Detection of BRAF mutations in thyroid nodules by allele-specific PCR using a dual priming oligonucleotide system

PEAC: An Ultrasensitive and Cost-Effective MRD Detection System in Non-small Cell Lung Cancer Using Plasma Specimen

Circulating tumor DNA (ctDNA), a tumor-derived fraction of cell-free DNA (cfDNA), has emerged as a promising marker in targeted therapy, immunotherapy, and minimal residual disease (MRD) monitoring in postsurgical patients. However, ctDNA level in early-stage cancers and postsurgical patients is very low, which posed many technical challenges to improve the detection rate and sensitivity, especially in the clinical practice of MRD detection. These challenges usually include insufficient DNA input amount, limit of detection (LOD), and high experimental costs. To resolve these challenges, we developed an ultrasensitive ctDNA MRD detection system in this study, namely PErsonalized Analysis of Cancer (PEAC), to simultaneously detect up to 37 mutations, which account for 70–80% non-small cell lung cancer (NSCLC) driver mutations from low plasma sample volume and enables LOD of 0.01% at a single-site level. We demonstrated the high performance achieved by PEAC on both cfDNA reference standards and clinical plasma samples from three NSCLC patient cohorts. For cfDNA reference standards, PEAC achieved a specificity of 99% and a sensitivity of 87% for the mutations at 0.01% allele fraction. In the second cohort, PEAC showed 100% concordance rate between ddPCR and Next-generation sequencing (NGS) among 29 samples. In the third cohort, 22 of 59 patients received EGFR TKI treatment. Among them, three in four patients identified low level actionable gene mutations only by PEAC had partial responses after targeted therapy, demonstrating high ctDNA detection ability of PEAC. Overall, the developed PEAC system can detect the majority of NSCLC driver mutations using 8–10 ml plasma samples, and has the advantages of high detection sensitivity and lower costs compared with the existing technologies such as ddPCR and NGS. These advantages make the PEAC system quite appropriate for ctDNA and MRD detection in early-stage NSCLC and postsurgical recurrence monitoring.

Copy Number Variations in Genetic Diagnosis of Congenital Adrenal Hyperplasia Children

Background: Congenital adrenal hyperplasia (CAH) is a monogenic disorder caused by genetic diversity in the CYP21A2 gene, with 21-hydroxylase deficiency (21-OHD) as the most common type. Early sex assignment and early diagnosis of different genetic variations with a proper technique are important to reduce mortality and morbidity. Proper early sex identification reduces emotional, social, and psychological stress.

Aim: Detection of a spectrum of aberrations in the CYP21A2 gene, including copy number variations, gene conversion, chimeric genes, and point variations.

Methods: The CYP21A2 gene was screened using MLPA assay in 112 unrelated Egyptian children with 21-OHD CAH (33 males and 79 females).

Results: In the studied group, 79.5% were diagnosed within the first month of life. 46.8% of the genetic females were misdiagnosed as males. Among the copy number variation results, large deletions in 15.4% and three types of chimeric genes in 9% (CH-1, CH-7, and CAH-X CH-1) were detected. Regarding gene dosage, one copy of CYP21A2 was found in 5 cases (4.5%), three copies were detected in 7 cases (6.3%), and one case (0.9%) showed four copies. Eight common genetic variants were identified, I2G, large deletions, large gene conversion (LGC), I172N, F306 + T, -113 SNP, 8bp Del, and exon 6 cluster (V237E and M239K) with an allelic frequency of 32.62%, 15.45%, 7.30%, 3.00%, 2.58%, 2.15%, 0.86%, and 0.86%, respectively.

Conclusion: High prevalence of copy number variations highlights the added value of using MLPA in routine laboratory diagnosis of CAH patients.

Prevalence of BRAFV600E mutation in Asian series of papillary thyroid carcinoma-a contemporary systematic review

Papillary thyroid carcinoma (PTC), the most common malignancy of the endocrine system, is frequently driven by BRAFV600E mutation, which was reported in 35-60% cases in Western series. Numerous studies have recently emerged from Asian countries and regions; however sufficient summary is lacking to date. BRAF mutation serves as a diagnostic and prognostic tool in thyroid cancer, therefore establishing a rate of BRAF on the national scale could be of practical significance. We performed systematic reviews of available literature to investigate the prevalence of BRAF mutation in series of PTC from various Asian countries and regions. Out of the total 3,966 reports identified via initial screening, 138 studies encompassing over 40,000 PTCs were included for the final analysis. A vast majority (90.2%) of PTCs with known BRAF status were from East Asia, including China, South Korea, and Japan, with BRAF mutation rates of 71.2%, 75.5%, and 70.6%, respectively. Less abundant Indian and Saudi Arabian series found 45.6% and 46.3% prevalence of BRAFV600E in PTC, respectively. Much limited evidence was available from Thailand, Iran, Kazakhstan, Taiwan, Singapore, Indonesia, Hong Kong, Philippines, Vietnam, Iraq, and Myanmar. No relevant publications were found from other highly populated countries, such as Pakistan, Bangladesh, and Malaysia. After grouping by geographic region, we found that the highest rate of BRAFV600E was reported in the PTC series from East Asia (76.4%). Much lower rate (45-48%) was seen in PTC cohorts from South Asia, Central Asia, and the Middle East while the Southeast Asian series were in between (57%). Further subgroup analysis revealed that studies employing fresh frozen tissue and fine-needle aspirates showed higher rates of BRAF compared to those used formalin-fixed paraffin-embedded tissues. We found that the PTC series enrolled patients' cohorts after 2010 demonstrated a higher rate of BRAF compared to the earlier series. Finally, pediatric PTCs had lower BRAF prevalence compared to the baseline rate for the country. In conclusion, despite considerable among and within countries heterogeneity, the Asian PTC series showed a higher prevalence of BRAFV600E mutation than that in Western series. Causes of geographic heterogeneity, whether genuine (etiology, genetics) or methodology-related should be further investigated.

