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Igder S, Zamani M, Fakher S, Siri M, Ashktorab H, Azarpira N, Mokarram P. Circulating Nucleic Acids in Colorectal Cancer: Diagnostic and Prognostic Value. DISEASE MARKERS 2024; 2024:9943412. [PMID: 38380073 PMCID: PMC10878755 DOI: 10.1155/2024/9943412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 01/07/2024] [Accepted: 01/25/2024] [Indexed: 02/22/2024]
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer in the world and the fourth leading cause of cancer-related mortality. DNA (cfDNA/ctDNA) and RNA (cfRNA/ctRNA) in the blood are promising noninvasive biomarkers for molecular profiling, screening, diagnosis, treatment management, and prognosis of CRC. Technological advancements that enable precise detection of both genetic and epigenetic abnormalities, even in minute quantities in circulation, can overcome some of these challenges. This review focuses on testing for circulating nucleic acids in the circulation as a noninvasive method for CRC detection, monitoring, detection of minimal residual disease, and patient management. In addition, the benefits and drawbacks of various diagnostic techniques and associated bioinformatics tools have been detailed.
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Affiliation(s)
- Somayeh Igder
- Department of Clinical Biochemistry, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mozhdeh Zamani
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Shima Fakher
- Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Morvarid Siri
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Hassan Ashktorab
- Department of Medicine, Gastroenterology Division and Cancer Center, Howard University College of Medicine, Washington, DC, USA
| | - Negar Azarpira
- Autophagy Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Pooneh Mokarram
- Autophagy Research Center, Department of Biochemistry, Shiraz University of Medical Sciences, Shiraz, Iran
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Xiong XJ, Xiao MM, Zhang YX, Liu DG, Jin ML, Wang J, Xu HT, Li QC, Wu GP. The Accurate Interpretation and Clinical Significance of Morphological Features of Fine Needle Aspiration Cells in Papillary Thyroid Carcinoma. Anal Cell Pathol (Amst) 2023; 2023:9397755. [PMID: 37181946 PMCID: PMC10171979 DOI: 10.1155/2023/9397755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/01/2023] [Accepted: 04/21/2023] [Indexed: 05/16/2023] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common malignant neoplasm of the thyroid gland; fine needle aspiration cytology is the most basic and reliable diagnostic method before PTC operation. However, it is not clear which cell morphological changes can be used as a reliable standard for the diagnosis of PTC. A retrospective analysis was performed on 337 patients with PTC confirmed by postoperative histology. An additional 197 randomly selected patients with benign thyroid lesions were included in the study and used as a control group. True papillary arrangements, swirl arrangements, and escape arrangements had high specificity, all of which were 100%, but only swirl arrangements had ideal sensitivity (77.61%). The nuclear volume characteristics had a high sensitivity of more than 90%, but the specificities of both nuclear crowding and nuclear overlap were too low, only 16.34% and 23.35%. The sensitivities of five nuclear structural characteristics were more than 90%, but only the specificity of intranuclear cytoplasmic pseudoinclusions (INCIs) reached 100%, nuclear contour irregularity and pale nuclei with powdery chromatin also had ideal interpretation value except for grooves and marginally placed micronucleoli. Although the sensitivity of psammoma bodies (PBs) was low, the specificity was 100%. In terms of preparation methods, the method of liquid-based preparation (LBP) is obviously better than that of conventional smears. The diagnostic efficiency by the combined detection method of parallel tests showed that without reducing the specificity, the sensitivity increased with the increase of the number of morphological characteristics and finally reached 98.81%. The INCIs and swirl arrangements are the most common and important indicators for the diagnosis of PTC, whereas papillary-like arrangements, the crowding and overlap of nuclear, grooves, marginally placed micronucleoli, and multinucleated giant cells are of little significance for the diagnosis of PTC.
