptor (EGFR) mutation status related to the treatment approach for advanced non-small cell lung cancer (NSCLC) patients. This study aimed to evaluate the diagnostic accuracy of peripheral blood circulating tumor DNA (ctDNA) in EGFR mutated advanced NSCLC patients.

METHOD

The related database was systematically searched with keywords until January 19, 2020. Studies contained the histopathological and cytological advanced NSCLC samples were included, and the diagnostic data were recorded for calculating sensitivity and specificity. I statistics were used for detecting heterogeneity across studies, and the meta-regression was performed to seek the source of heterogeneity.

RESULT

A total of 32 studies with 4527 advanced NSCLC patients were included in our meta-analysis. Among them, 87% of the patients were diagnosed as stage IV. The pooled sensitivity of peripheral blood ctDNA was 0.70 (95% CI: 0.63-0.75, I = 81.76) and the pooled specificity was 0.98 (95% CI: 0.96-0.99, I = 88.33). The meta-regression showed that the prospective study design and the ARMS detection method were the main source of heterogeneity for sensitivity (P < .05), and the publication country (Asia or non-Asia) was the main source of heterogeneity for specificity (P < .01).

CONCLUSION

ctDNA biopsy has high specificity and diagnostic accuracy in detection of EGFR mutation in advanced NSCLC patients. When the ctDNA gene test result is negative, we should fully consider the risk of missed diagnosis, and further tissue biopsy is still needed to undertake.

The Diagnostic Accuracy of Liquid Biopsy in EGFR-Mutated NSCLC: A Systematic Review and Meta-Analysis of 40 Studies

Epidermal growth factor receptor (EGFR) mutations are the most common carcinogenic driver mutations in non-small-cell lung cancer (NSCLC) patients, while invasive tissue biopsy has certain inherent defects. PubMed, Ovid Medline, Embase, and the Cochrane Library were systematically searched on January 4, 2020, using the keywords "liquid biopsy," "EGFR," and "NSCLC." The pooled sensitivity and specificity of EGFR mutations in paired tissue and blood were calculated. The accuracy was assessed by receiver operating characteristic curve. The meta-regression of the subgroup was performed to analyze the heterogeneity. Hazard ratio (HR) and 95% confidence interval (CI) were combined for evaluating the impact of EGFR mutation in tissue and liquid blood biopsy. A total of 40 studies with 5,995 patients were involved in the study. The pooled sensitivity was 68% (95% CI = 60-75%), and the specificity was 98% (95% CI = 95-99%). The diagnostic odds ratio was 88 (95% CI = 40-195), and the area under the curve was 0.91 (95% CI = 0.88-0.93). In the meta-regression, the sensitivity and specificity remain lower in the Asian studies than non-Asian studies (sensitivity: 66% vs. 73%, P = 0.04; specificity: 96% vs. 97%, P = 0.03, respectively). The EGFR mutation was associated with a better progression-free survival than wild type in both tissue (HR = 0.54, 95% CI = 0.34-0.85, P = 0.007) and blood (HR = 0.81, 95% CI = 0.71-0.92, P = 0.001) detection. Peripheral blood liquid biopsy had a better specificity for detecting EGFR mutation in NSCLC patients, while tissue biopsy still needs to be undertaken for negative blood biopsy patients due to its lower sensitivity.

Comparison detection methods for EGFR in formalin-fixed paraffin-embedded tissues of patients with NSCLC

Epidermal growth factor receptor (EGFR) is an important gene in the development of lung cancer. Non-small cell lung cancer (NSCLC) is the most common lung cancer. In the present study, the expression of EGFR in 717 patients with NSCLC was detected by Ventana automatic immunohistochemical technique, and the samples was verified by Real-time PCR, and then the results were compared with the data acquired by next-generation sequencing technology (NGS), which is the high throughput, multiple sites for EGFR gene mutation testing. The expression of Ventana EGFR in 717 cases of NSCLC was detected by immunohistochemistry, and the positive rate was 60.70 % (435 / 717). The mutation rate of EGFR was 57.60 % (413/717). The coincidence rate of Ventana EGFR immunohistochemical assay and Real-time PCR assay reached 94.94 %, and the two had high consistency. The coincidence rate of Ventana EGFR immunohistochemical assay and NGS were high correlation. Based on these results, Ventana EGFR automatic immunohistochemical detection has high accuracy, simple operation process, low price and easy interpretation. It can be used as the preferred method for EGFR detection.

Comparison of next-generation sequencing and immunohistochemistry analysis for targeted therapy-related genomic status in lung cancer patients

Background

Some drugs that target molecular pathways are available for the targeted treatment of lung cancer. Multiple tests are needed to detect the status of the known molecular targets to determine whether the patients can respond to the drugs. An integrated platform for various gene alteration detection including both mutations and rearrangements is necessary for patients, especially those without enough tissue.

Methods

In our study, detections of EGFR mutations, ALK rearrangement, ROS1 rearrangement, and alterations of other nine important lung cancer-related genes were integrated into a single next-generation sequencing (NGS) platform. The NGS analysis was performed in 107 cases of non-small cell lung cancer (NSCLC). Meanwhile, hot spots such as EGFR L858R, EGFR E746-A750Del mutations and gene rearrangement of ALK and ROS1 were detected by immunohistochemical (IHC) staining.

Results

NGS could explore various gene mutations and gene rearrangements with a reduced experiment time and lower amounts of tumor tissues than multiple IHC staining experiments. NGS results were more informative and reliable than IHC staining for EGFR gene alterations, especially for the exon 19 region. NGS could also increase the positive rate of ALK rearrangement and decrease the false positive results of ROS1 rearrangements detected by IHC staining.

