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Silva AL, Powalowska PK, Stolarek M, Gray ER, Palmer RN, Herman B, Frayling CA, Balmforth BW. Single-copy detection of somatic variants from solid and liquid biopsy. Sci Rep 2021; 11:6068. [PMID: 33727644 PMCID: PMC7966381 DOI: 10.1038/s41598-021-85545-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/03/2021] [Indexed: 12/15/2022] Open
Abstract
Accurate detection of somatic variants, against a background of wild-type molecules, is essential for clinical decision making in oncology. Existing approaches, such as allele-specific real-time PCR, are typically limited to a single target gene and lack sensitivity. Alternatively, next-generation sequencing methods suffer from slow turnaround time, high costs, and are complex to implement, typically limiting them to single-site use. Here, we report a method, which we term Allele-Specific PYrophosphorolysis Reaction (ASPYRE), for high sensitivity detection of panels of somatic variants. ASPYRE has a simple workflow and is compatible with standard molecular biology reagents and real-time PCR instruments. We show that ASPYRE has single molecule sensitivity and is tolerant of DNA extracted from plasma and formalin fixed paraffin embedded (FFPE) samples. We also demonstrate two multiplex panels, including one for detection of 47 EGFR variants. ASPYRE presents an effective and accessible method that simplifies highly sensitive and multiplexed detection of somatic variants.
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Affiliation(s)
- Ana-Luisa Silva
- Biofidelity Ltd, 330 Cambridge Science Park, Cambridge, CB4 0WN, UK
| | | | | | | | | | - Bram Herman
- Agilent Technologies LDA UK Ltd, 5500 Lakeside, Cheadle, SK8 3GR, UK
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2
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Varshavi D, Varshavi D, McCarthy N, Veselkov K, Keun HC, Everett JR. Metabolic characterization of colorectal cancer cells harbouring different KRAS mutations in codon 12, 13, 61 and 146 using human SW48 isogenic cell lines. Metabolomics 2020; 16:51. [PMID: 32300895 PMCID: PMC7162829 DOI: 10.1007/s11306-020-01674-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/02/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION Kirsten Rat Sarcoma Viral Oncogene Homolog (KRAS) mutations occur in approximately one-third of colorectal (CRC) tumours and have been associated with poor prognosis and resistance to some therapeutics. In addition to the well-documented pro-tumorigenic role of mutant Ras alleles, there is some evidence suggesting that not all KRAS mutations are equal and the position and type of amino acid substitutions regulate biochemical activity and transforming capacity of KRAS mutations. OBJECTIVES To investigate the metabolic signatures associated with different KRAS mutations in codons 12, 13, 61 and 146 and to determine what metabolic pathways are affected by different KRAS mutations. METHODS We applied an NMR-based metabonomics approach to compare the metabolic profiles of the intracellular extracts and the extracellular media from isogenic human SW48 CRC cell lines with different KRAS mutations in codons 12 (G12D, G12A, G12C, G12S, G12R, G12V), 13 (G13D), 61 (Q61H) and 146 (A146T) with their wild-type counterpart. We used false discovery rate (FDR)-corrected analysis of variance (ANOVA) to determine metabolites that were statistically significantly different in concentration between the different mutants. RESULTS CRC cells carrying distinct KRAS mutations exhibited differential metabolic remodelling, including differences in glycolysis, glutamine utilization and in amino acid, nucleotide and hexosamine metabolism. CONCLUSIONS Metabolic differences among different KRAS mutations might play a role in their different responses to anticancer treatments and hence could be exploited as novel metabolic vulnerabilities to develop more effective therapies against oncogenic KRAS.
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Affiliation(s)
- Dorna Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, Kent, ME4 4TB, UK
| | - Dorsa Varshavi
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, Kent, ME4 4TB, UK
| | - Nicola McCarthy
- Horizon Discovery Ltd., Cambridge Research Park, 8100 Beach Dr, Waterbeach, Cambridge, CB25 9TL, UK
| | - Kirill Veselkov
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College, London, SW7 2AZ, UK
| | - Hector C Keun
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital Campus, London, W12 ONN, UK
| | - Jeremy R Everett
- Medway Metabonomics Research Group, University of Greenwich, Chatham Maritime, Kent, ME4 4TB, UK.
