1
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Wang T, Liu Y, Sun HH, Yin BC, Ye BC. An RNA-Guided Cas9 Nickase-Based Method for Universal Isothermal DNA Amplification. Angew Chem Int Ed Engl 2019; 58:5382-5386. [PMID: 30773764 DOI: 10.1002/anie.201901292] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Indexed: 12/11/2022]
Abstract
We have developed an ingenious method, termed Cas9 nickase-based amplification reaction (Cas9nAR), to amplify a target fragment from genomic DNA at a constant temperature of 37 °C. Cas9nAR employs a sgRNA:Cas9n complex with a single-strand nicking property, a strand-displacing DNA polymerase, and two primers bearing the cleavage sequence of Cas9n, to promote cycles of DNA replication through priming, extension, nicking, and displacement reaction steps. Cas9nAR exhibits a zeptomolar limit of detection (2 copies in 20 μL of reaction system) within 60 min and a single-base discrimination capability. More importantly, the underlying principle of Cas9nAR offers simplicity in primer design and universality in application. Considering the superior sensitivity and specificity, as well as the simple-to-implement, rapid, and isothermal features, Cas9nAR holds great potential to become a routine assay for the quantitative detection of nucleic acids in basic and applied studies.
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Affiliation(s)
- Ting Wang
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Yong Liu
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Huan-Huan Sun
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Bin-Cheng Yin
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
| | - Bang-Ce Ye
- Lab of Biosystem and Microanalysis, State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, Shanghai, 200237, China
- Institute of Engineering Biology and Health, Collaborative Innovation Center of Yangtze River Delta Region Green Pharmaceuticals, College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, 310014, Zhejiang, China
- School of Chemistry and Chemical Engineering, Shihezi University, Xinjiang, 832000, China
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2
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Wang T, Liu Y, Sun H, Yin B, Ye B. An RNA‐Guided Cas9 Nickase‐Based Method for Universal Isothermal DNA Amplification. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201901292] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Ting Wang
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Yong Liu
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Huan‐Huan Sun
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Bin‐Cheng Yin
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
| | - Bang‐Ce Ye
- Lab of Biosystem and MicroanalysisState Key Laboratory of Bioreactor EngineeringEast China University of Science & Technology Shanghai 200237 China
- Institute of Engineering Biology and HealthCollaborative Innovation Center of Yangtze River Delta Region Green PharmaceuticalsCollege of Pharmaceutical SciencesZhejiang University of Technology Hangzhou 310014 Zhejiang China
- School of Chemistry and Chemical EngineeringShihezi University Xinjiang 832000 China
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3
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Dong L, Wang S, Fu B, Wang J. Evaluation of droplet digital PCR and next generation sequencing for characterizing DNA reference material for KRAS mutation detection. Sci Rep 2018; 8:9650. [PMID: 30504843 PMCID: PMC6269532 DOI: 10.1038/s41598-018-27368-3] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 05/23/2018] [Indexed: 01/05/2023] Open
Abstract
KRAS gene mutations are predictive markers of non-response to anti-epidermal growth factor receptor. An increasing number of techniques are being developed to detect KRAS mutations. To obtain consistent and comparable results, a traceable reference material (RM) is necessary for validation the routinely used method. However, a lack of reference methods is a main impediment for deriving traceability and measurement comparability. In this study, droplet digital PCR (ddPCR) and next generation sequencing (NGS) were evaluated. No cross- reactivity was detected with any of the probe by ddPCR. The measured fraction of KRAS mutant allele by ddPCR and NGS agreed with the prepared value by gravimetrical dilution (concordance (k) >0.95 and >0.93 for ddPCR and NGS, respectively). The reliable limit of quantification (LOQ) was 0.1% and 1% for ddPCR and NGS, respectively. In conclusion, the validated ddPCR and NGS are suitable to characterize the KRAS RM due to the high specificity and accuracy. Verification of the LOD of three commercial kits by using the NIM-KRAS-8 RM showed that the LOD was inconsistent with the claimed LOD of the kits (1%) for some assays. This indicates a traceable RM was important for setting up the criteria regarding the LOD for the commercial kit.