Conclusions

NGS is effective for confirmation the status of various important lung cancer-related gene alterations. Furthermore, NGS is necessary for the confirmation of the IHC results of ALK and ROS1 rearrangements.

BRAFV600E mutation analysis in fine-needle aspiration cytology specimens for diagnosis of thyroid nodules: The influence of false-positive and false-negative results

Background

The accurate evaluation of BRAF^V600E mutation in preoperative fine‐needle aspiration cytology (FNAC) specimens is important for making management decisions in thyroid nodules (TNs). The aim of this study was to assess the false‐positive and false‐negative BRAF^V600E mutations in thyroid FNAC specimens and their influence on diagnosis of TN.

Methods

This prospective study enrolled 292 nodules in 269 patients who underwent BRAF^V600E mutation analysis using amplification refractory mutation system‐quantitative real‐time polymerase chain reaction (ARMS‐qPCR) both in FNAC specimens and formalin‐fixed, paraffin‐embedded (FFPE) tissue samples after surgery. The false‐positive and false‐negative mutations for BRAF^V600E analysis using ARMS‐qPCR in FNAC specimens were recorded, with reference to the results of BRAF^V600E mutation analysis using ARMS‐qPCR in FFPE tissue sample. Diagnostic performances of FNAC, BRAF^V600E mutation analysis in FNAC specimens, BRAF^V600E mutation analysis in FFPE tissue sample, and the combination of FNAC and BRAF^V600E mutation analysis for predicting thyroid malignancy were assessed.

Results

The false‐positive and false‐negative mutations for BRAF^V600E analysis using ARMS‐qPCR in FNAC specimens were 10.1% (19/189) and 7.1% (7/98), respectively. FNAC combined with preoperative BRAF^V600E mutation analysis significantly increased the diagnostic sensitivity from 75.7% to 92.3%, and accuracy from 78.7% to 90.6% in comparison with FNAC alone (both P < .001). No significant differences were found between the combination of FNAC and BRAF^V600E mutation analysis in FNAC specimens and the combination of FNAC and BRAF^V600E mutation analysis in FFPE tissue sample (sensitivity: 92.3% vs 91.9%; accuracy: 90.6% vs 91.3%; both P > .05).

Conclusions

FNAC combined with preoperative BRAF^V600E mutation analysis can significantly increase the diagnostic performance in comparison with FNAC alone. False‐positive and false‐negative BRAF^V600E mutation results are found in preoperative FNAC specimens, whereas it does not affect the overall auxiliary diagnosis of TNs.

Development of a rapid and reliable single-tube multiplex real-time PCR method for HLA-A*24:02 genotyping

Aim: HLA-A*24:02 is significantly associated with cutaneous adverse drug reactions caused by aromatic antiepileptic drugs. Here, we aimed to establish a fast and reliable detection method for HLA-A*24:02 genotyping. Methods: A single-tube multiplex quantitative real-time polymerase chain reaction (qPCR) assay for HLA-A*24:02 genotyping was established by combining allele-specific primers with TaqMan probes. Results: A 100% concordance was observed between qPCR and SBT result in 106 Han subjects. The detection limit of the new method was 0.05 ng DNA. The positive rate of HLA-A*24:02 in Tibetans (55.6%, n = 81) was significantly higher than those in Han (34%, n = 106), Uighur (27.5%, n = 102), Bouyei (25.9%, n = 116) and Miao populations (26.5%, n = 113). Conclusion: The newly established qPCR assay was reliable for HLA-A*24:02 screening in clinical applications.

Relationship between BRAF V600E and clinical features in papillary thyroid carcinoma

OBJECTIVE

To investigate the mutant status of BRAF gene and analyze its relationship to epidemiological risk factors and clinical outcomes among patients with papillary thyroid cancer (PTC) in the largest, single-institution Chinese cohort to date.

METHODS

The medical records of 2048 PTC patients were reviewed in this retrospective study. Single-factor and multiple logistic regression analyses were applied to identify risk factors for BRAF V600E mutation. Survival outcomes including distant metastatic and persistent or recurrent PTC were examined, with a mean follow-up time of 23.4 (5-47) months.

RESULTS

The BRAF V600E mutation was present in 83.7% of patients (1715 of 2048). Correlation was found between BRAF V600E mutation and several epidemiological features, including age, concomitant hypertension and Hashimoto thyroiditis (HT). For the clinicopathological features, BRAF V600E was significantly associated with bilateral multifocality (odds ratio (OR) 1.233, 95% confidence interval (CI) 1.063-1.431, P < 0.01) and less lateral lymph node metastases (OR 0.496, 95% CI 0.357-0.689, P < 0.01). Smaller tumor size and advanced disease stage were significant in single-factor analyses but became insignificant after multivariate adjustment. No association was found between BRAF V600E mutation and extrathyroidal invasion, distant metastatic and disease persistence or recurrence.

CONCLUSION

Part of epidemiological features are independent risk or protective factors for BRAF V600E mutation. The presence of BRAF V600E mutation is not an aggressive prognosis on poor clinical outcomes in PTC. However, the high prevalence of BRAF V600E may provide guidance for surgery strategy and opportunity for targeted treatment in recurrent and advanced stage disease.