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Affiliation(s)
- Xue-Jiao Xiong
- Department of Pathology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Ming-Ming Xiao
- Department of Pathology, The People's Hospital of Liaoning Province, Shenyang 110016, China
| | - Yi-Xia Zhang
- Department of Ultrasound, The First Hospital of China Medical University, Shenyang 110001, China
| | - Dong-Ge Liu
- Department of Pathology, Beijing Hospital, National Geriatric Center, Beijing 100730, China
| | - Mu-Lan Jin
- Department of Pathology, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Jian Wang
- Department of Pathology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Hong-Tao Xu
- Department of Pathology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Qing-Chang Li
- Department of Pathology, The First Hospital of China Medical University, Shenyang 110001, China
| | - Guang-Ping Wu
- Department of Pathology, The First Hospital of China Medical University, Shenyang 110001, China
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Shi W, Gong Y, Zhang D, Yang T, Yi M, Tan J, Ding S, Cheng W. A dual identification strategy based on padlock ligation and CRISPR/Cas14a for highly specific detection of BRAF V600E mutation in clinical samples. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:1913-1921. [PMID: 35522948 DOI: 10.1039/d2ay00319h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
BRAF V600E mutation is a single-nucleotide variation (SNV) that is widely found in various cancers and has been demonstrated to have a strong association with the prognosis and development of some diseases. Thus, we developed a strategy based on rolling circle amplification (RCA) and CRISPR/Cas14a to meet the great need for detecting highly specific BRAF V600E mutation in fine-needle biopsy samples. In this study, a padlock probe was designed to recognize and trigger subsequent ligase chain reactions (LCR). And due to the Taq DNA ligase, a great number of ligated annular padlock probes were generated in the presence of BRAF V600E mutation, subsequently generating long repeated single-strand DNA by RCA. The obtained amplicons were activators triggering the trans-cleavage of CRISPR/Cas14a. CRISPR/Cas14a shows outstanding performance in identifying ssDNA with single base mutation, which significantly increases the specificity of mutation discrimination. Under the optimal conditions, our strategy can identify BRAF V600E mutation down to 0.307 fM with a wide linear range from 1 fM to 10 pM. On the other hand, the dual identification strategy endows the method with terrific specificity for the detection of SNV. Furthermore, our method has been successfully employed to identify BRAF V600E mutation in clinical fine-needle aspiration samples, proving great potential for ultra-specific identification of low abundance BRAF V600E mutation and providing a novel method for diagnosis and treatment of cancer.
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Affiliation(s)
- Weicheng Shi
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Yao Gong
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Decai Zhang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Tiantian Yang
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Ming Yi
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Jingyi Tan
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
| | - Shijia Ding
- Key Laboratory of Clinical Laboratory Diagnostics (Ministry of Education), College of Laboratory Medicine, Chongqing Medical University, Chongqing, 400016, China
| | - Wei Cheng
- The Center for Clinical Molecular Medical Detection, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China.
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Rashid FA, Bhat GH, Khan MS, Tabassum S, Bhat MH. Variations in MAP kinase gladiators and risk of differentiated thyroid carcinoma. Mol Clin Oncol 2022; 16:45. [PMID: 35003743 PMCID: PMC8739702 DOI: 10.3892/mco.2021.2478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 10/27/2021] [Indexed: 12/02/2022] Open
Abstract
Thyroid carcinoma (TC) accounts for ~2.1% of newly diagnosed cancer cases. Mutations in KRAS, HRAS, NRAS and BRAF are primary participants in the development and progression of various types of malignancy, including differentiated TC (DTC). Therefore, the present prospective cohort study aimed to screen patients with DTC for variations in RAS gene family and BRAF gene. Exon 1 and 2 of KRAS, HRAS, NRAS and exon 15 of BRAF gene were screened for hotspot mutations in 72 thyroid tumor and adjacent normal tissue samples using di-deoxy Sanger sequencing. HRAS T81C mutation was found in 21% (15 of 72) of DTC tissue samples, therefore this mutation was investigated in blood samples from patients with DTC and controls as a genetic polymorphism. In addition, HRAS T81C genotypes were determined in 180 patients with DTC and 220 healthy controls by performing restriction fragment length polymorphism. BRAFV600E mutation was confined to classical variant of papillary thyoid cancer (CPTC; 44.4%) and was significantly associated with multifocality and lymph node (LN) metastasis. No mutation was found in exons 1 and 2 of KRAS and NRAS and exon 2 of HRAS genes, however, mutation was detected in exon 1 of HRAS gene (codon 27) at nucleotide position 81 in 21% (15 of 72) of DTC tumor tissue samples. Furthermore, HRAS T81C single nucleotide polymorphism was significantly associated with the risk of DTC with variant genotypes more frequently detected in cases compared with controls (P≤0.05). Moreover, frequency of variant genotypes (TC+CC) was significantly higher among DTC cases with no history of smoking, males, greater age, multifocality and LN metatasis compared with healthy controls (P<0.05). BRAFV600E mutation was primarily present in CPTC and associated with an aggressive tumor phenotype but mutations in RAS gene family were not present in patients with DTC. HRAS T81C polymorphism may be involved in the etiopathogenesis of DTC in a Pakistani cohort. Furthermore, testing for the BRAFV600E mutation may be useful for selecting initial therapy and follow-up monitoring.