Simultaneous Detection of Bovine Rotavirus, Bovine Parvovirus, and Bovine Viral Diarrhea Virus Using a Gold Nanoparticle-Assisted PCR Assay With a Dual-Priming Oligonucleotide System

Bovine rotavirus (BRV), bovine parvovirus (BPV), and bovine viral diarrhea virus (BVDV) are the pathogens that cause diarrhea primarily in newborn calves. A mixed infection of BRV, BPV, and BVDV makes clinical diagnosis difficult. In this study, we designed dual-priming oligonucleotide (DPO) primers the VP6 gene of BRV, VP2 gene of BPV, and 5′UTR gene of BVDV and synthesized gold nanoparticles (GNPs) with an average diameter of 10 nm. We combined the DPOs with the GNPs to develop a DPO-nanoPCR assay for detecting BRV, BPV, and BVDV. The annealing temperature, primer concentration, and GNP concentration were optimized for this assay. Compared to a conventional PCR assay, the DPO-nanoPCR assay allowed the use of a wider range of annealing temperatures (41–65°C) to effectively amplify target genes. PCR amplification was the most efficient at 56.2°C using conventional primers. The optimal volume of all the primers (10 μM) was 1.0 μL. The optimal volume of GNPs (10 nM) for all the reactions was 0.5 μL. The detection limits of DPO-nanoPCR for pMD19-T-VP6, pMD19-T-VP2, and pMD19-T-5′UTR were 9.40 × 10² copies/μL, 5.14 × 10³ copies/μL, and 4.09 × 10¹ copies/μL, respectively; and those using conventional PCR were 9.40 × 10⁴ copies/μL, 5.14 × 10⁵ copies/μL, and 4.09 × 10⁴ copies/μL, respectively. The sensitivity of DPO-nanoPCR was at least 100-fold higher than that of conventional PCR. The specificity detection showed that the DPO-nanoPCR was able to specifically detect BRV, BPV, and BVDV. Use of clinical samples indicated that target viruses can be detected accurately. Thus, DPO-nanoPCR is a new powerful, simple, specific, and sensitive tool for detecting mixed infections of BRV, BPV, and BVDV.

Prevalence and prognostic relevance of BrafV600E mutation in colorectal carcinomas from Kashmir (North India) valley

Molecular studies have implicated mutant B-type Raf kinase (BRAFMut) of MAP-kinase signalling pathway in the pathogenesis of several cancers including colorectal cancer. Recently, the prognostic and therapeutic relevance of the most frequent BRAFV600E mutation also has been highlighted in colorectal carcinomas (CRC). Thus, the aim of this study was to investigate the prevalence of BRAFV600E mutation and to determine the correlation between this mutation and indicators of poor prognosis and outcome in patients with CRCs from Kashmir, North India. Here, we developed a highly sensitive technique, mutation allele-specific multiplex PCR (MASMP), for detection of BRAFV600E/BRAFc.1799T>A mutation, the results of which were confirmed by sequencing the product and compared to direct DNA sequencing. In total, BRAFV600E mutation status was analyzed in 57 colorectal tumour samples and an equal number of adjacent normal tissues. A high frequency of BRAFV600E mutation 21% (12/57) was identified in tumour tissues by MASMP compared to only 5.2% by direct DNA sequencing. Statistical analysis indicated that compared to BRAF-negative colorectal tumours, patients with BRAFV600E colorectal tumours were more likely to be >50 years old (61%) (P < 0.03). These tumours were more likely to be of clinical tumour stages III and IV (63%) (P < 0.04) with lymph node metastasis (52%) (P < 0.02) and characterised by a high-grade histology (63%) (P < 0.04). Colorectal patients harbouring BRAFV600E mutation experience more relapse/recurrence (52%) (P < 0.02). We, therefore, conclude that BRAFV600E mutation can be used as an indicator of poor prognosis to predict the outcome for CRC patients from Kashmir. MASMP proved to be a simple, sensitive and reliable technique for screening patients for BRAFV600E mutation. Testing for this mutation may be useful for selecting initial therapy mode and for follow-up monitoring in CRC patients.

Molecular pathology of thyroid tumours of follicular cells: a review of genetic alterations and their clinicopathological relevance

Thyroid cancer is the most common endocrine malignancy. Knowledge of the molecular pathology of thyroid tumours originating from follicular cells has greatly advanced in the past several years. Common molecular alterations, such as BRAF p.V600E, RAS point mutations, and fusion oncogenes (RET-PTC being the prototypical example), have been, respectively, associated with conventional papillary carcinoma, follicular-patterned tumours (follicular adenoma, follicular carcinoma, and the follicular variant of papillary carcinoma/non-invasive follicular thyroid neoplasm with papillary-like nuclear features), and with papillary carcinomas from young patients and arising after exposure to ionising radiation, respectively. The remarkable correlation between genotype and phenotype shows how specific, mutually exclusive molecular changes can promote tumour development and initiate a multistep tumorigenic process that is characterised by aberrant activation of mitogen-activated protein kinase and phosphoinositide 3-kinase-PTEN-AKT signalling. Molecular alterations are becoming useful biomarkers for diagnosis and risk stratification, and as potential treatment targets for aggressive forms of thyroid carcinoma. What follows is a review of the principal genetic alterations of thyroid tumours originating from follicular cells and of their clinicopathological relevance.