Comparative Analysis of Two Methods for the Detection of EGFR Mutations in Plasma Circulating Tumor DNA from Lung Adenocarcinoma Patients

Mutations in the epidermal growth factor receptor (EGFR) are associated with various solid tumors. This study aimed to compare two methods for the detection of EGFR mutations in circulating tumor DNA (ctDNA) from lung adenocarcinoma (LUAD) patients and to evaluate the clinical significance of EGFR mutations in ctDNA. In this prospective cohort study, the EGFR mutation status of 77 patients with stage IIIB or IV LUAD was first determined using lung cancer tissue. The amplification refractory mutation system (ARMS) and single allele base extension reaction combined with mass spectroscopy (SABER/MassARRAY) methods were also used to detect EGFR mutations in plasma ctDNA from these patients and then compared using the EGFR mutation status in lung cancer tissue as a standard. Furthermore, the relationship between the presence of EGFR mutations in ctDNA after receiving first-line EGFR-tyrosine kinase inhibitor (EGFR-TKI) therapy and survival was evaluated. The overall sensitivity and specificity for the detection of EGFR mutations in plasma ctDNA by ARMS and SABER/MassARRAY were 49.1% vs. 56% and 90% vs. 95%, respectively. The agreement level between these methods was very high, with a kappa-value of 0.88 (95% CI 0.77-0.99). Moreover, 43 of the patients who carried EGFR mutations also received first-line EGFR-TKI therapy. Notably, patients with EGFR mutations in plasma ctDNA had significantly shorter progression-free survival (9.0 months, 95% CI 7.0-11.8, vs. 15.0 months, 95% CI 11.7-28.2; p = 0.02) and overall survival (30.6 months, 95% CI 12.4-37.2, vs. 55.6 months, 95% CI 25.8-61.8; p = 0.03) compared to those without detectable EGFR mutations. The detection of EGFR mutations in plasma ctDNA is a promising, minimally invasive, and reliable alternative to tumor biopsy, and the presence of EGFR mutations in plasma ctDNA after first-line EGFR-TKI therapy is associated with poor prognosis.

BRAF V600E vs. TIRADS in predicting papillary thyroid cancers in Bethesda system I, III, and V nodules

Objective

Bethesda System for Reporting Thyroid Cytopathology (BSRTC) categories I, III, and V account for a significant proportion of fine needle aspiration cytology (FNAC) diagnoses. This study aimed to compare the diagnostic efficacy of BRAF^V600E mutation and the Thyroid Imaging Reporting and Data System (TIRADS) classification in differentiating papillary thyroid cancers (PTCs) from benign lesions among BSRTC I, III, and V nodules.

Methods

A total of 472 patients with 479 nodules were enrolled in this prospective study. Ultrasound, BRAF^V600E mutation testing, and FNAC were performed in each nodule, followed by surgery or regular ultrasound examination.

Results

In the BSRTC I category, BRAF^V600E showed similar sensitivity, higher specificity, and lower accuracy when compared with TIRADS. In the BSRTC III/V category, the sensitivity, specificity, and accuracy of BRAF^V600E were similar to those of TIRADS. In comparison to BRAF^V600E alone, the combination of the two methods significantly improved sensitivity (BSRTC I: 93.6% vs. 67.7%, P < 0.01; BSRTC III: 93.8% vs. 75.0%, P < 0.01; BSRTC V: 96.0% vs. 85.3%, P < 0.001). When compared with TIRADS alone, the combination improved sensitivity in BSRTC I nodules (93.6% vs. 74.2%, P < 0.05), increased sensitivity and decreased accuracy in BSRTC III nodules (93.8% vs. 75.0%, P < 0.01, 91.0% vs. 93.6%, P < 0.01), and improved both sensitivity and accuracy in BSRTC V nodules (96.0% vs. 82.0%, P < 0.001; 94.2% vs. 81.3%, P < 0.001).

Conclusions

BRAF^V600E exhibited higher specificity and lower accuracy compared with TIRADS in BSRTC I nodules, while the two methods showed similar diagnostic value in BSRTC III/V nodules. The combination of the two methods distinctly improved sensitivity in the diagnosis of PTCs in BSRTC I, III, and V nodules.

Efficacy of first-line treatment with epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) alone or in combination with chemotherapy for advanced non-small cell lung cancer (NSCLC) with low-abundance mutation

OBJECTIVE

The objective of this study was to investigate whether first-line treatment with epidermal growth factor receptor-tyrosine kinase inhibitor (EGFR-TKI) in combination with chemotherapy improves the prognosis of patients with advanced non-small cell lung cancer (NSCLC) who harbour low-abundance EGFR mutations.

PATIENTS AND METHODS

We retrospectively analysed the clinical data of 76 patients with advanced NSCLC who harboured low-abundance EGFR mutations. The patients were divided into the combination group and the monotherapy group. The combination group received EGFR-TKI combined with a platinum-based regimen. After the end of chemotherapy, EGFR-TKI was administered daily. The monotherapy group was administered EGFR-TKI therapy daily.

RESULTS

No significant difference was observed in response rate between the different groups. The median PFS and OS were significantly longer in the combination group than in the monotherapy group (PFS: 7.9 months [95% CI,5.73-10.07] vs 5.9 months [95% CI, 4.99-6.81], p = 0.015; OS: 25.8 months[95% CI,16.27-35.33] vs 19.8 months [95% CI, 18.60-21.00], p = 0.047). Subgroup analysis showed that, for patients with the exon 21 L858R mutation, the PFS and OS were significantly longer in the combination group than in the monotherapy group (PFS: 7.2 months vs 5.8 months, p = 0.013; OS: 22.0 months vs 18.7 months, p = 0.024). The incidence of adverse events was significantly higher in the combination group.