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Affiliation(s)
- Faiza A Rashid
- Department of Biological Sciences, International Islamic University, Islamabad 1243, Pakistan
| | - Ghulam Hassan Bhat
- Department of Biochemistry, Government Medical College and Associated Shri Maharaja Hari Singh and Super Speciality Hospital, Srinagar, Jammu and Kashmir 190010, India
| | - Mosin S Khan
- Department of Biochemistry, Government Medical College and Associated Shri Maharaja Hari Singh and Super Speciality Hospital, Srinagar, Jammu and Kashmir 190010, India
| | - Sobia Tabassum
- Department of Biological Sciences, International Islamic University, Islamabad 1243, Pakistan
| | - Mohammad Hayat Bhat
- Department of Endocrinology, Government Medical College and Associated Shri Maharaja Hari Singh and Super Speciality Hospital, Srinagar, Jammu and Kashmir 190010, India
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5
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Agrawal T, Xi L, Navarro W, Raffeld M, Patel SB, Roth MJ, Klubo‐Gwiezdzinska J, Filie AC. An Effective Approach for
BRAF V600E
Mutation Analysis of Routine Thyroid Fine Needle Aspirates. Cytopathology 2021; 33:344-349. [DOI: 10.1111/cyt.13093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 11/30/2021] [Accepted: 12/22/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Tanupriya Agrawal
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
- Department of Pathology University of Rochester Medical Center Rochester
| | - Liqiang Xi
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
| | - Winnifred Navarro
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
| | - Mark Raffeld
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
| | - Snehal B. Patel
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
- Snehal B. Patel ‐ HeloGenika LLC Dexter
| | - Mark J. Roth
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
| | - Joanna Klubo‐Gwiezdzinska
- National Institute of Diabetes and Digestive and Kidney Diseases National Institutes of Health 9000 Rockville Pike Bethesda MD 20892 USA
| | - Armando C. Filie
- Laboratory of Pathology National Cancer Institute National Institutes of Health 10 Center Drive Bethesda MD 20892 USA
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Fu G, Chazen RS, MacMillan C, Witterick IJ. Development of a Molecular Assay for Detection and Quantification of the BRAF Variation in Residual Tissue From Thyroid Nodule Fine-Needle Aspiration Biopsy Specimens. JAMA Netw Open 2021; 4:e2127243. [PMID: 34613404 PMCID: PMC8495535 DOI: 10.1001/jamanetworkopen.2021.27243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/09/2021] [Indexed: 12/14/2022] Open
Abstract
Importance Thyroid cancer, predominantly papillary thyroid carcinoma (PTC), is common, but an estimated 30% of ultrasonography-guided fine-needle aspiration (FNA) biopsies of thyroid nodules are indeterminate. BRAF variation, associated with poor clinicopathological characteristics, is a useful molecular marker for diagnostics. Objective To develop a sensitive molecular assay for BRAF V600E detection in remaining tissue of thyroid FNA biopsies to identify patients with cancer carrying a BRAF variation. Design, Setting, and Participants This diagnostic study used tumor tissue from surgical formalin-fixed, paraffin-embedded (FFPE) specimens and residual tissue from thyroid FNA biopsies for genomic DNA extraction. FFPE specimens served as the validation set, and residual tissue from FNA biopsies served as the test set. A molecular assay was developed for accurate detection of BRAF V600E variation using locked nucleic acid (LNA) probe-based droplet digital polymerase chain reaction (dPCR), and the assay was validated by BRAF V600E immunohistochemical staining (IHC). The study was conducted between February 2019 and May 2021. Results A total of 271 specimens, including 77 FFPE specimens (with a follow-up of 48 matched surgical specimens) and 146 residual FNA samples, were collected from 223 patients (mean [SD] age, 53.8 [15.3] years; 174 [78.0%] women; 49 [22.0%] men). The molecular assay by dPCR was first established to specifically and accurately detect and quantify wild-type BRAF and variant BRAF in DNA from human follicular thyroid carcinoma-derived FTC-133 and papillary thyroid carcinoma-derived BCPAP cells. The linearity of quantification of BRAF V600E was calculated (y = 0.7339x; R2 = 0.9996) with sensitivity at 0.02 copies/μL and reproducibility in detecting variant DNA at various dilutions(coefficient of variance in 0.3% DNA, 9.63%; coefficient of variance in 1.0% DNA, 7.41%). In validation testing, the dPCR assay and IHC staining exhibited 100% specificity in concordantly identifying BRAF V600E in PTCs (κ = 0.873; P < .001) and sensitivity of 32.0% (95% CI, 19.1% to 44.9%) in dPCR and 26.0% (95% CI, 13.1% to 38.9%) in IHC staining, with an improvement by 23.08% in dPCR compared with the IHC staining. The dPCR assay further detected BRAF V600E in 39 of 146 residual FNA specimens (26.7%). At short-term follow-up, 48 patients, including 14 of 39 patients with BRAF variation and 34 of 107 patients without BRAF variation on residual FNA specimens, underwent resection. The dPCR assay of BRAF status in the matched surgical specimens showed BRAF V600E variations in 12 patients and wild-type BRAF in 36 patients, with a high agreement to that in residual tissue of FNA specimens (κ = 0.789; P < .001). Among 14 patients with BRAF variations on residual FNA, 13 were diagnosed with PTC and 1 was diagnosed with anaplastic thyroid cancer at the thyroidectomy. Conclusions and Relevance This diagnostic study developed a sensitive molecular assay for detection and quantification of BRAF V600E variation in residual tissue from thyroid FNA biopsies to identify patients with cancer harboring BRAF V600E in a cost-effective manner, highlighting the clinical value of molecular assay of the remaining FNA tissue in the management of thyroid nodules.