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Affiliation(s)
- Lianhua Dong
- National Institute of Metrology, Beijing, 100013, P. R. China.
| | - Shangjun Wang
- Nanjing Institute of Measurement and Testing Technology, Nanjing, 210049, P. R. China
| | - Boqiang Fu
- National Institute of Metrology, Beijing, 100013, P. R. China
| | - Jing Wang
- National Institute of Metrology, Beijing, 100013, P. R. China
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4
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Susanti S, Fadhil W, Murtaza S, Hassall JC, Ebili HO, Oniscu A, Ilyas M. Positive association of PIK3CA mutation with KRAS mutation but not BRAF mutation in colorectal cancer suggests co-selection is gene specific but not pathway specific. J Clin Pathol 2018; 72:263-264. [PMID: 30361395 DOI: 10.1136/jclinpath-2018-205483] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 11/03/2022]
Affiliation(s)
- Susanti Susanti
- Molecular Pathology Group, Unit of Academic Molecular Pathology, Division of Cancer and Stem Cell, School of Medicine, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK.,Deparment of Pharmacology and Clinical Pharmacy, Faculty of Pharmacy, University of Muhammadiyah Purwokerto, Central Java, Indonesia.,Nottingham Molecular Pathology Node, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK
| | - Wakkas Fadhil
- Molecular Pathology Group, Unit of Academic Molecular Pathology, Division of Cancer and Stem Cell, School of Medicine, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK.,Nottingham Molecular Pathology Node, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK
| | - Shamayal Murtaza
- Molecular Pathology Group, Unit of Academic Molecular Pathology, Division of Cancer and Stem Cell, School of Medicine, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK
| | - James C Hassall
- Molecular Pathology Group, Unit of Academic Molecular Pathology, Division of Cancer and Stem Cell, School of Medicine, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK.,Nottingham Molecular Pathology Node, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK
| | - Henry O Ebili
- Molecular Pathology Group, Unit of Academic Molecular Pathology, Division of Cancer and Stem Cell, School of Medicine, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK.,Nottingham Molecular Pathology Node, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK.,Department of Morbid Anatomy and Histopathology, Olabisi Onabanjo University, Ago-Iwoye, Nigeria
| | - Anca Oniscu
- Molecular Pathology, Royal Infirmary of Edinburgh, Edinburgh, UK
| | - Mohammad Ilyas
- Molecular Pathology Group, Unit of Academic Molecular Pathology, Division of Cancer and Stem Cell, School of Medicine, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK .,Nottingham Molecular Pathology Node, University of Nottingham, Queen's Medical Centre Campus, Nottingham, UK
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5
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Susanti S, Fadhil W, Ebili HO, Asiri A, Nestarenkaite A, Hadjimichael E, Ham-Karim HA, Field J, Stafford K, Matharoo-Ball B, Hassall JC, Sharif A, Oniscu A, Ilyas M. N_LyST: a simple and rapid screening test for Lynch syndrome. J Clin Pathol 2018; 71:713-720. [DOI: 10.1136/jclinpath-2018-205013] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 02/07/2018] [Accepted: 02/08/2018] [Indexed: 01/13/2023]
Abstract
AimsWe sought to use PCR followed by high-resolution melting analysis to develop a single closed-tube screening panel to screen for Lynch syndrome. This comprises tests for microsatellite instability (MSI), MLH1 methylation promoter and BRAF mutation.MethodsFor MSI testing, five mononucleotide markers (BAT25, BAT26, BCAT25, MYB, EWSR1) were developed. In addition, primers were designed to interrogate Region C of the MLH1 promoter for methylation (using bisulphite-modified DNA) and to test for mutations in codon 600 of BRAF. Two separate cohorts from Nottingham (n=99, 46 with MSI, 53 being microsatellite stable (MSS)) and Edinburgh (n=88, 45 MSI, 43 MSS) were tested.ResultsAll the cases (n=187) were blind tested for MSI and all were correctly characterised by our panel. The MLH1 promoter and BRAF were tested only in the Nottingham cohort. Successful blinded analysis was performed on the MLH1 promoter in 97 cases. All MSS cases showed a pattern of non-methylation while 41/44 cases with MSI showed full methylation. The three cases with MSI and a non-methylated pattern had aberrations in MSH2 and MSH6 expression. BRAF mutation was detected in 61% of MSI cases and 11% of MSS cases.Finally, 12 cases were blind screened by using the whole panel as a single test. Of these, five were identified as MSS, four as MSI/non-LS and three as MSI/possible LS. These results were concordant with the previous data.ConclusionWe describe the Nottingham Lynch Syndrome Test (N_LyST). This is a quick, simple and cheap method for screening for Lynch syndrome.