CONCLUSION

For patients with advanced NSCLC and low-abundance EGFR mutations, first-line treatment with EGFR-TKI plus chemotherapy significantly improved PFS and OS. The combination therapy increased the incidence of adverse reactions, but all adverse reactions were expected and tolerated.

Value of BRAF V600E in High-Risk Thyroid Nodules with Benign Cytology Results

BACKGROUND AND PURPOSE

Limitations of ultrasound-guided fine-needle aspiration include nondiagnostic, indeterminate cytology and false-negative results. The BRAF V600E mutation is a specific biomarker for papillary thyroid carcinoma. This study aimed to investigate the additional diagnostic role of the BRAF V600E mutation in high-risk thyroid nodules with benign cytology results.

MATERIALS AND METHODS

A total of 787 high-risk nodules in 720 patients underwent ultrasound-fine-needle aspiration. A subsequent BRAF V600E mutation test was performed on thyroid nodules with benign cytology. Final pathology confirmed thyroid nodules with benign cytology that were positive for the BRAF V600E mutation. Ultrasound was performed on thyroid nodules with benign cytology results that were negative for the BRAF V600E mutation. Fine-needle aspiration was repeated on thyroid nodules with enlarged size or changed ultrasound features.

RESULTS

Among the 787 nodules, 292 thyroid nodules had benign cytology results with 256 nodules negative for the BRAF V600E mutation and 36 nodules positive for the BRAF V600E mutation. Thirty-one nodules positive for the BRAF V600E mutation were confirmed malignant, and 5 nodules were confirmed benign by pathology. Fine-needle aspiration was repeated on 11 enlarged thyroid nodules with benign cytology findings that were negative for the BRAF V600E mutation. The results of repeat fine-needle aspiration were 4 benign nodules, 2 follicular neoplasms or suspected follicular neoplasms, 3 suspected malignancies, and 2 malignant nodules. Among the 36 thyroid nodules positive for the BRAF V600E mutation, 25 (69.4%) had ≥2 suspicious ultrasound features and 11 (30.6%) nodules had 1 suspicious ultrasound feature.

CONCLUSIONS

The BRAF V600E mutation test can detect papillary thyroid carcinomas that might be missed by fine-needle aspiration. We recommend that fine-needle aspiration be routinely accompanied by the BRAF V600E mutation test in high-risk thyroid nodules with ≥2 suspicious ultrasound features.

EGFR-TKI-sensitive mutations in lung carcinomas: are they related to clinical features and CT findings?

Background

Epidermal growth factor receptor (EGFR) mutation testing is restricted to several limitations. In this study, we examined the relationship between EGFR mutation status and clinicoradiological characteristics in a Chinese cohort of patients.

Materials and methods

The data of patients who were diagnosed with lung carcinoma and underwent both EGFR testing and chest computed tomography (CT) at our hospital between January 1, 2011, and November 31, 2015, were retrospectively analyzed. The age, sex, and smoking index of the patients, the size, margin, and density of the tumor, and the presence of specific signs visible on the CT images were assessed.

Results

The results showed a higher rate of EGFR-tyrosine kinase inhibitor (TKI)-sensitive group than nonsensitive group in female patients and patients with a low smoking index (P<0.001, both). In logistic regression analyses, tumor size (P<0.001), smooth margins (P=0.015), and angular margins (P<0.001) were independent negative predictors of EGFR-TKI-sensitive group. Pleural indentation (P<0.001) and air bronchogram (P=0.025) were independent positive predictors of EGFR-TKI-sensitive group. Patients with squamous cell carcinoma had fewer sensitive mutations than those with either adenocarcinoma (P<0.001) or adenosquamous carcinoma (P<0.001).

Conclusion

Clinical and CT characteristics differed significantly between EGFR-TKI-sensitive and nonsensitive groups. Our findings may be useful in deciding therapeutic strategies for patients in whom EGFR testing is not possible.

Characterization of genetic alterations in brain metastases from non-small cell lung cancer

Brain metastasis (BM) is the primary contributor to mortality in non‐small cell lung cancer (NSCLC) patients. Although the findings of NSCLC genetic sequencing studies suggest the potential for personalizing therapeutic approaches, the genetic profiles and underlying mechanisms of BM progression remain poorly understood. Here, we investigated the genetic profiles of brain metastases from NSCLC in six patients with primary tumors and corresponding BM samples via whole exome sequencing and targeted panel sequencing. We have demonstrated considerable genetic heterogeneity between primary lung cancer and corresponding brain metastases specimens. High‐frequency mutations were found in NOTCH2,NOTCH2NL,FANCD2,EGFR, and TP53. Additionally, EGFR and TP53 consistently exhibited high frequencies of mutation between primary tumors and corresponding brain metastases. The implication is that most of the genetic alterations may be acquired or lost during malignant progression, and the stable EGFR and TP53 mutational status between paired primary tumors and metastatic sites confirms that most mutations detected on analysis of the primary tumor or metastases are sufficient for clinical decision‐making, and suggest there is no need to re‐biopsy recurrent tumors or metastases for most NSCLC patients.

Highly Sensitive and Reliable Detection of EGFR Exon 19 Deletions by Droplet Digital Polymerase Chain Reaction

BACKGROUND

Analysis of EGFR mutations is becoming a routine clinical practice but the optimal EGFR mutation testing method is still to be determined.

METHODS

We determined the nucleotide sequence of deletions located in exon 19 of the EGFR gene in lung tumor samples of patients residing in different regions of Russia (153 tumor DNA specimens), using Sanger sequencing. We developed a droplet digital polymerase chain reaction assay capable of detecting all common EGFR deletions in exon 19. We also compared the therascreen amplification refractory mutation system assay with a droplet digital polymerase chain reaction assay for the detection of all the deletions in our study.