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Affiliation(s)
- Guodong Fu
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Mount Sinai Hospital, Toronto, Canada
| | - Ronald S. Chazen
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Mount Sinai Hospital, Toronto, Canada
| | - Christina MacMillan
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Mount Sinai Hospital, Toronto, Canada
- Department of Pathology and Laboratory Medicine, Sinai Health System, Mount Sinai Hospital, University of Toronto, Toronto, Canada
| | - Ian J. Witterick
- Alex and Simona Shnaider Research Laboratory in Molecular Oncology, Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Mount Sinai Hospital, Toronto, Canada
- Joseph and Mildred Sonshine Family Centre for Head and Neck Diseases, Sinai Health System, Mount Sinai Hospital, Toronto, Canada
- Department of Otolaryngology-Head and Neck Surgery, Sinai Health System, Mount Sinai Hospital, University of Toronto, Toronto, Canada
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7
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Jing C, Cao H, Ma R, Wu J, Wang Z. Association between mutation profiles and clinicopathological features in Chinese patients with thyroid cancer. PRECISION MEDICAL SCIENCES 2021. [DOI: 10.1002/prm2.12048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- Changwen Jing
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
| | - Haixia Cao
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
| | - Rong Ma
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
| | - Jianzhong Wu
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
| | - Zhuo Wang
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
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Wadee R, Grayson W. BRAF testing in a South African cohort of MLH1 deficient endometrial carcinomas: lessons learnt. SOUTHERN AFRICAN JOURNAL OF GYNAECOLOGICAL ONCOLOGY 2021. [DOI: 10.1080/20742835.2021.1884348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Reubina Wadee
- Department of Anatomical Pathology, University of the Witwatersrand/National Health Laboratory Services (NHLS), Johannesburg, South Africa
| | - Wayne Grayson
- AMPATH National Laboratories/Department of Anatomical Pathology, University of the Witwatersrand, Johannesburg, South Africa
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Rashid FA, Tabassum S, Khan MS, Ansari HR, Asif M, Sheikh AK, Sameer Aga S. VE1 immunohistochemistry is an adjunct tool for detection of BRAF V600E mutation: Validation in thyroid cancer patients. J Clin Lab Anal 2020; 35:e23628. [PMID: 33305405 PMCID: PMC7891529 DOI: 10.1002/jcla.23628] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/09/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022] Open
Abstract
Papillary thyroid carcinoma (PTC) is the most common endocrine malignancy among other endocrine tumors, and BRAFV600E is a frequent genetic mutation occurring in the disease. Although different molecular techniques, most importantly sequencing has been widely recognized as a gold standard but molecular diagnosis remains an expensive, laborious, and time‐intensive process. Recently, immunohistochemistry (IHC) with anti‐BRAF V600E (VE1) antibody has increased practical utility and implemented clinically for the detection of BRAFV600E mutation. Therefore, the study aimed to evaluate diagnostic accuracy of VE1 IHC for detecting the BRAFV600E mutation frequency and clinical implementation in diagnostic laboratories. In this study, 72 formalin fixed paraffin‐embedded tissues (FFPE) were used to determine the BRAFV600E mutation status using IHC and Sanger sequencing. The mutation was found in 29% and 28% cases using IHC and Sanger sequencing, respectively. Furthermore, the results showed 100% sensitivity, 98.07% specificity, 95.2% positive predictive value, and 100% negative predictive value. Notably, significant associations were found between BRAFV600E status and tumor stage, tumor focality, and extrathyroidal extensions, respectively. VE1 IHC was found to be a highly sensitive, specific, and diagnostically accurate method in this cohort. Therefore, BRAFV600E detection through IHC has been considered as the best tailored technique for routine pathology laboratories.