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Wang QL, Zhou CL, Yin YF, Xiao L, Wang Y, Li K. An enzymatic on/off switch-mediated assay for KRAS hotspot point mutation detection of circulating tumor DNA. J Clin Lab Anal 2020; 34:e23305. [PMID: 32207862 PMCID: PMC7439329 DOI: 10.1002/jcla.23305] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 12/10/2019] [Accepted: 01/07/2020] [Indexed: 12/13/2022] Open
Abstract
Background To detect the mutations of KRAS gene in colorectal cancer patients and other cancer patients, it is of value to develop non‐invasive, sensitive, specific, easy, and low‐cost assays. Methods Templates harboring hotspot mutations of the KRAS gene were constructed, and primers were designed for evaluation of the specificity, and sensitivity of detection system consisted of exonuclease polymerase‐mediated on/off switch; then, gel electrophoresis and real‐time PCR were performed for verification. The assay was verified by testing the DNA pool of normal controls and circulating DNA (ctDNA) samples from 14 tumor patients, as compared to Sanger sequencing. Results A specific and sensitive assay consisted of exonuclease polymerase‐mediated on/off switch, and multiplex real‐time PCR method has been established. This assay could detect <100 copies of KRAS mutation in more than 10 million copies of wild‐type KRAS gene fragments. This assay was applied to test KRAS gene mutations in three cases of fourteen ctDNA samples, and the results were consistent with Sanger sequencing. However, this PCR‐based assay was more sensitive and easier to be interpreted. Conclusion This assay can detect the presence of KRAS hotspot mutations in clinical circulating tumor DNA samples. The assay has a potential to be used in early diagnosis of colorectal cancer as well as other types of cancer.
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Affiliation(s)
- Qing-Lin Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Cui-Lan Zhou
- Department of Human Anatomy, University of South China, Hengyang, China
| | - Yu-Fang Yin
- Department of Pharmacology and Neuroscience, SIU Medical School, Springfield, IL, USA
| | - Li Xiao
- Laboratory of Molecular Medicine, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Yuan Wang
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China
| | - Kai Li
- Jiangsu Key Laboratory of Neuropsychiatric Diseases and College of Pharmaceutical Sciences, Soochow University, Suzhou, China.,GeneTalks Biotechnology Inc., Changsha, China
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Yun HG, Lee HJ, Kim BR, Lee JH, Lee JH, Lee MY, Kim DH, Sohn JH, Chae SW, Do IG, Do SI, Kim K. Factors affecting KRAS mutation detection in colorectal cancer tissue. Pathol Res Pract 2019; 215:1071-1075. [PMID: 30846412 DOI: 10.1016/j.prp.2019.02.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 01/30/2019] [Accepted: 02/26/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND With the recent development of molecular tests for various biomarkers, it has become even more important to prepare adequate tissue samples. However, little is known about how the effect of cold ischemia time or formalin fixation time can affect KRAS mutation detection in colorectal cancer. METHODS This study included the results of KRAS mutation tests for colorectal cancer in 401 specimens. We investigated clinicopathologic factors that may affect DNA quality of formalin-fixed, paraffin-embedded (FFPE) tissue including specimen type, cold ischemia time, and formalin fixation time and assessed the detection rate of the KRAS mutation in samples with varying DNA quality. RESULTS Sample DNA quality for KRAS mutation test was better in biopsy specimens, which showed markedly shorter cold ischemia time and shorter formalin fixation time compared to resection specimens. A cold ischemia time of one hour or less was associated with better sample DNA quality. But the formalin fixation time was not a significant factor when it fell within the range performed in routine pathology diagnosis. When prolonged formalin fixation was tested, we confirmed that the specimen DNA quality gradually got worse from one month to three months. CONCLUSIONS The biopsy specimens showed better sample DNA quality for KRAS mutation test compared to resection specimens. In a routine diagnostic pathology setting, the cold ischemia time was an important factor affecting DNA quality and the formalin fixation had a wide time range for optimal DNA quality.
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Affiliation(s)
- Hyon-Goo Yun
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Hyun Joo Lee
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Bo-Ra Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Joo-Hee Lee
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jun-Hyeong Lee
- IT Support, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Mi-Yeon Lee
- Division of Biostatistics, Department of R&D Management, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Dong-Hoon Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Jin Hee Sohn
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Seoung Wan Chae
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - In Gu Do
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Sung-Im Do
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
| | - Kyungeun Kim
- Department of Pathology, Kangbuk Samsung Hospital, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.
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Li Q, Zhou D, Pan J, Liu Z, Chen J. An ultrasensitive and simple fluorescence biosensor for detection of the Kras wild type by using the three-way DNA junction-driven catalyzed hairpin assembly strategy. Analyst 2019; 144:3088-3093. [DOI: 10.1039/c9an00195f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A label-free platform for simple detection of the Kras gene was proposed by using the three-way DNA junction-driven catalyzed hairpin assembly strategy.