The usefulness of a novel fully automated PCR-based Idylla test for detection of the BRAF V600E mutation in thyroid tissue: comparison with PNA-clamping PCR, real-time PCR and pyrosequencing

INTRODUCTION

The BRAF V600E mutation is the most common genetic event in papillary thyroid carcinoma (PTC). The BRAF V600E mutational status has a significant diagnostic and prognostic role in PTC since it can be detected in 32%-87% of PTC by various molecular methods.

AIMS

A novel, fully automated real-time PCR-based Idylla test is assessed to detect the BRAF mutation in formalin-fixed paraffin-embedded (FFPE) thyroid samples.

METHODS

99 PTC and 11 nodular hyperplasia FFPE thyroid tissues are evaluated for the BRAF V600E mutation by the Idylla tests and compared with peptide nucleic acid-clamping PCR, real-time PCR and pyrosequencing.

RESULTS

The sensitivity and specificity of the Idylla test to detect BRAF V600E are 98.8% and 100%, which is superior to real-time PCR and pyrosequencing. The concordance between Idylla and true positive is highest at 0.974.

CONCLUSIONS

This study validates that the Idylla test is a sensitive and specific method to detect BRAF V600E in FFPE thyroid tissues. A simple, quick and easy to handle Idylla test is a useful and reliable molecular technique to evaluate BRAF mutations.

Usefulness of NRAS codon 61 mutation analysis and core needle biopsy for the diagnosis of thyroid nodules previously diagnosed as atypia of undetermined significance

A repeat fine needle aspiration (FNA) is recommended for thyroid nodules diagnosed as atypia of undetermined significance (AUS) in a previous cytology. We evaluated the utility of NRAS codon 61 (NRAS61) mutation analysis and core needle biopsy (CNB) for the diagnosis of thyroid nodules previously diagnosed as AUS. This study enrolled 236 patients who underwent both NRAS61 mutation analysis and CNB of thyroid nodules previously diagnosed as AUS at cytology. The NRAS61 mutation was detected in 36 nodules and was more frequently detected in the AUS and follicular neoplasm (FN)/suspicious for follicular neoplasm (SFN) categories, as determined by histological analysis of CNB, than in the benign group (p = 0.005). Sixty-one patients underwent surgery, and 29 nodules were finally diagnosed as malignant after surgery. Among 61 patients who underwent surgery, nodules with the NRAS61 mutation (42-65 %) had a significantly higher malignancy rate than nodules with wild-type NRAS61 (7-37 %, p = 0.038). The association between malignancy and the NRAS61 mutation was significant after adjusting for age, sex, nodule size, and histological diagnosis of CNB (p = 0.01). NRAS61 mutation analysis together with CNB could be helpful for arriving at a clinical decision in patients with thyroid nodules showing AUS in a previous cytology.

Initial clinical experience with BRAF(V600E) mutation analysis of core-needle biopsy specimens from thyroid nodules

OBJECTIVE

The accurate diagnosis of thyroid nodules is important for making management decisions. The purpose of this study was to evaluate the feasibility of core-needle biopsy with BRAF(V600E) mutation analysis (CNB + BRAF(V600E) ) and to compare the clinical usefulness of CNB + BRAF(V600E) and fine-needle aspiration with BRAF(V600E) mutation analysis (FNA + BRAF(V600E) ) in the diagnosis of thyroid malignancy.

DESIGN, PATIENTS AND MEASUREMENTS

The results of BRAF(V600E) mutation analyses of 820 nodules from 820 patients (153 men, 667 women; mean age, 51·1 years), who underwent CNB + BRAF(V600E) (n = 256) or FNA + BRAF(V600E) (n = 564) between January 2011 and March 2012 were retrospectively evaluated. The feasibility of CNB + BRAF(V600E) was assessed by comparing its rate of detection of BRAF(V600E) mutations and positive predictive value with those of FNA + BRAF(V600E) . The clinical usefulness of CNB + BRAF(V600E) was determined by comparing rates of inconclusive results, the additional value of BRAF(V600E) mutation analysis, diagnostic surgery and diagnostic performance with those of FNA + BRAF(V600E) .

RESULTS

CNB + BRAF(V600E) and FNA + BRAF(V600E) had similar rates of BRAF(V600E) mutation detection (66·3% vs 64·4%, P = 0·883) and positive predictive value (100·0% vs 96·6%, P = 0·135). CNB + BRAF(V600E) had a significantly higher diagnostic accuracy rate (95·7% vs 85·9%, P < 0·001), and significantly lower rates of inconclusive results (8·2% vs 51·8%, P < 0·001), and diagnostic surgery (8·9% vs 22·3%, P = 0·006), than FNA + BRAF(V600E) .

CONCLUSIONS

The greater diagnostic performance of CNB + BRAF(V600E) and its lower rate of inconclusive results than FNA + BRAF(V600E) suggest that CNB + BRAF(V600E) can reduce rates of preventable diagnostic surgery.

BRAF mutations in non-small cell lung cancer: has finally Janus opened the door?

B-Raf mutations occur in about 1-2% of non-small cell lung cancers (NSCLC). These mutations generate a permanent activation of the mitogen activated protein kinase (MAPK) pathway, which promotes tumor growth and proliferation. In the present review, we discuss B-Raf mutation epidemiology, diagnostic methods to detect B-Raf mutations, the role of B-Raf as a driver mutation and a potential therapeutic target in NSCLC. The results of clinical trials involving B-Raf or MAPK pathway inhibitors for the treatment of NSCLC are also discussed. Clinical trials evaluating B-Raf inhibitors in BRAF mutated NSCLC patients have shown promising results, and larger prospective studies are warranted to validate these findings. Enrollment of these patients in clinical trials is an interesting strategy to offer a potentially more effective and less toxic targeted therapy.