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Affiliation(s)
- Faiza A. Rashid
- Department of Biological SciencesInternational Islamic UniversityIslamabadPakistan
| | - Sobia Tabassum
- Department of Biological SciencesInternational Islamic UniversityIslamabadPakistan
| | - Mosin S. Khan
- Government Medical College Srinagar and Associated SMHS and Superspeciality HospitalSrinagarIndia
| | - Hifzur R. Ansari
- King Abdullah International Medical Research CenterKing Saud bin Abdulaziz University for Health SciencesMinistry of National Guard Health AffairsJeddahSaudi Arabia
| | - Muhammad Asif
- Department of HistopathologyArmed Forces Institute of Pathologycentral Military HospitalRawalpindiPakistan
| | - Ahmareen K. Sheikh
- Department of PathologyPakistan Institute of Medical SciencesIslamabadPakistan
| | - Syed Sameer Aga
- Basic Medical SciencesCollege of Medicine‐ JeddahKing Saud bin Abdulaziz University for Health Sciences, King Abdullah International Medical Research CenterMinistry of National Guard Health AffairsJeddahKingdom of Saudi Arabia
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10
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Parker KG, White MG, Cipriani NA. Comparison of Molecular Methods and BRAF Immunohistochemistry (VE1 Clone) for the Detection of BRAF V600E Mutation in Papillary Thyroid Carcinoma: A Meta-Analysis. Head Neck Pathol 2020; 14:1067-1079. [PMID: 32358715 PMCID: PMC7669962 DOI: 10.1007/s12105-020-01166-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 04/23/2020] [Indexed: 10/24/2022]
Abstract
The evaluation of surgically resected papillary thyroid carcinomas (PTC) by immunohistochemistry (IHC) for BRAF mutation has diagnostic, prognostic and therapeutic implications. The goal of this meta-analysis was to perform a systematic review of studies using the VE1 clone (specific for detection of the BRAF V600E mutation) on formalin-fixed paraffin embedded (FFPE) thyroid surgical resection specimens for primary papillary thyroid carcinoma. The authors' molecular techniques, immunohistochemistry protocols, and scoring methods for VE1 immunostaining were also evaluated. This study included 4079 PTCs representing data from 23 studies. The results extracted from each study were split into two different groups, direct sequencing group or PCR group, based on the molecular "gold standard" method used to compare VE1 IHC staining. In the direct sequencing group, the IHC sensitivity was 100% (95% CI 0.97-1.00) and specificity 84% (95% 0.72-0.91). In the PCR group the sensitivity was 98% (95% CI 0.96-0.99) and specificity 89% (95% CI 0.82-0.94). Although immunohistochemical procedures varied by author, the overall performance of the VE1 clone shows that it is highly sensitive and relatively specific for detecting the BRAF V600E mutation in surgical resection specimens. However, standardization of immunohistochemical procedural method and scoring/interpretation criteria may improve the reliability and reproducibility for the use of VE1 clone for future practice.
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Affiliation(s)
- Kyle G Parker
- Department of Pathology, University of Chicago Medical Center, Chicago, IL, USA.
| | - Michael G White
- Department of General Surgery, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Nicole A Cipriani
- Department of Pathology, University of Chicago Medical Center, Chicago, IL, USA
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11
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Wang Z, Jing C, Cao H, Liu S, Wu J, Ma R. Next generation sequencing
based detection of 15 target genes mutations in papillary thyroid carcinoma. PRECISION MEDICAL SCIENCES 2020. [DOI: 10.1002/prm2.12028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Zhuo Wang
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
| | - Changwen Jing
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
| | - Haixia Cao
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
| | - SiWen Liu
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
| | - Jianzhong Wu
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
| | - Rong Ma
- Clinical Cancer Research Center Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University Nanjing Jiangsu China
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12
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Rashid FA, Munkhdelger J, Fukuoka J, Bychkov A. Prevalence of BRAFV600E mutation in Asian series of papillary thyroid carcinoma-a contemporary systematic review. Gland Surg 2020; 9:1878-1900. [PMID: 33224863 PMCID: PMC7667088 DOI: 10.21037/gs-20-430] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/04/2020] [Indexed: 12/30/2022]
Abstract
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.