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Affiliation(s)
- Qiong Li
- College of Bioscience and Biotechnology
- Hunan Agricultural University
- Changsha 410128
- China
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
| | - Danhua Zhou
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental and Science &Technology
- Guangzhou 510650
- China
| | - Jiafeng Pan
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental and Science &Technology
- Guangzhou 510650
- China
| | - Zhi Liu
- College of Bioscience and Biotechnology
- Hunan Agricultural University
- Changsha 410128
- China
| | - Junhua Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental and Science &Technology
- Guangzhou 510650
- China
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Evaluation of a DNA Extraction and Purification Protocol Using Archived Formalin-fixed Paraffin-embedded Tissues for BRAF Mutations Analysis in Papillary Thyroid Microcarcinomas. Appl Immunohistochem Mol Morphol 2019; 27:70-76. [DOI: 10.1097/pai.0000000000000535] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Chat-Uthai N, Vejvisithsakul P, Udommethaporn S, Meesiri P, Danthanawanit C, Wongchai Y, Teerapakpinyo C, Shuangshoti S, Poungvarin N. Development of ultra-short PCR assay to reveal BRAF V600 mutation status in Thai colorectal cancer tissues. PLoS One 2018; 13:e0198795. [PMID: 29879227 PMCID: PMC5991739 DOI: 10.1371/journal.pone.0198795] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 05/25/2018] [Indexed: 02/06/2023] Open
Abstract
The protein kinase BRAF is one of the key players in regulating cellular responses to extracellular signals. Somatic mutations of the BRAF gene, causing constitutive activation of BRAF, have been found in various types of human cancers such as malignant melanoma, and colorectal cancer. BRAF V600E and V600K, most commonly observed mutations in these cancers, may predict response to targeted therapies. Many techniques suffer from a lack of diagnostic sensitivity in mutation analysis in clinical samples with a low cancer cell percentage or poor-quality fragmented DNA. Here we present allele-specific real-time PCR assay for amplifying 35- to 45-base target sequences in BRAF gene. Forward primer designed for BRAF V600E detection is capable of recognizing both types of BRAF V600E mutation, i.e. V600E1 (c.1799T>A) and V600E2 (c.1799_1800delTGinsAA), as well as complex tandem mutation caused by nucleotide changes in codons 600 and 601. We utilized this assay to analyze Thai formalin-fixed paraffin-embedded tissues. Forty-eight percent of 178 Thai colorectal cancer tissues has KRAS mutation detected by highly sensitive commercial assays. Although these DNA samples contain low overall yield of amplifiable DNA, our newly-developed assay successfully revealed BRAF V600 mutations in 6 of 93 formalin-fixed paraffin-embedded colorectal cancer tissues which KRAS mutation was not detected. Ultra-short PCR assay with forward mutation-specific primers is potentially useful to detect BRAF V600 mutations in highly fragmented DNA specimens from cancer patients.
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Affiliation(s)
- Nunthawut Chat-Uthai
- Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Sutthirat Udommethaporn
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Puttarakun Meesiri
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chetiya Danthanawanit
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Yannawan Wongchai
- Research Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Chinachote Teerapakpinyo
- Chulalongkorn GenePRO Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Shanop Shuangshoti
- Chulalongkorn GenePRO Center, Research Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Department of Pathology, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Naravat Poungvarin
- Clinical Molecular Pathology Laboratory, Department of Clinical Pathology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- * E-mail:
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Zhang Y, Wang L, Luo F, Qiu B, Guo L, Weng Z, Lin Z, Chen G. An electrochemiluminescence biosensor for Kras mutations based on locked nucleic acid functionalized DNA walkers and hyperbranched rolling circle amplification. Chem Commun (Camb) 2018; 53:2910-2913. [PMID: 28154878 DOI: 10.1039/c7cc00009j] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Herein, an electrochemiluminescence (ECL) biosensor for ultrasensitive and specific detection of Kras mutant genes has been developed on the basis of the high discrimination capability of locked nucleic acid (LNA) and dual signal amplification techniques including DNA walkers and hyperbranched rolling circle amplification (HRCA).
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Affiliation(s)
- Ying Zhang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Lixu Wang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Fang Luo
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian 350116, China.
| | - Bin Qiu
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Longhua Guo
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zuquan Weng
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian 350116, China.
| | - Zhenyu Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Guonan Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
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Guarnaccia M, Iemmolo R, Petralia S, Conoci S, Cavallaro S. Miniaturized Real-Time PCR on a Q3 System for Rapid KRAS Genotyping. SENSORS 2017; 17:s17040831. [PMID: 28398227 PMCID: PMC5422192 DOI: 10.3390/s17040831] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Revised: 03/29/2017] [Accepted: 04/05/2017] [Indexed: 12/13/2022]
Abstract
Colorectal cancer (CRC) is an aggressive human malignancy with a complex genomic landscape harboring KRAS mutations. In 40%–60% of patients with CRC, constantly active KRAS proteins affect the prognosis, surgical strategy, and clinical benefit from therapy with anti-epidermal growth factor receptor (EGFR) agents. For this reason, there is a greater demand for minimally-invasive diagnostic devices to characterize the genetic pattern and prevent the acquired mechanism to drug resistance. The rapid developments in cutting-edge diagnostic techniques are expected to play a growing role in medicine and represent an attractive promise to identify potential responders to personalized medicine. Here we propose a new method to simultaneously detect the main KRAS mutations on the portable real-time PCR Q3 platform. This platform is based on hybrid silicon-plastic technology implemented in a miniaturized chip able to achieve a sample-in answer-out rapid analysis, allowing a new approach to genetic counseling and testing.