DNA degradation in liquid-based cytology and its comparison with conventional smear

BACKGROUND

In fine needle aspiration biopsy (FNAB) of thyroid nodules, LBC is adopted in most of the hospitals and clinics in Korea for its convenience. BRAF mutation test has been introduced as an important ancillary test, but its applicability has not been completely proven with LBC samples.

METHODS

Five aspirates from thyroidectomy specimens were simultaneously processed into LBC and CS slides, in which BRAF mutation tests were performed using three primer sets with PCR products of 72, 164, and 226 base pairs (bp) at 6, 9, and 12 months after processing. In addition, BRAF mutation tests were performed in nine clinical samples that had been prepared by LBC or CS and stored for 3-5 years after processing.

RESULTS

At 9 months after processing, LBC failed to provide DNA of sufficient quality for PCR, whereas CS succeeded with primers for amplifying a 226 bp fragment. Furthermore, CS had successful amplification of DNA despite a delay of more than 1 year. The failure of DNA amplification in LBC was overcome by using primers to amplify shorter PCR products, suggesting that DNA degradation occurred in LBC. However, false positive or negative results were observed in primers for amplifying shorter size. The kind of preservative solutions used in LBC did not affect test results.

CONCLUSION

LBC may have disadvantages in long-term DNA preservation because of its accelerated DNA degradation compared with alcohol-fixed CS. Using primers to amplify shorter size fragments might be helpful in mitigating loss of signal due to DNA degradation in LBC.

Proficiency of DNA repair genes and microsatellite instability in operated colorectal cancer patients with clinical suspicion of lynch syndrome

BACKGROUND

Lynch syndrome (LS) diagnosis is underestimated, and most of the patients remain undetected after colorectal resections. The study aims to assess the frequency of LS in patients undergoing surgical treatment for colorectal cancer (CRC).

METHODS

A total of 458 CRC patients were operated from January 2005 to December 2008. Positive CRC family history (FH) was present in 118 (25.8%) patients. Histologic sections were reviewed for microsatellite instability (MSI) criteria (Bethesda guidelines), immunohistochemical (IHC) analysis for MLH1, MSH2, MSH6, PMS2 proteins, through the avidin-biotin-peroxidase complex, MSI (BAT-25, BAT-26, NR-21, NR-24 and MONO-27) and BRAF somatic mutation.

RESULTS

Of the 118 patients with FH, 61 (51.69%) met at least one of the revised Bethesda criteria. IHC was abnormal in 8 (13.1%) and MSI in 12 patients (20%). BRAF was negative in all cases. MSI histopathological included: intratumoral lymphocytes (47.5%), expansive tumors (29.5%) mucinous component (27.8%) and Crohn's like reaction in (14.7%). There was an association between the revised Bethesda criteria with: sex, mucinous histology and Crohn's like reaction; MSI and IHC with PMS2 and MLH1. Revised Bethesda criteria 4 had 10.6 increased chances to display positive MSI. We have proposed a score to contribute as a practical tool in the diagnosis of LS.

CONCLUSIONS

The frequence of LS in resected CRC patients was 2.6%. The criterion 4 Revised Bethesda was associated more strongly with the presence of MSI.

BRAF Immunohistochemistry Using Clone VE1 is Strongly Concordant with BRAF(V600E) Mutation Test in Papillary Thyroid Carcinoma

The aim of this study was to investigate the concordance between BRAF(V600E) mutation test and immunohistochemistry (IHC) and determine the diagnostic accuracy of IHC for papillary thyroid carcinoma (PTC) through a systematic review, meta-analysis, and diagnostic test accuracy review. The current systematic review and meta-analysis included 1141 PTCs in 11 eligible studies. We investigated the concordance rate and performed subgroup analysis using tissue and cytologic samples. Diagnostic test accuracy review was conducted and calculated using the value of area under curve (AUC) on the summary receiver operating characteristic (SROC) curve. The positive rate of BRAF IHC was 79.1% (903 of 1141 cases), and the BRAF(V600E) mutation was found in 76.6% (874 of 1141 cases). The concordance rates were 0.921 (95% confidence interval (CI) 0.877-0.950) and 0.894 (95% CI 0.801-0.946) in IHC positive and negative subgroups, respectively. In the diagnostic test accuracy review, the pooled sensitivity and specificity were 0.97 (95% CI 0.95-0.98) and 0.78 (95% CI 0.72-0.83). The value of AUC on SROC curve was 0.983, and diagnostic odds ratio was 164.28 (95% CI 57.69-467.80). Our results showed that BRAF IHC was strongly concordant with BRAF mutation test and had high diagnostic accuracy in BRAF mutation analysis of PTC.

Evaluation of the Clinical Usefulness of BRAFV600E Mutation Analysis of Core-Needle Biopsy Specimens in Thyroid Nodules with Previous Atypia of Undetermined Significance or Follicular Lesions of Undetermined Significance Results

BACKGROUND

The accurate diagnosis of thyroid nodules is important for making management decisions. The purpose of this study is to evaluate the clinical usefulness of BRAF(V600E) mutation analysis with core-needle biopsy (CNB+BRAF(V600E)) in thyroid nodules with previous atypia of undetermined significance (AUS) or follicular lesions of undetermined significance (FLUS) results.