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Affiliation(s)
- Faiza Abdul Rashid
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, International Islamic University, Islamabad, Pakistan
| | | | - Junya Fukuoka
- Department of Pathology, Kameda Medical Center, Kamogawa, Chiba, Japan
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
| | - Andrey Bychkov
- Department of Pathology, Kameda Medical Center, Kamogawa, Chiba, Japan
- Department of Pathology, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan
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13
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Tran TV, Dang KX, Pham QH, Nguyen UD, Trinh NTT, Hoang LV, Ho SA, Nguyen BV, Nguyen DT, Trinh DT, Tran DN, Orpana A, Stenman UH, Stenman J, Ho TH. Evaluation of the expression levels of BRAF V600E mRNA in primary tumors of thyroid cancer using an ultrasensitive mutation assay. BMC Cancer 2020; 20:368. [PMID: 32357861 PMCID: PMC7195771 DOI: 10.1186/s12885-020-06862-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Accepted: 04/14/2020] [Indexed: 12/05/2022] Open
Abstract
Background The BRAFV600E gene encodes for the mutant BRAFV600E protein, which triggers downstream oncogenic signaling in thyroid cancer. Since most currently available methods have focused on detecting BRAFV600E mutations in tumor DNA, there is limited information about the level of BRAFV600E mRNA in primary tumors of thyroid cancer, and the diagnostic relevance of these RNA mutations is not known. Methods Sixty-two patients with thyroid cancer and non-malignant thyroid disease were included in the study. Armed with an ultrasensitive technique for mRNA-based mutation analysis based on a two step RT-qPCR method, we analysed the expression levels of the mutated BRAFV600E mRNA in formalin-fixed paraffin-embedded samples of thyroid tissues. Sanger sequencing for detection of BRAFV600E DNA was performed in parallel for comparison and normalization of BRAFV600E mRNA expression levels. Results The mRNA-based mutation detection assay enables detection of the BRAFV600E mRNA transcripts in a 10,000-fold excess of wildtype BRAF counterparts. While BRAFV600E mutations could be detected by Sanger sequencing in 13 out of 32 malignant thyroid cancer FFPE tissue samples, the mRNA-based assay detected mutations in additionally 5 cases, improving the detection rate from 40.6 to 56.3%. Furthermore, we observed a surprisingly large, 3-log variability, in the expression level of the BRAFV600E mRNA in FFPE samples of thyroid cancer tissue. Conclusions The expression levels of BRAFV600E mRNA was characterized in the primary tumors of thyroid cancer using an ultrasensitive mRNA-based mutation assay. Our data inspires further studies on the prognostic and diagnostic relevance of the BRAFV600E mRNA levels as a molecular biomarker for the diagnosis and monitoring of various genetic and malignant diseases.
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Affiliation(s)
- Tien Viet Tran
- 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Kien Xuan Dang
- Minerva Foundation Institute for Medical Research, Helsinki, Finland
| | - Quynh Huong Pham
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung street, Ha Dong district, Hanoi, Vietnam
| | - Ung Dinh Nguyen
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung street, Ha Dong district, Hanoi, Vietnam
| | - Nhung Thi Trang Trinh
- Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung street, Ha Dong district, Hanoi, Vietnam
| | - Luong Van Hoang
- Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, Hanoi, Vietnam
| | - Son Anh Ho
- Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, Hanoi, Vietnam
| | - Ba Van Nguyen
- Oncology Centre, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Duc Trong Nguyen
- School of Medicine and Pharmacy, Vietnam National University, Hanoi, Vietnam
| | - Dung Tuan Trinh
- Pathology Department, 108 Military Central Hospital, Hanoi, Vietnam
| | - Dung Ngoc Tran
- Department of Pathology, 103 Military Hospital, Vietnam Military Medical University, Hanoi, Vietnam
| | - Arto Orpana
- Laboratory of Genetics, HUSLAB, Helsinki University Central Hospital, Helsinki, Finland
| | - Ulf-Håkan Stenman
- Department of Clinical Chemistry, Medicum, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Jakob Stenman
- Minerva Foundation Institute for Medical Research, Helsinki, Finland.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Tho Huu Ho
- Minerva Foundation Institute for Medical Research, Helsinki, Finland. .,Department of Genomics and Cytogenetics, Institute of Biomedicine and Pharmacy (IBP), Vietnam Military Medical University, 222 Phung Hung street, Ha Dong district, Hanoi, Vietnam. .,Department of Medical Microbiology, 103 Military Hospital, Vietnam Medical University, Hanoi, Vietnam.