RESULTS

The droplet digital polymerase chain reaction assay demonstrated 100% sensitivity against polymerase chain reaction fragment length analysis and detected all possible types of deletions revealed in our study (22 types). At the same time, the therascreen EGFR RGQ PCR Kit was not able to detect deletions c.2252-2276>A and c.2253-2276 and showed low performance for another long deletion.

CONCLUSION

Thus, we can conclude that the extraordinary length of deletions and their atypical locations (shift at the 3'-region compared to known deletions) could be problematic for the therascreen EGFR RGQ PCR Kit and should be taken into account during targeted mutation test development. However, droplet digital polymerase chain reaction is a promising and reliable assay that can be used as a diagnostic tool to genotype formalin-fixed paraffin-embedded cancer samples for EGFR or another clinically relevant somatic mutation.

Methodological comparison of the allele refractory mutation system and direct sequencing for detecting EGFR mutations in NSCLC, and the association of EGFR mutations with patient characteristics

Gefitinib is effective for patients with non-small cell lung cancer (NSCLC) with a mutation in the epidermal growth factor receptor (EGFR) gene, which makes the detection of EGFR mutations a critical step prior to determining a treatment schedule. Therefore, the present study determined the EGFR mutation status in patients with NSCLC using an allele refractory mutation system (ARMS) and analyzed the detection ratio for different specimen types. A total of 1,596 NSCLS samples were collected and EGFR gene mutations were detected on exons 18-21 using ARMS and direct sequencing. The concordance of two methods reached 89.21%, with a total mutation rate of 45.55% (727/1,596), in which the mutation rate in lung adenocarcinoma samples was markedly increased compared with squamous cell carcinoma (51.77 vs. 8.68%). In patients with lung adenocarcinoma, EGFR mutations were more frequent in female patients than male patients (65.53 vs. 39.80%, P<0.01); there was no observable difference depending on age. Similar results were obtained for squamous cell carcinoma. In the present study, certain rare mutations were also identified; these may be subjects for further study. The impact of different sample types on the consistency between the methods was determined to be insignificant. ARMS is a more applicable approach for large-scale clinical detection than direct sequencing, and we hypothesize that ARMS may replace direct sequencing if the drawbacks of ARMS, including its narrow detection range, can be amended.

EGFR mutations in early-stage and advanced-stage lung adenocarcinoma: Analysis based on large-scale data from China

Background

EGFR‐tyrosine kinase inhibitors play an important role in the treatment of advanced non‐small cell lung cancer (NSCLC). EGFR mutations in advanced NSCLC occur in approximately 35% of Asian patients and 60% of patients with adenocarcinoma. However, the frequency and type of EGFR mutations in early‐stage lung adenocarcinoma remain unclear.

Methods

We retrospectively collected data on patients diagnosed with lung adenocarcinoma tested for EGFR mutation. Early stage was defined as pathological stage IA–IIIA after radical lung cancer surgery, and advanced stage was defined as clinical stage IIIB without the opportunity for curative treatment or stage IV according to the American Joint Committee on Cancer Staging Manual, 7th edition.

Results

A total of 1699 patients were enrolled in this study from May 2014 to May 2016; 750 were assigned to the early‐stage and 949 to the advanced‐stage group. Baseline characteristics of the two groups were balanced, except that there were more smokers in the advanced‐stage group (P < 0.001). The total EGFR mutation rate in the early‐stage group was similar to that in the advanced‐stage group (53.6% vs. 51.4%, respectively; P = 0.379). There was no significant difference in EGFR mutation type between the two groups. In subgroup analysis of smoking history, there was no difference in EGFR mutation frequency or type between the early‐stage and advanced‐stage groups.

Conclusion

Early‐stage and advanced‐stage groups exhibited the same EGFR mutation frequencies and types.

Mutation abundance affects the therapeutic efficacy of EGFR-TKI in patients with advanced lung adenocarcinoma: A retrospective analysis

PURPOSE

To investigate the influence of mutation abundance and sites of epidermal growth factor receptor (EGFR) on therapeutic efficacies of EGFR-tyrosine kinase inhibitor (EGFR-TKIs) treatments of patients with advanced non-small cell lung carcinoma (NSCLC).

METHODS

EGFR mutational sites and mutation abundance were analyzed by amplification refractory mutation system (ARMS) in paraffin-embedded tissue sections taken from primary or metastatic tumors of 194 NSCLC patients.

RESULTS

The median progression-free survival (PFS) time of the enrolled patients was 9.3 months (95% CI, 8.2-10.8 months). The PFS was significantly different with EGFR gene mutation abundance after EGFR-TKI therapy (P = 0.014). The median PFS was significantly longer when the cut-off value of EGFR mutation abundance of exon 19 or exon 21, and solely exon 19 was > 26.7% and 61.8%, respectively. For patients who received EGFR-TKI as first-line treatment, the median PFS was significantly longer in the high mutation abundance group than in the low mutation abundance group (12.7 vs 8.7 months, P = 0.002).

CONCLUSION

The PFS benefits were greater in patients with a higher abundance of exon 19 deletion mutations in the EGFR gene after EGFR-TKI treatment and first line EGFR-TKI treatment led to improved PFS in high mutation abundance patients.