MATERIALS AND METHODS

From January 2011 to December 2012, 590 CNB+BRAF(V600E) mutation analyses were performed. We analyzed 200 nodules from 200 patients with previous AUS/FLUS results (22 men, 178 women; mean age, 48.6 years). The clinical usefulness of CNB+BRAF(V600E) was assessed by comparing the rates of conclusive results, the additional value of BRAF(V600E) mutation analysis, diagnostic performances, and therapeutic/diagnostic surgery results with those of CNB alone. For the subgroup analysis, the study patients were divided into those with nodules with previous AUS results and those with previous FLUS results.

RESULTS

All CNB+BRAF(V600E) procedures were well-tolerated. CNB+BRAF(V600E) did not show significantly better diagnostic performance than CNB alone in thyroid nodules with previous AUS/FLUS results. However, the conclusive result rate of CNB+BRAF(V600E) was improved in thyroid nodules with previous AUS/FLUS results (76.5% vs. 73.0%, p=0.016), especially with previous AUS results (81.1% vs. 76.4%, p=0.031). Of the 56 previous AUS result thyroid nodules with surgical management, BRAF(V600E) mutation analysis led to therapeutic surgery in 5.4% by decreasing unnecessary diagnostic surgery.

CONCLUSIONS

In general, CNB+BRAF(V600E) did not show significantly higher diagnostic accuracy than CNB alone. Although CNB+BRAF(V600E) may add additional value in nodules with previous AUS results, routinely adding BRAF(V600E) mutation analysis to CNB is not recommended.

High-Resolution Melting Is a Sensitive, Cost-Effective, Time-Saving Technique for BRAF V600E Detection in Thyroid FNAB Washing Liquid: A Prospective Cohort Study

OBJECTIVE

The diagnostic accuracy of thyroid fine needle aspiration biopsy (FNAB) can be improved by the combination of cytological and molecular analysis. In this study, washing liquids of FNAB (wFNAB) were tested for the BRAF V600E mutation, using the sensitive and cost-effective technique called high-resolution melting (HRM). The aim was to demonstrate the feasibility of BRAF analysis in wFNAB and its diagnostic utility, combined with cytology.

DESIGN

Prospective cohort study.

METHODS

481 patients, corresponding to 648 FNAB samples, were subjected to both cytological (on cells smeared onto a glass slide) and molecular analysis (on fluids obtained washing the FNAB needle with 1 ml of saline) of the same aspiration. BRAF V600E analysis was performed by HRM after methodological validation for application to wFNAB (technique sensitivity: 5.4%).

RESULTS

The cytological results of the FNAB were: 136 (21%) nondiagnostic (THY1); 415 (64%) benign (THY2); 80 (12.4%) indeterminate (THY3); 9 (1.4%) suspicious for malignancy (THY4); 8 (1.2%) diagnostic of malignancy (THY5). The BRAF V600E mutation was found in 5 THY2, 2 THY3, 6 THY4 and 6 THY5 samples. Papillary carcinoma diagnosis was histologically confirmed in all BRAF+ thyroidectomized patients. BRAF combined with cytology improved the diagnostic value compared to cytology alone in a subgroup of 74 operated patients.

CONCLUSIONS

HRM was demonstrated to be a feasible method for BRAF analysis in wFNAB. Thanks to its sensitivity and cost-effectiveness, it might be routinely used on a large scale in clinical practice. In perspective, standby wFNAB samples could be analyzed a posteriori in case of indeterminate cytology and/or suspicious findings on ultrasound.

Dual priming oligonucleotide (DPO)-based multiplex PCR assay for specific detection of four diarrhoeagenic Escherichia coli in food

In this study, a dual priming oligonucleotide (DPO)-based multiplex PCR assay was developed for the specific detection of four foodborne diarrhoeagenic Escherichia coli (DEC) in food, including enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enterohemorrhagic E. coli (EHEC) O157:H7 and enteroinvasive E. coli (EIEC). Species-specific DPO primers were designed based on rfbE, LT, ipaH and bfpA genes for EHEC O157:H7, ETEC, EIEC and EPEC respectively. Our optimized DPO-based multiplex PCR assay was able to simultaneously detect these DEC from pure cultures, spiked food or environmental sample with an analytical detection limit of <120 CFU ml(-1) (or g(-1) ) for each at annealing temperature from 45 to 65°C. A total of 336 bacterial strains including 51 target and 285 other bacterial strains were used to evaluate the specificity of the assay, and results showed that specific PCR products were only amplified in strains belonging to target bacteria. Applying the assay to 982 samples collected from food, clinical patients and environmental sources revealed that 73 samples were positive, which were confirmed by conventional culture-based assays combined with serological tests. Taken together, the DPO-based multiplex PCR assay developed in this study is a rapid, specific and reliable tool for efficient screening single or multiple DEC from food in laboratory diagnosis.

SIGNIFICANCE AND IMPACT OF THE STUDY

The high specificity of the DPO-based multiplex PCR assay developed in this study without false positive results indicates its great potential to be a rapid, reliable, practical and cost-effective method for the monitoring of diarrhoeagenic E. coli in food.

BRAF(V600E) Mutation, RET/PTC1 and PAX8-PPAR Gamma Rearrangements in Follicular Epithelium Derived Thyroid Lesions - Institutional Experience and Literature Review

BACKGROUND

Thyroid cancers are the most frequently occurring endocrine malignancy worldwide. In Turkey, thyroid cancers are ranked 2(nd) on the incidence list in women, with a rate of 16.2%, but they are not included among the top 10 cancer types in men.

AIMS

To identify the contribution of the BRAF(V600E) mutation, and the RET/PTC1 and PAX8-PPARγ rearrangements in the diagnosis and differential diagnosis of follicular epithelial-derived thyroid lesions.

STUDY DESIGN

Retrospective clinical and molecular genetic study.