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14
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VE1 Immunohistochemistry Improves the Limit of Genotyping for Detecting BRAFV600E Mutation in Papillary Thyroid Cancer. Cancers (Basel) 2020; 12:cancers12030596. [PMID: 32150939 PMCID: PMC7139976 DOI: 10.3390/cancers12030596] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 02/29/2020] [Accepted: 03/04/2020] [Indexed: 02/07/2023] Open
Abstract
Detection of BRAFV600E is useful for making diagnosis and risk stratification of papillary thyroid carcinoma (PTC). Molecular testing, however, is not always available for routine clinical use. To assess the clinical utility and reliability of VE1 immunohistochemistry (IHC) for detecting BRAFV600E mutation in PTC, VE1 IHC was performed on the tissue microarrays of 514 patients with PTC and was compared with Sanger sequencing results. Of 514 PTC cases, 433 (84.2%) were positive for VE1 expression. Among 6 discordant cases between VE1 IHC and Sanger sequencing, 3 initial VE1-false negative cases turned out to be true false negative on repeat testing, and 3 VE1-false positive cases showed BRAFV600E mutation using digital PCR analysis. PTCs with low variant allele fraction were positive for VE1 IHC but were not detected using sequencing. VE1 IHC showed 99.3% sensitivity, 100% specificity, 100% positive predictive value, and 96.4% negative predictive value. The BRAFV600E mutation was significantly associated with older age, multifocality, extrathyroidal extension, lymph node metastasis, and advanced tumor stage. In conclusion, VE1 IHC is a reliable method for detecting BRAFV600E mutation in PTC specimens.
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15
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Singarayer R, Mete O, Perrier L, Thabane L, Asa SL, Van Uum S, Ezzat S, Goldstein DP, Sawka AM. A Systematic Review and Meta-Analysis of the Diagnostic Performance of BRAF V600E Immunohistochemistry in Thyroid Histopathology. Endocr Pathol 2019; 30:201-218. [PMID: 31300997 DOI: 10.1007/s12022-019-09585-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Immunohistochemistry (IHC) in evaluating thyroid surgical specimens may facilitate diagnostic and prognostic evaluation, with potential therapeutic implications. We performed a systematic review and meta-analysis examining the analytic validity of IHC in detecting BRAFV600E mutations in thyroid cancer (primary or metastatic). We screened citations from three electronic databases (until December 20, 2018), supplemented by a hand search of authors' files and cross-references of reviews. Citations and full-text papers were independently reviewed in duplicate, and consensus was achieved on inclusion of papers. Two reviewers independently critically appraised and abstracted data from included papers. Random-effect meta-analyses were conducted for sensitivity and specificity estimates. We reviewed 1499 unique citations and 93 full-text articles. We included 1 systematic review and 30 original articles. The published review (from 2015) needed to be updated as there were multiple subsequent original studies. The pooled sensitivity of IHC in detecting a BRAFV600E mutation was 96.8% (95% confidence interval [CI] at 94.1%, 98.3%) (29 studies, including 2659 BRAFV600E mutant tumors). The IHC pooled specificity was 86.3% (95% CI 80.7%, 90.4%) (28 studies, including 1107 BRAFV600E wild-type specimens). These meta-analyses were subject to statistically significant heterogeneity, partly explained by antibody type (sensitivity and specificity) and tissue/tumor type (specificity). In conclusion, BRAF IHC is highly sensitive and reasonably specific in detecting the BRAFV600E mutation; however, there is some variability in analytic performance.