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Affiliation(s)
- Maria Guarnaccia
- Institute of Neurological Sciences, Italian National Research Council, Via Paolo Gaifami, 18-95125 Catania, Italy.
| | - Rosario Iemmolo
- Institute of Neurological Sciences, Italian National Research Council, Via Paolo Gaifami, 18-95125 Catania, Italy.
| | | | - Sabrina Conoci
- STMicroelectronics, Stradale Primosole, 50-95121 Catania, Italy.
| | - Sebastiano Cavallaro
- Institute of Neurological Sciences, Italian National Research Council, Via Paolo Gaifami, 18-95125 Catania, Italy.
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Fiorentino M, Scarpelli M, Lopez-Beltran A, Cheng L, Montironi R. Considerations for standardizing predictive molecular pathology for cancer prognosis. Expert Rev Mol Diagn 2016; 17:47-55. [PMID: 27897454 DOI: 10.1080/14737159.2017.1266258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Molecular tests that were once ancillary to the core business of cyto-histopathology are becoming the most relevant workload in pathology departments after histopathology/cytopathology and before autopsies. This has resulted from innovations in molecular biology techniques, which have developed at an incredibly fast pace. Areas covered: Most of the current widely used techniques in molecular pathology such as FISH, direct sequencing, pyrosequencing, and allele-specific PCR will be replaced by massive parallel sequencing that will not be considered next generation, but rather, will be considered to be current generation sequencing. The pre-analytical steps of molecular techniques such as DNA extraction or sample preparation will be largely automated. Moreover, all the molecular pathology instruments will be part of an integrated workflow that traces the sample from extraction to the analytical steps until the results are reported; these steps will be guided by expert laboratory information systems. In situ hybridization and immunohistochemistry for quantification will be largely digitalized as much as histology will be mostly digitalized rather than viewed using microscopy. Expert commentary: This review summarizes the technical and regulatory issues concerning the standardization of molecular tests in pathology. A vision of the future perspectives of technological changes is also provided.
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Affiliation(s)
- Michelangelo Fiorentino
- a Pathology Service , Addarii Institute of Oncology, S. Orsola-Malpighi Hospital , Bologna , Italy
| | - Marina Scarpelli
- b Section of Pathological Anatomy , Marche Polytechnic University, School of Medicine, United Hospitals , Ancona , Italy
| | | | - Liang Cheng
- d Department of Pathology and Laboratory Medicine , Indiana University School of Medicine , Indianapolis , IN , USA
| | - Rodolfo Montironi
- a Pathology Service , Addarii Institute of Oncology, S. Orsola-Malpighi Hospital , Bologna , Italy
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Orue A, Rieber M. Optimized Multiplex Detection of 7 KRAS Mutations by Taqman Allele-Specific qPCR. PLoS One 2016; 11:e0163070. [PMID: 27632281 PMCID: PMC5025196 DOI: 10.1371/journal.pone.0163070] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Accepted: 09/01/2016] [Indexed: 12/23/2022] Open
Abstract
UNLABELLED Establishing the KRAS mutational status of tumor samples is essential to manage patients with colorectal or lung cancer, since these mutations preclude treatment with monoclonal anti-epidermal growth factor receptor (EGFR) antibodies. We report an inexpensive, rapid multiplex allele-specific qPCR method detecting the 7 most clinically relevant KRAS somatic mutations with concomitant amplification of non-mutated KRAS in tumor cells and tissues from CRC patients. Positive samples evidenced in the multiplex assay were further subjected to individual allele-specific analysis, to define the specific mutation. Reference human cancer DNA harbouring either G12A, G12C, G12D, G12R, G12S, G12V and G13D confirmed assay specificity with ≤1% sensitivity of mutant alleles. KRAS multiplex mutation analysis usefulness was also demonstrated with formalin-fixed paraffin embedded (FFPE) from CRC biopsies. CONCLUSION Co-amplification of non-mutated DNA avoided false negatives from degraded samples. Moreover, this cost effective assay is compatible with mutation detection by DNA sequencing in FFPE tissues, but with a greater sensitivity when mutant DNA concentrations are limiting.
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Affiliation(s)
- Andrea Orue
- IVIC, Tumor Cell Biology Laboratory, Apartado 21827, Caracas, 1020A, Venezuela
| | - Manuel Rieber
- IVIC, Tumor Cell Biology Laboratory, Apartado 21827, Caracas, 1020A, Venezuela
- * E-mail:
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