METHODS

A total of 86 thyroid cases diagnosed between 2001 and 2012 at the Department of Pathology were included in the retrospective study group. Samples best representing the lesion and comprising capsules were chosen in the selection of paraffin blocks pertaining to the cases. The BRAF(V600E) mutation, and the RET/PTC1 and PAX8-PPARγ rearrangements were investigated in all cases.

RESULTS

The BRAF(V600E) mutation was observed in 12 out of 37 papillary carcinoma cases (32.4%), in 1 out of 15 follicular carcinoma cases (6.6%), and in 1 out of 7 undifferentiated carcinoma cases (14.3%). No mutation was detected in benign lesions. The RET/PTC1 rearrangement was detected in 2 out of 7 undifferentiated carcinoma cases (28.6%), and in 1 out of 15 follicular carcinoma cases (6.6%). No gene rearrangement was detected in benign lesions. The PAX8-PPARγ rearrangement was detected in 5 out of 15 follicular thyroid carcinoma cases (33.3%) and in 1 out of 15 follicular adenoma cases (6.6%).

CONCLUSION

The BRAF(V600E) mutation and RET/PTC1 rearrangement were effective in distinguishing the follicular epithelium-derived benign and malignant lesions of the thyroid in the resection materials. The BRAF(V600E) mutation was rather specific to papillary carcinoma in the thyroid, and in cases where the BRAF(V600E) mutation was detected, multi-centricity, lymph node metastasis and capsular invasion findings were observed more frequently compared to cases in which no mutation was observed. The PAX8-PPARγ rearrangement was observed to be more effective in the differentiation of adenomas and carcinomas in follicular neoplasms of the thyroid, whereas the RET/PTC1 analysis contributed to the differential diagnosis of papillary carcinoma histogenesis at a frequency of 29% in undifferentiated thyroid carcinomas.

Comparison of Three BRAF Mutation Tests in Formalin-Fixed Paraffin Embedded Clinical Samples

BACKGROUND

Recently, BRAF inhibitors showed dramatic treatment outcomes in BRAF V600 mutant melanoma. Therefore, the accuracy of BRAF mutation test is critical.

METHODS

BRAF mutations were tested by dual-priming oligonucleotide-polymerase chain reaction (DPO-PCR), direct sequencing and subsequently retested with a real-time PCR assay, cobas 4800 V600 mutation test. In total, 64 tumors including 34 malignant melanomas and 16 papillary thyroid carcinomas were analyzed. DNA was extracted from formalin-fixed paraffin embedded tissue samples and the results of cobas test were directly compared with those of DPO-PCR and direct sequencing.

RESULTS

BRAF mutations were found in 23 of 64 (35.9%) tumors. There was 9.4% discordance among 3 methods. Out of 6 discordant cases, 4 cases were melanomas; 3 cases were BRAF V600E detected only by cobas test, but were not detected by DPO-PCR and direct sequencing. One melanoma patient with BRAF mutation detected only by cobas test has been on vemurafenib treatment for 6 months and showed a dramatic response to vemurafenib. DPO-PCR failed to detect V600K mutation in one case identified by both direct sequencing and cobas test.

CONCLUSIONS

In direct comparison of the currently available DPO-PCR, direct sequencing and real-time cobas test for BRAF mutation, real-time PCR assay is the most sensitive method.

Clinical utility of immunohistochemistry for the detection of the BRAF v600e mutation in papillary thyroid carcinoma

BACKGROUND

BRAF V600E mutation is the most common genetic alteration in papillary thyroid cancer (PTC). We used a mutation-specific antibody for immunohistochemical (IHC) detection of the BRAF V600E mutation and correlated expression with clinicopathologic features. The study was designed to validate the accuracy and determine the clinical importance of IHC detection of the BRAF V600E mutation in PTC.

METHODS

Direct sequencing and IHC for BRAF V600E mutation was performed in 37 consecutive patients with PTCs. IHC was scored on an intensity proportion scale. IHC positive tumors were stratified into intensity categories. The categories were assessed for clinicopathologic variables, including age, extrathyroidal extension, lymphovascular invasion, and lymph node metastases.

RESULTS

A total of 25 PTCs were BRAF V600E-positive and 12 were BRAF mutation-negative on IHC. The BRAF V600E mutation-specific antibody had a sensitivity of 89% and specificity of 100% for detecting the mutation. Tumors with high-intensity staining were more likely to have extrathyroidal extension.

CONCLUSION

IHC is an accurate method for the detection of the BRAF V600E mutation in PTC, and its ability to quantify the mutation expression may serve as a better predictor of tumor behavior than molecular sequencing. It provides a potentially rapid, easily applicable, and economic alternative to current techniques.

Immunohistochemical detection of mutated BRAF V600E supports the clonal origin of BRAF-induced thyroid cancers along the spectrum of disease progression

BACKGROUND

The mutated BRAF V600E protein has been specifically detected in papillary thyroid carcinomas (PTCs) using immunohistochemical (IHC) analysis. The clonal origin of PTCs harboring BRAF mutations has recently been called into question.

OBJECTIVES

The purpose of this study was 2-fold: (1) to compare BRAF V600E IHC expression in PTCs, poorly differentiated thyroid carcinomas (PDTCs), and anaplastic thyroid carcinomas (ATCs) with DNA mutation analysis; and (2) to study the distribution of BRAF V600E IHC staining within thyroid cancer tissues.

METHODS

Whole sections and tissue microarrays from 31 PTCs, 38 PDTCs, and 22 ATCs were subjected to both mass spectrometry genotyping for the BRAF(T1799A) mutation as well as IHC staining for BRAF V600E protein.