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Affiliation(s)
- Ranjit Singarayer
- Thyroid Fellow, University of Toronto, Toronto, Canada
- Toronto General Hospital, 200 Elizabeth Street, 12 EN-212, Toronto, Ontario, M5G 2C, Canada
| | - Ozgur Mete
- Department of Pathology, University Health Network and University of Toronto, Toronto, Canada
- Toronto General Hospital, 200 Elizabeth Street, 11 EN-422, Toronto, Ontario, M5G 2C4, Canada
| | - Laure Perrier
- University of Toronto Libraries, University of Toronto, 130 St. George St, Toronto, Ontario, Canada
| | - Lehana Thabane
- Department of Health Research Methods, Evidence, and Impact, McMaster University, Hamilton, Ontario, Canada
- St. Joseph's Healthcare Hamilton, Biostatistics Unit, 3rd Floor, Martha Wing, Room H-325, 50 Charlton Avenue East, Hamilton, Ontario, L8N 4A6, Canada
| | - Sylvia L Asa
- Department of Pathology, University Health Network and University of Toronto, Toronto, Canada
- Toronto General Hospital, 200 Elizabeth Street, 11 EN-422, Toronto, Ontario, M5G 2C4, Canada
| | - Stan Van Uum
- Division of Endocrinology, Western University, London, Ontario, Canada
- Division of Endocrinology & Metabolism, St Joseph's Health Care London, Room B5-130, 268 Grosvenor Street, London, Ontario, Canada
| | - Shereen Ezzat
- Department of Endocrine Oncology, Princess Margaret Cancer Centre, Toronto, Ontario, Canada
- Toronto General Hospital, 585 University Avenue, 9NU-986, Toronto, Ontario, M5G 2N2, Canada
| | - David P Goldstein
- Department of Otolaryngology, Head and Neck Surgery, University Health Network and University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, 610 University Avenue, Suite 3-950, Toronto, Ontario, M5G 2M9, Canada
| | - Anna M Sawka
- Division of Endocrinology, University Health Network and University of Toronto, Toronto, Canada.
- Toronto General Hospital, 200 Elizabeth Street, 12 EN-212, Toronto, Ontario, M5G 2C4, Canada.
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Sukswai N, Khoury JD. Immunohistochemistry Innovations for Diagnosis and Tissue-Based Biomarker Detection. Curr Hematol Malig Rep 2019; 14:368-375. [DOI: 10.1007/s11899-019-00533-9] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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17
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Wang Z, Sun K, Jing C, Cao H, Ma R, Wu J. Comparison of droplet digital PCR and direct Sanger sequencing for the detection of the BRAF V600E mutation in papillary thyroid carcinoma. J Clin Lab Anal 2019; 33:e22902. [PMID: 31021028 PMCID: PMC6642310 DOI: 10.1002/jcla.22902] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Revised: 03/27/2019] [Accepted: 03/28/2019] [Indexed: 12/19/2022] Open
Abstract
Background The BRAFV600E mutation status is a useful diagnostic and prognostic marker for papillary thyroid carcinoma (PTC). Although it is a commonly used method, Sanger sequencing has several limitations in detecting the BRAFV600E mutation. The aim of this study was to evaluate the efficiency of droplet digital PCR (ddPCR) as an alternative method for the detection of the BRAFV600E mutation in PTC patients. Methods Samples from a total of 120 patients with PTC and 30 patients with benign nodular thyroid disease who underwent thyroid surgery were collected. The BRAFV600E mutation status of the PTC patients was tested by Sanger sequencing and ddPCR. Results The BRAFV600E mutation was detected in 67 samples (44.67%) by Sanger sequencing and 92 samples (61.33%) by ddPCR. The detection of the mutation by the two methods was inconsistent in twenty‐five samples (16.67%). The sensitivity and specificity of the ddPCR method were 100% and 69.88%, respectively, and the positive predictive and negative predictive values were 72.83% and 100%, respectively. The concordance rate between the two methods in detecting the BRAFV600E mutation was 83.33%. Neither Sanger sequencing nor ddPCR detected BRAFV600E in 30 patients with benign nodular thyroid disease. The 92 samples with the BRAFV600E mutation were detected by ddPCR at a fractional abundance from 0.28% to 45.40% as follows: ≥10% (59 samples, 64.13%), 5%‐10% (8 samples, 8.70%), and ≤5% (25 samples, 27.17%). The BRAFV600E mutation was detected in all 59 samples at a fractional abundance ≥10% and in four samples at a fractional abundance from 5% to 10%, and no BRAFV600E mutation was detected at a fractional abundance ≤5% by Sanger sequencing. Conclusions ddPCR was a reliable, highly sensitive alternative method for the detection of the BRAFV600E mutation in PTC patients.
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Affiliation(s)
- Zhuo Wang
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | | | - Changwen Jing
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Haixia Cao
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Rong Ma
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
| | - Jianzhong Wu
- Clinical Cancer Research Center, Jiangsu Cancer Hospital & Jiangsu Institute of Cancer Research & The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, China
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Immunohistochemistry is a feasible method to screen BRAF V600E mutation in colorectal and papillary thyroid carcinoma. Exp Mol Pathol 2018; 105:153-159. [DOI: 10.1016/j.yexmp.2018.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Revised: 06/08/2018] [Accepted: 07/11/2018] [Indexed: 12/27/2022]
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