Extending Circulating Tumor DNA Analysis to Ultralow Abundance Mutations: Techniques and Challenges

Liquid biopsies that analyze circulating tumor DNA (ctDNA) hold great promise in the guidance of clinical treatment for various cancers. However, the innate characteristics of ctDNA make it a difficult target: ctDNA is highly fragmented, and found at very low concentrations, both in absolute terms and relative to wildtype species. Clinically relevant target sequences often differ from the wildtype species by a single DNA base pair. These characteristics make analyzing mutant ctDNA a uniquely difficult process. Despite this, techniques have recently emerged for analyzing ctDNA, and have been used in pilot studies that showed promising results. These techniques each have various drawbacks, either in their analytical capabilities or in practical considerations, which restrict their application to many clinical situations. Many of the most promising potential applications of ctDNA require assay characteristics that are not currently available, and new techniques with these properties could have benefits in companion diagnostics, monitoring response to treatment and early detection. Here we review the current state of the art in ctDNA detection, with critical comparison of the analytical techniques themselves. We also examine the improvements required to expand ctDNA diagnostics to more advanced applications and discuss the most likely pathways for these improvements.

Assessment of EGFR mutation status in Tunisian patients with pulmonary adenocarcinoma

BACKGROUND

Despite recent advances, non-small cell lung cancer carries a grim prognosis. For appropriate treatment selection, the updated guidelines recommend broad molecular profiling for all patients with pulmonary adenocarcinoma. Precise histological subtyping and targeted epidermal growth factor receptor (EGFR) and anaplastic lymphoma kinase (ALK) testing are mandatory.

METHODS

Herein, we assessed the EGFR mutation status of 26 formalin fixed-paraffin embedded (FFPE) samples of lung adenocarcinoma. Mutational analysis concerned exons 18-21 of EGFR by real-time polymerase chain reaction (Real time-PCR) using the Therascreen EGFR RGQ PCR mutation kit. ALK status was established on 22 among 26 patients using D5F3 antibody with a fully automated Ventana CDx technique.

RESULTS

Activating EGFR mutations were found in 3 men among 26 patients (11.5%). Positive ALK expression was found in 2 cases among 22 patients (9.09%).

CONCLUSION

Frequency of EGFR mutations in pulmonary adenocarcinomas of our series is similar to that found in the European ones with some particularities. The mutations detected are uncommon. Whereas, we found a high frequency of positive ALK expression in our series compared to frequency reported in literature. Further studies with larger Tunisian series are required to obtain more conclusive results.

A novel ARMS-based assay for the quantification of EGFR mutations in patients with lung adenocarcinoma

Quantification of epidermal growth factor receptor (EGFR) mutations is important for the prediction of tyrosine kinase inhibitor (TKI) efficacy in patients with non-small cell lung cancer (NSCLC). However, clinicians lack a sensitive and convenient method to quantify EGFR mutant abundance. The present study introduces a novel method, namely amplification refractory mutation system (ARMS)-Plus, for the quantitative analysis of EGFR exon 19 deletion (19Del), L858R and T790M mutations. Formalin-fixed paraffin-embedded tumor samples were collected from 77 patients with lung adenocarcinoma. DNA was extracted and analyzed for EGFR mutations using ARMS-Plus. The performance of ARMS-Plus was then compared with that of conventional ARMS-polymerase chain reaction (ARMS-PCR) and droplet digital PCR (ddPCR). The results demonstrated that the concordance rate of EGFR mutation testing between ARMS-Plus and ddPCR was 98.7% (76/77, Kappa=0.9739). 19Del and L858R mutations were detected in 23 and 12 patients, respectively. There was a significant difference between ARMS-Plus and ddPCR in the evaluation of 19Del mutant abundance (P=0.0002); however, not in that of L858R mutant abundance (P=0.7334). The ARMS-Plus results in L858R mutant abundance were concordant with that of ddPCR (R2=0.8081). These results indicated that the sensitivity and specificity of ARMS-Plus in identifying EGFR mutations were similar to that of ddPCR. For quantitative analysis, the results of ARMS-Plus in evaluating L858R mutant abundance revealed a positive correlation with the ddPCR results. Thus, ARMS-Plus provides an alternative method, which is reliable and cost-effective, to quantify EGFR mutations and thereby, aid treatment decisions in patients with lung adenocarcinoma.

Clinical efficacy and safety of afatinib in the treatment of non-small-cell lung cancer in Chinese patients

Compared with various malignant tumors, lung cancer has high incidence and the highest mortality worldwide. Non-small-cell lung cancer (NSCLC), the most common kind of lung cancer, is still a great threat to the world, including China. Surgery, platinum-based chemotherapy, and radiotherapy are still the primary treatments for NSCLC patients in the clinic, whereas immunotherapy and targeted therapy are gradually playing more important roles. A next-generation tyrosine kinase inhibitor (TKI), afatinib, was developed as a targeted reagent for epidermal growth factor receptor (EGFR). This targeted drug was effective in a series of trials. The US Food and Drug Administration then approved afatinib as a new first-line treatment for EGFR L858R and exon 19 deletion mutant patients in 2013. This review focused on current clinical studies of afatinib. Although this TKI was not widely available in China until recently, we aim to provide a reference for its future use in China.