RESULTS

Of the 31 PTCs, 16 (52%) showed strong (3+) IHC staining and harbored BRAF(T1799A), whereas the remaining 15 (48%) showed absent/faint (0/1+) staining, and were wild type for BRAF (BRAF-wt). Only 5 of 38 (13%) PDTCs harbored mutant BRAF, and these were the only ones with moderate (2+) or 3+ IHC staining. All 14 ATCs with a staining intensity of 3+ harbored BRAF(T1799A), whereas the 2 ATCs with 0/1+ staining were BRAF-wt. Six ATCs showed staining of 2+, 5 of which had high background staining. Of those 6 cases, BRAF(T1799A) was present only in the tumor without background. Homogeneous staining was found in 13 of 14 (93%) PTCs, 3 of 3 (100%) PDTCs, and 12 of 14 ATCs (86%).

CONCLUSIONS

First, absent/faint staining for BRAF V600E correlates perfectly with the lack of the BRAF(T1799A) mutation, whereas strong staining is highly specific for the BRAF(T1799A) mutation in PTCs, PDTCs, and ATCs. Moderate staining intensity cannot be relied on and should lead to genotypic analysis. Second, homogeneous staining occurs in the vast majority of cases, demonstrating that the BRAF(T1799A) mutation is a clonal event in thyroid cancer.

Detection of BRAF V600E mutation with thyroid tissue using pyrosequencing: comparison with PNA-clamping and real-time PCR

We used pyrosequencing, peptide nucleic acid (PNA)-clamping polymerase chain reaction (PCR), and real-time PCR to detect the BRAF V600E mutation and to investigate the prognostic effect of the BRAF V600E mutation in paraffin block specimens from 100 patients diagnosed with papillary thyroid carcinoma. Positive rates of PNA-clamping PCR, real-time PCR, and pyrosequencing were 66%, 70%, and 68%, respectively. Pyrosequencing and PNA-clamping PCR detected mutant type in a 99:1 (wild-type: mutant) DNA concentration, and PNA-clamping PCR detected mutant type in a 99.5:0.5 DNA concentration. Clamping PCR showed higher κ value than real-time PCR (0.729 vs 0.626). The BRAF V600E mutation was associated with an advanced stage of cancer (P = .045) and was found to be associated with poor prognostic factors. This study suggests that pyrosequencing can be as sensitive as real-time PCR and that PNA-clamping PCR is a sensitive and reliable method to detect the BRAF V600E mutation.

Sonographically suspicious thyroid nodules with initially benign cytologic results: the role of a core needle biopsy

PURPOSE

To evaluate the diagnostic role of core needle biopsy (CNB) in sonographically suspicious thyroid nodules with initially benign cytologic results through a histologic analysis of CNB specimens.

METHODS

Between October 2008 and July 2011, 88 patients underwent ultrasound (US)-guided CNB for initially benign cytologic results with suspicious US features at our institution. In all, 85 patients with 85 focal thyroid nodules were included in the study after surgery or concordant benign readings following fine-needle aspiration biopsy (FNAB) and CNB. We evaluated the risk of malignancy, diagnostic performance of CNB, and histologic findings for these nodules.

RESULTS

Of the 85 nodules, 28 (32.9%) were histologically upgraded on CNB specimens including one case of atypia of undetermined significance (AUS), seven cases of follicular neoplasm, one case of suspicious for malignancy, and 19 cases of malignancy. Of these, 27 (31.8%) were finally confirmed as malignant, and one as follicular adenoma at surgery. The 27 malignant nodules included 21 papillary thyroid carcinomas (PTCs), five follicular thyroid carcinomas, and one Hürthle cell carcinoma. All PTCs were diagnosed from CNB readings of AUS suspicious for malignancy or malignancy. Follicular thyroid carcinomas and Hürthle cell carcinoma were diagnosed from CNB readings of follicular neoplasm. Histologic analysis of benign CNB specimens revealed severe fibrosis (96.4%), hemosiderin (21.4%), calcification (17.9%), granulation tissue (12.5%), and focal lymphocytic thyroiditis (12.5%).

CONCLUSIONS

The histologic information obtained by analysis of CNB specimens may enable more confident diagnosis for benign nodules with suspicious US features and reduce the need for repetitive FNABs or diagnostic surgery.

B-Raf and the inhibitors: from bench to bedside

The B-Raf protein is a key signaling molecule in the mitogen activated protein kinase (MAPK) signaling pathway and has been implicated in the pathogenesis of a variety of cancers. An important V600E mutation has been identified and can cause constitutive B-Raf activation. Recent studies have evaluated a variety of small molecule inhibitors targeting B-Raf, including PLX4032/vemurafenib, dabrafenib, LGX818, GDC0879, XL281, ARQ736, PLX3603 (RO5212054), and RAF265. Therapeutic resistance has been identified and various mechanisms described. This review also discussed the current understanding of B-Raf signaling mechanism, methods of mutation detection, treatment strategies as well as potential methods of overcoming therapeutic resistance.

Activation of nuclear factor-κB contributes to growth and aggressiveness of papillary thyroid carcinoma

Nuclear factor-κB (NF-κB) is involved in proliferation, angiogenesis, and metastasis in various malignancies; however, the role of NF-κB in papillary thyroid carcinoma (PTC) has not been fully elucidated. The purpose of this study was to elucidate the role and clinicopathological significance of the NF-κB signaling pathway in PTC. We investigated NF-κB RelA expression in 122 patients with conventional PTC by immunohistochemistry, and evaluated the correlation between RelA expression and clinicopathological parameters, including BRAF(V600E) mutation. Nuclear expression of NF-κB RelA, regardless of cytoplasmic expression, was identified in 91 of 122 PTCs (74.6%), and was more frequent in PTCs larger than 1cm (overt PTC) (P=0.001). There were significant differences in clinicopathological parameters, such as extrathyroidal extension (P=0.031), nodal metastasis (P=0.021) and BRAF(V600E) mutation (P=0.039), between NF-κB-positive and negative PTCs. Proliferation index was strongly associated with NF-κB activation (P=0.045) but not with BRAF(V600E) mutation (P=0.141). Taken together, our results suggest that NF-κB RelA activation contributes, at least in part, to tumor growth and aggressiveness of PTC after tumor transformation. The expression pattern of NF-κB may serve as a prognostic marker and a potential therapeutic target.