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6
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Ilyas M. Next-Generation Sequencing in Diagnostic Pathology. Pathobiology 2017; 84:292-305. [PMID: 29131018 DOI: 10.1159/000480089] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/06/2017] [Indexed: 12/26/2022] Open
Abstract
Interrogation of tissue informs on patient management through delivery of a diagnosis together with associated clinically relevant data. The diagnostic pathologist will usually evaluate the morphological appearances of a tissue sample and, occasionally, the pattern of expression of a limited number of biomarkers. Recent developments in sequencing technology mean that DNA and RNA from tissue samples can now be interrogated in great detail. These new technologies, collectively known as next-generation sequencing (NGS), generate huge amounts of data which can be used to support patient management. In order to maximize the utility of tissue interrogation, the molecular data need to be interpreted and integrated with the morphological data. However, in order to interpret the molecular data, the pathologist must understand the utility and the limitations of NGS data. In this review, the principles behind NGS technologies are described. In addition, the caveats in the interpretation of the data are discussed, and a scheme is presented to "classify" the types of data which are generated. Finally, a glossary of new terminology is included to help pathologists become familiar with the lexicon of NGS-derived molecular data.
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7
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Ebili HO, Hassall J, Asiri A, Ham-Karim H, Fadhil W, Agboola AJ, Ilyas M. QMC-PCRx: a novel method for rapid mutation detection. J Clin Pathol 2017; 70:702-711. [PMID: 28153952 DOI: 10.1136/jclinpath-2016-204264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/09/2017] [Accepted: 01/10/2017] [Indexed: 11/03/2022]
Abstract
AIMS We previously described the quick multiplex consensus PCR (QMC-PCR) as a method for rapid mutation screening in low-quality template. QMC-PCR has two-stages: a prediagnostic multiplex (PDM) reaction followed by a single specific diagnostic reaction with high-resolution melting (HRM) analysis. We aimed to develop QMC-PCRx in which second stage was multiplexed to allow testing of multiple targets. METHODS The PDM reaction was retained without change. For the second stage, in silico design was used to identify targets amenable to a multiplex specific diagnostic reaction and multiplex HRM (mHRM) analysis. Following optimisation, 17 colorectal cancers were tested for mutation in five hotspots. For QMC-PCR, each target was tested individually. For QMC-PCRx, the targets were tested in the following combinations (i) KRAS exon 3/PIK3CA exon 20/PTEN exon 3 in triplex and (ii) PTEN exon 7/NRAS exon 2 in duplex. The degree of agreement between the novel QMC-PCRx and the standard QMC-PCR was tested by the percentage concordance. RESULTS Optimisation of mHRM showed that peaks needed to be separated (without overlap) and the optimal number was three targets per test. Our experimental design produced distinct and widely separated peaks for the individual targets although one of the primers needed a GC-tail. A total of 85 individual targets were tested; this required 85 second-stage PCR/HRM tests by QMC-PCR versus 34 second-stage tests by QMC-PCRx. The percentage concordance between the singleplex and multiplex methodologies was 100%. CONCLUSIONS A multiplexed analysis using HRM is possible without loss of diagnostic accuracy. The novel QMC-PCRx protocol can significantly reduce workload and costs of mutation screening.