An evaluation of the challenges to developing tumor BRCA1 and BRCA2 testing methodologies for clinical practice

Ovarian cancer patients with germline or somatic pathogenic variants benefit from treatment with poly ADP ribose polymerase (PARP) inhibitors. Tumor BRCA1/2 testing is more challenging than germline testing as the majority of samples are formalin-fixed paraffin embedded (FFPE), the tumor genome is complex, and the allelic fraction of somatic variants can be low. We collaborated with 10 laboratories testing BRCA1/2 in tumors to compare different approaches to identify clinically important variants within FFPE tumor DNA samples. This was not a proficiency study but an inter-laboratory comparison to identify common issues. Each laboratory received the same tumor DNA samples ranging in genotype, quantity, quality, and variant allele frequency (VAF). Each laboratory performed their preferred next-generation sequencing method to report on the variants. No false positive results were reported in this small study and the majority of methods detected the low VAF variants. A number of variants were not detected due to the bioinformatics analysis, variant classification, or insufficient DNA. The use of hybridization capture or short amplicon methods are recommended based on a bioinformatic assessment of the data. The study highlights the importance of establishing standards and standardization for tBRCA testing particularly when the test results dictate clinical decisions regarding life extending therapies.

Key differences between 13 KRAS mutation detection technologies and their relevance for clinical practice

Introduction

This study assessed KRAS mutation detection and functional characteristics across 13 distinct technologies and assays available in clinical practice, in a blinded manner.

Methods

Five distinct KRAS-mutant cell lines were used to study five clinically relevant KRAS mutations: p.G12C, p.G12D, p.G12V, p.G13D and p.Q61H. 50 cell line admixtures with low (50 and 100) mutant KRAS allele copies at 20%, 10%, 5%, 1% and 0.5% frequency were processed using quantitative PCR (qPCR) (n=3), matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-TOF) (n=2), next-generation sequencing (NGS) (n=6), digital PCR (n=1) and Sanger capillary sequencing (n=1) assays. Important performance differences were revealed, particularly assay sensitivity and turnaround time.

Results

Overall 406/728 data points across all 13 technologies were identified correctly. Successful genotyping of admixtures ranged from 0% (Sanger sequencing) to 100% (NGS). 5/6 NGS platforms reported similar allelic frequency for each sample. One NGS assay detected mutations down to a frequency of 0.5% and correctly identified all 56 samples (Oncomine Focus Assay, Thermo Fisher Scientific). One qPCR (Idylla, Biocartis) and MALDI-TOF (UltraSEEK, Agena Bioscience) assay identified 96% (all 100 copies and 23/25 at 50 copies input) and 92% (23/25 at 100 copies and 23/25 at 50 copies input) of samples, respectively. The digital PCR assay (KRAS PrimePCR ddPCR, Bio-Rad Laboratories) identified 60% (100 copies) and 52% (50 copies) of samples correctly. Turnaround time from sample to results ranged from ~2 hours (Idylla CE-IVD) to 2 days (TruSight Tumor 15 and Sentosa CE-IVD), to 2 weeks for certain NGS assays; the level of required expertise ranged from minimal (Idylla CE-IVD) to high for some technologies.

Discussion

This comprehensive parallel assessment used high molecular weight cell line DNA as a model system to address key questions for a laboratory when implementing routine KRAS testing. As most of the technologies are available for additional molecular biomarkers, this study may be informative for other applications.

Guidance Statement On BRCA1/2 Tumor Testing in Ovarian Cancer Patients

The approval, in 2015, of the first poly (adenosine diphosphate-ribose) polymerase inhibitor (PARPi; olaparib, Lynparza) for platinum-sensitive relapsed high-grade ovarian cancer with either germline or somatic BRCA1/2 deleterious mutations is changing the way that BRCA1/2 testing services are offered to patients with ovarian cancer. Ovarian cancer patients are now being referred for BRCA1/2 genetic testing for treatment decisions, in addition to familial risk estimation, and irrespective of a family history of breast or ovarian cancer. Furthermore, testing of tumor samples to identify the estimated 3%-9% of patients with somatic BRCA1/2 mutations who, in addition to germline carriers, could benefit from PARPi therapy is also now being considered. This new testing paradigm poses some challenges, in particular the technical and analytical difficulties of analyzing chemically challenged DNA derived from formalin-fixed, paraffin-embedded specimens. The current manuscript reviews some of these challenges and technical recommendations to consider when undertaking BRCA1/2 testing in tumor tissue samples to detect both germline and somatic BRCA1/2 mutations. Also provided are considerations for incorporating genetic analysis of ovarian tumor samples into the patient pathway and ethical requirements.

Comparison of direct sequencing and amplification refractory mutation system for detecting epidermal growth factor receptor mutation in non-small-cell lung cancer patients: a systematic review and meta-analysis

BACKGROUND

Direct sequencing and amplification refractory mutation system (ARMS) are commonly used to detect epidermal growth factor receptor (EGFR) mutation status in patients with non-small-cell lung cancer to inform the decision-making on tyrosine kinase inhibitors treatment. This study aimed to systematically compare the two methods in terms of the rate of detected mutations and the association of detected mutations with clinical outcomes.

MATERIAL AND METHODS

PubMed, EMBASE, China National Knowledge Infrastructure (in Chinese) and Wanfang database (in Chinese) were searched to identify relevant studies. Meta-analyses of EGFR mutation rates, rate differences, and the associations of EGFR mutations with clinical outcomes of tyrosine kinase inhibitors treatment were conducted.

RESULTS

Eight hundred and sixty-six records were retrieved and 26 studies with 3282 patients were included. The pooled rate of mutations detected by ARMS (41%, 95% confidence interval (CI) 35% to 47%) was significantly higher than that by direct sequencing (28%, 95%CI 22% to 34%), with a weighted rate difference of 11% (95%CI 8% to 13%). There was a consistent trend that the associations between ARMS-detected mutations and clinical outcomes were stronger than those between direct-sequencing-detected mutations and clinical outcomes (pooled risk ratio for objective response: 5.18 vs. 2.25; hazard ratio for progression-free survival: 0.30 vs. 0.42; hazard ratio for overall survival: 0.46 vs. 0.54).