Immunohistochemistry with a mutation-specific monoclonal antibody as a screening tool for the BRAFV600E mutational status in primary cutaneous malignant melanoma

The V600E mutation of BRAF has emerged as both an effective biomarker and therapeutic target for select benign and malignant cutaneous and non-cutaneous human tumors and is typically determined using DNA-based techniques that include allele-specific PCR and direct DNA sequencing. Recently however, the development of new antibodies directed against the V600E protein has opened the door for an easier and more efficient strategy for identifying this mutation. Our present aim was to determine the efficacy of one such antibody, anti-B-Raf (V600E), a mouse monoclonal antibody in which the immunogen is a synthetic peptide derived from the internal region of BRAFV600E. A total of 35 cases of primary cutaneous melanoma were evaluated using a combination of DNA-based techniques that included allele-specific PCR and/or direct DNA sequencing and immunohistochemistry. Cases of papillary thyroid carcinomas (n=5) and colorectal carcinomas (n=5), known to harbor the BRAFV600E mutation, served as positive controls for the study. DNA analyses revealed that 6 of 35 (17%) cases of the primary cutaneous malignant melanoma possessed the BRAFV600E mutation. For immunohistochemical analyses, cytoplasmic positivity with anti-B-Raf was noted in 7 of 35 (20%) cases of primary melanoma and in all 10 positive controls. Statistical analyses of the data demonstrated that the sensitivity of the immunohistochemistry was 100% and specificity was 97%. Findings from the current study support the potential use of immunohistochemistry as an ancillary screening tool to assess the BRAFV600E mutation status in primary cutaneous melanoma.

Study of peripheral BRAF(V600E) mutation as a possible novel marker for papillary thyroid carcinomas

BACKGROUND

The BRAF(V600E) mutation can be detected peripherally in the serum of patients with thyroid cancer. The purpose of this study was to establish the value of detecting the peripheral BRAF(V600E) mutation as a serum tumor marker in this population.

METHODS

In this study, we obtained 94 serum samples from patients with papillary thyroid cancer positive for the BRAF(V600E) mutation in the tumor itself. The serum samples were analyzed for BRAF(V600E) mutation using real-time polymerase chain reaction (PCR).

RESULTS

Sixty-seven patients (71.3%) had papillary thyroid microcarcinoma and 26 patients (27.7%) had underlying lymphocytic thyroiditis. Forty-three patients (45.7%) were found to have stage III or stage IV thyroid cancer. None of the patients had a detectable serum BRAF(V600E) mutation.

CONCLUSION

We were unable to identify peripheral BRAF(V600E) mutations in patients with papillary thyroid cancer using real-time PCR. Further studies will be needed to validate our results using various diagnostic methods.

Detection of BRAF(V600E) Mutations in Papillary Thyroid Carcinomas by Peptide Nucleic Acid Clamp Real-Time PCR: A Comparison with Direct Sequencing

BACKGROUND

Papillary thyroid carcinoma (PTC) of the thyroid is the most common endocrine malignancy. High prevalence of an activating point mutation of BRAF gene, BRAF(V600E), has been reported in PTC. We assessed the efficiency of peptide nucleic acid clamp real-time polymerase chain reaction (PNAcqPCR) for the detection of BRAF(V600E) mutation in PTC in comparison with direct sequencing (DS).

METHODS

A total of 265 thyroid lesions including 200 PTCs, 5 follicular carcinomas, 60 benign lesions and 10 normal thyroid tissues were tested for BRAF(V600E) mutation by PNAcqPCR and DS.

RESULTS

The sensitivity and accuracy of the PNAcqPCR method were both higher than those of DS for the detection of the BRAF(V600E) mutation. In clinical samples, 89% of PTCs harbored the BRAF(V600E) mutation, whereas 5 follicular carcinomas, 50 benign lesions and 10 normal thyroid tissues lacked the mutation. The mutation was associated with aggressive clinical behaviors as extrathyroid invasion (p=0.015), lymph node metastasis (p=0.002) and multiple tumor numbers (p=0.016) with statistical significance.

CONCLUSIONS

The PNAcqPCR method is efficiently applicable for the detection of the BRAF(V600E) mutation in PTCs in a clinical setting.

The utility of BRAF testing in the management of papillary thyroid cancer

This review summarizes the current literature surrounding BRAF and its significance in thyroid cancer.

Over the last decade, investigators have developed a clearer understanding of the genetic alterations underlying thyroid carcinogenesis. A number of biomarkers involved in the pathogenesis of differentiated thyroid cancer have undergone intensive study, not only for their role in tumorigenesis, but also for their potential utility as diagnostic and prognostic indicators and therapeutic targets. This review summarizes the current literature surrounding BRAF and its significance in thyroid cancer. Further, we discuss how molecular analysis can be integrated into management algorithms for thyroid nodules and papillary thyroid cancer. We also review what is known, to date, about the association of BRAF and papillary microcarcinoma as well as using targeted therapies for BRAF as adjuvant treatment for metastatic papillary thyroid cancer.