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Affiliation(s)
- Henry O Ebili
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK.,Department of Morbid Anatomy and Histopathology, Olabisi Onabanjo University, Ago-Iwoye, Nigeria
| | - James Hassall
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK
| | - Abutaleb Asiri
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK
| | - Hersh Ham-Karim
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK
| | - Wakkas Fadhil
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK.,Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, UK
| | - Ayodeji Johnson Agboola
- Department of Morbid Anatomy and Histopathology, Olabisi Onabanjo University, Ago-Iwoye, Nigeria
| | - Mohammad Ilyas
- Division of Cancer and Stem Cell, Faculty of Medicine & Health Sciences, University of Nottingham, Nottingham, UK.,Nottingham Molecular Pathology Node, University of Nottingham, Nottingham, UK
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8
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Martinuzzi C, Pastorino L, Andreotti V, Garuti A, Minuto M, Fiocca R, Bianchi-Scarrà G, Ghiorzo P, Grillo F, Mastracci L. A combination of immunohistochemistry and molecular approaches improves highly sensitive detection of BRAF mutations in papillary thyroid cancer. Endocrine 2016; 53:672-80. [PMID: 26296380 DOI: 10.1007/s12020-015-0720-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 08/08/2015] [Indexed: 12/19/2022]
Abstract
The optimal method for BRAF mutation detection remains to be determined despite advances in molecular detection techniques. The aim of this study was to compare, against classical Sanger sequencing, the diagnostic performance of two of the most recently developed, highly sensitive methods: BRAF V600E immunohistochemistry (IHC) and peptide nucleic-acid (PNA)-clamp qPCR. BRAF exon 15 mutations were searched in formalin-fixed paraffin-embedded tissues from 86 papillary thyroid carcinoma using the three methods. The limits of detection of Sanger sequencing in borderline or discordant cases were quantified by next generation sequencing. BRAF mutations were found in 74.4 % of cases by PNA, in 71 % of cases by IHC, and in 64 % of cases by Sanger sequencing. Complete concordance for the three methods was observed in 80 % of samples. Better concordance was observed with the combination of two methods, particularly PNA and IHC (59/64) (92 %), while the combination of PNA and Sanger was concordant in 55 cases (86 %). Sensitivity of the three methods was 99 % for PNA, 94.2 % for IHC, and 89.5 % for Sanger. Our data show that IHC could be used as a cost-effective, first-line method for BRAF V600E detection in daily practice, followed by PNA analysis in negative or uninterpretable cases, as the most efficient method. PNA-clamp quantitative PCR is highly sensitive and complementary to IHC as it also recognizes other mutations besides V600E and it is suitable for diagnostic purposes.
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Affiliation(s)
- Claudia Martinuzzi
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
- Department of Surgical Sciences (DISC), University of Genoa, Genoa, Italy
| | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Virginia Andreotti
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Anna Garuti
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
| | - Michele Minuto
- Department of Surgical Sciences (DISC), University of Genoa, Genoa, Italy
- Surgery 1 Unit, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Roberto Fiocca
- Department of Surgical Sciences (DISC), University of Genoa, Genoa, Italy
- Pathology Unit, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Giovanna Bianchi-Scarrà
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy
- Genetics of Rare Tumors, IRCCS AOU San Martino-IST, University of Genoa, Genoa, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, V.le Benedetto XV 6, 16132, Genoa, Italy.
- Genetics of Rare Tumors, IRCCS AOU San Martino-IST, University of Genoa, Genoa, Italy.