CONCLUSIONS

More patients with EGFR mutations can be identified by ARMS than by direct sequencing, and those identified by ARMS seems to be able to benefit more from tyrosine kinase inhibitors than those identified by direct sequencing.

[Detection and Clinical Significance of Abundance of EGFR Mutation]

Non-small cell lung cancer (NSCLC) patients, with sensitive epidermal growth factor receptor (EGFR) mutations react well to tyrosine kinase inhibitors (TKIs). However, the efficacy of TKIs on patients with the same mutant types differs dramatically. It is implied that the different quantities of mutant alleles could be one of the reasons underlying. Patients with high abundance of EGFR mutation might benefit more from TKIs. There are no universal standards for the definition of EGFR mutant abundance. Abundance could be semi-quantified according to the different sensitivities of detection methods, quantified with quantifying detection techniques such as digital PCR or next generation sequencing, or quantified based on the expression of mutant proteins. The different abundances of primary and metastatic diseases could reflect the heterogeneity of the tumors. The pre-treatment level or the dynamic change of EGFR mutant abundance could help observe the course of the diseases and predict the efficacy of TKIs. TKIs resistance could be detected by change of abundance prior to image manifestations. Besides, the abundance of T790M could also predict drug efficacy and resistance of the first and third generation TKIs. Thus the detection of EGFR mutant abundance has important clinical significance. The standardization and correction of abundance needs more exploration.

Clinical value and indication for the dissection of lymph nodes posterior to the right recurrent laryngeal nerve in papillary thyroid carcinoma

Lymph nodes posterior to the right recurrent laryngeal nerve (LN-prRLN) are common sites of nodal recurrence after the resection of papillary thyroid carcinoma (PTC). However, the indication for LN-prRLN dissection remains debatable. We therefore studied the relationships between LN-prRLN metastasis and the clinicopathological characteristics in 306 patients with right or bilateral PTC who underwent LN-prRLN dissection. We found that LN-prRLN metastasis occurred in 16.67% of PTC and was associated with a number of the clinicopathological features. The receiver-operator characteristic (ROC) analysis showed that the areas under the ROC curves for the prediction of LN-prRLN metastasis by the risk factors age < 35.5 years, right tumor size > 0.85 cm, lymph node (right cervical central VI-1) number > 1.5, metastatic lymph node (right cervical central VI-1) size > 0.45 cm, and lymph node number in the right cervical lateral compartment > 0.5 were 0.601, 0.815, 0.813, 0.725, and 0.743, respectively.

In conclusion, the risk factors for LN-prRLN metastasis in patients suffering right thyroid lobe or bilateral PTC include age ≤ 35.5 years, right tumor size ≥ 0.85 cm, capsular invasion, metastatic lymph node (right cervical central VI-1) number ≥ 2, metastatic lymph node (right cervical central VI-1) size ≥ 0.45 cm, and metastatic lymph node number in the right cervical lateral compartment ≥ 1. In patients whose risk factors can be identified pre-operatively or intraoperatively, the dissection of LN-pr-RLN should be considered during right cervical central compartment dissection.

Impact of germline and somatic BRCA1/2 mutations: tumor spectrum and detection platforms

The BRCA1/2 genes are long and complex and mutation carriers are at risk of developing malignancies, mainly of gynecological origin. Various mutations arise in these genes and their characterization is a time-consuming, cost intensive, complicated process. Tumors of BRCA1/2 origin have distinct molecular and histological features that can impact responses to therapy. Therefore, detection of these mutations constitutes an important step in the risk assessment, prevention strategy and treatment of subjects. Although Sanger sequencing is the gold standard for the detection of genetic mutations, several next generation sequencing-based high throughput platforms have been developed and adapted for the detection of BRCA1/2 mutations. This review provides a comprehensive overview of the sequencing platforms available for the screening and identification of these mutations. We also summarize what is known about the different types of mutations that arise in these genes and the tumor spectra they result in. Finally, we present a short discussion on existing clinical guidelines which assist physicians in the decision-making process. These parameters have important consequences for the management of patients and an urgent need exists for the development of detection platforms that are cost effective and can provide clinicians with conclusive results within a significantly shorter time.

Association between BRAF V600E Mutation and Ultrasound Features in Papillary Thyroid Carcinoma Patients with and without Hashimoto's Thyroiditis

To assess the association between BRAF V600E mutation and ultrasound (US) features in papillary thyroid carcinoma (PTC) patients with and without Hashimoto’s thyroiditis (HT). We retrospectively reviewed the US features and status of BRAF V600E mutation in 438 consecutive patients with surgically confirmed PTCs. The association between BRAF mutation and US features were analyzed. In addition, we conducted subgroup analyses in terms of coexistent HT. The BRAF mutation was found in 86.5% of patients (379 of 438). Patient age (OR: 1.028, P = 0.010), age ≥ 50 y (OR: 1.904, P = 0.030), and microcalcification (OR: 2.262, P = 0.015) on US were significantly associated with BRAF mutation in PTC patients. Solid component (OR: 5.739, P = 0.019) on US was the significant predictor for BRAF mutation in patients with HT, while age (OR: 1.036, P = 0.017) and microcalcification (OR: 3.093, P = 0.017) were significantly associated with BRAF mutation in patients without HT. In conclusion, older age and microcalcification are risk factors for BRAF mutation in PTC patients, especially in those without HT. For those with HT, however, PTCs with BRAF mutation tend to be solid on ultrasound. These factors might be considered when making treatment planning or prognosis evaluation.