| | - Federica Grillo
- Department of Surgical Sciences (DISC), University of Genoa, Genoa, Italy
- Pathology Unit, IRCCS AOU San Martino-IST, Genoa, Italy
| | - Luca Mastracci
- Department of Surgical Sciences (DISC), University of Genoa, Genoa, Italy
- Pathology Unit, IRCCS AOU San Martino-IST, Genoa, Italy
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9
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Van Krieken JHJM, Rouleau E, Ligtenberg MJL, Normanno N, Patterson SD, Jung A. RAS testing in metastatic colorectal cancer: advances in Europe. Virchows Arch 2016; 468:383-96. [PMID: 26573425 PMCID: PMC4830882 DOI: 10.1007/s00428-015-1876-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 12/22/2022]
Abstract
Personalized medicine shows promise for maximizing efficacy and minimizing toxicity of anti-cancer treatment. KRAS exon 2 mutations are predictive of resistance to epidermal growth factor receptor-directed monoclonal antibodies in patients with metastatic colorectal cancer. Recent studies have shown that broader RAS testing (KRAS and NRAS) is needed to select patients for treatment. While Sanger sequencing is still used, approaches based on various methodologies are available. Few CE-approved kits, however, detect the full spectrum of RAS mutations. More recently, "next-generation" sequencing has been developed for research use, including parallel semiconductor sequencing and reversible termination. These techniques have high technical sensitivities for detecting mutations, although the ideal threshold is currently unknown. Finally, liquid biopsy has the potential to become an additional tool to assess tumor-derived DNA. For accurate and timely RAS testing, appropriate sampling and prompt delivery of material is critical. Processes to ensure efficient turnaround from sample request to RAS evaluation must be implemented so that patients receive the most appropriate treatment. Given the variety of methodologies, external quality assurance programs are important to ensure a high standard of RAS testing. Here, we review technical and practical aspects of RAS testing for pathologists working with metastatic colorectal cancer tumor samples. The extension of markers from KRAS to RAS testing is the new paradigm for biomarker testing in colorectal cancer.
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Affiliation(s)
- J Han J M Van Krieken
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands.
| | | | - Marjolijn J L Ligtenberg
- Department of Pathology, Radboud University Medical Center, P.O. Box 9101, 6500 HB, Nijmegen, Netherlands
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, INT-Fondazione Pascale, Naples, Italy
| | - Scott D Patterson
- Amgen Inc., Thousand Oaks, CA, USA
- Gilead Sciences, Inc., Foster City, CA, USA
| | - Andreas Jung
- Institute of Pathology, University of Munich, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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10
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Azuara D, Santos C, Lopez-Doriga A, Grasselli J, Nadal M, Sanjuan X, Marin F, Vidal J, Montal R, Moreno V, Bellosillo B, Argiles G, Elez E, Dienstmann R, Montagut C, Tabernero J, Capellá G, Salazar R. Nanofluidic Digital PCR and Extended Genotyping of RAS and BRAF for Improved Selection of Metastatic Colorectal Cancer Patients for Anti-EGFR Therapies. Mol Cancer Ther 2016; 15:1106-12. [PMID: 27037411 DOI: 10.1158/1535-7163.mct-15-0820] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 02/17/2016] [Indexed: 11/16/2022]
Abstract
The clinical significance of low-frequent RAS pathway-mutated alleles and the optimal sensitivity cutoff value in the prediction of response to anti-EGFR therapy in metastatic colorectal cancer (mCRC) patients remains controversial. We aimed to evaluate the added value of genotyping an extended RAS panel using a robust nanofluidic digital PCR (dPCR) approach. A panel of 34 hotspots, including RAS (KRAS and NRAS exons 2/3/4) and BRAF (V600E), was analyzed in tumor FFPE samples from 102 mCRC patients treated with anti-EGFR therapy. dPCR was compared with conventional quantitative PCR (qPCR). Response rates, progression-free survival (PFS), and overall survival (OS) were correlated to the mutational status and the mutated allele fraction. Tumor response evaluations were not available in 9 patients and were excluded for response rate analysis. Twenty-two percent of patients were positive for one mutation with qPCR (mutated alleles ranged from 2.1% to 66.6%). Analysis by dPCR increased the number of positive patients to 47%. Mutated alleles for patients only detected by dPCR ranged from 0.04% to 10.8%. An inverse correlation between the fraction of mutated alleles and radiologic response was observed. ROC analysis showed that a fraction of 1% or higher of any mutated alleles offered the best predictive value for all combinations of RAS and BRAF analysis. In addition, this threshold also optimized prediction both PFS and OS. We conclude that mutation testing using an extended gene panel, including RAS and BRAF with a threshold of 1% improved prediction of response to anti-EGFR therapy. Mol Cancer Ther; 15(5); 1106-12. ©2016 AACR.
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Affiliation(s)
- Daniel Azuara
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Cristina Santos
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Adriana Lopez-Doriga
- Unit of Biomarkers and Susceptibility, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Julieta Grasselli
- Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Marga Nadal
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Xavier Sanjuan
- Department of Pathology, University Hospital Bellvitge (HUB-IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Fátima Marin
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Joana Vidal
- Department of Medical Oncology, Hospital Universitari del Mar, Barcelona, Spain
| | - Robert Montal
- Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Unit of Biomarkers and Susceptibility, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain
| | - Beatriz Bellosillo
- Department of Pathology, Hospital Universitari del Mar, Barcelona, Spain
| | - Guillem Argiles
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Elena Elez
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rodrigo Dienstmann
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Clara Montagut
- Department of Medical Oncology, Hospital Universitari del Mar, Barcelona, Spain
| | - Josep Tabernero
- Department of Medical Oncology, Vall d'Hebron University Hospital and Institute of Oncology (VHIO), Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Gabriel Capellá
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
| | - Ramon Salazar
- Translational Research Laboratory, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain. Department of Medical Oncology, Catalan Insitute of Oncology (ICO), Bellvitge Biomedical Research Institute (IDIBELL), L'Hospitalet de Llobregat, Barcelona, Spain.
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11
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Molecular Taxonomy and Tumourigenesis of Colorectal Cancer. Clin Oncol (R Coll Radiol) 2016; 28:73-82. [DOI: 10.1016/j.clon.2015.11.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/22/2015] [Accepted: 10/26/2015] [Indexed: 12/16/2022]
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12
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Spagnolo F, Ghiorzo P, Orgiano L, Pastorino L, Picasso V, Tornari E, Ottaviano V, Queirolo P. BRAF-mutant melanoma: treatment approaches, resistance mechanisms, and diagnostic strategies. Onco Targets Ther 2015; 8:157-68. [PMID: 25653539 PMCID: PMC4303458 DOI: 10.2147/ott.s39096] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BRAF inhibitors vemurafenib and dabrafenib achieved improved overall survival over chemotherapy and have been approved for the treatment of BRAF-mutated metastatic melanoma. More recently, the combination of BRAF inhibitor dabrafenib with MEK inhibitor trametinib has shown improved progression-free survival, compared to dabrafenib monotherapy, in a Phase II study and has received approval by the US Food and Drug Administration. However, even when treated with the combination, most patients develop mechanisms of acquired resistance, and some of them do not achieve tumor regression at all, because of intrinsic resistance to therapy. Along with the development of BRAF inhibitors, immunotherapy made an important step forward: ipilimumab, an anti-CTLA-4 monoclonal antibody, was approved for the treatment of metastatic melanoma; anti-PD-1 agents achieved promising results in Phase I/II trials, and data from Phase III studies will be ready soon. The availability of such drugs, which are effective regardless of BRAF status, has made the therapeutic approach more complex, as first-line treatment with BRAF inhibitors may not be the best choice for all BRAF-mutated patients. The aim of this paper is to review the systemic therapeutic options available today for patients affected by BRAF V600-mutated metastatic melanoma, as well as to summarize the mechanisms of resistance to BRAF inhibitors and discuss the possible strategies to overcome them. Moreover, since the molecular analysis of tumor specimens is now a pivotal and decisional factor in the treatment strategy of metastatic melanoma patients, the advances in the molecular detection techniques for the BRAF V600 mutation will be reported.
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Affiliation(s)
- Francesco Spagnolo
- Department of Plastic and Reconstructive Surgery, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Paola Ghiorzo
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genova, Italy ; Genetics of Rare Cancers, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Laura Orgiano
- Department of Medical Oncology, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Lorenza Pastorino
- Department of Internal Medicine and Medical Specialties (DiMI), University of Genoa, Genova, Italy ; Genetics of Rare Cancers, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Virginia Picasso
- Department of Medical Oncology, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Elena Tornari
- Department of Medical Oncology, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Vincenzo Ottaviano
- Department of Medical Oncology, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
| | - Paola Queirolo
- Department of Medical Oncology, IRCCS Azienda Ospedaliera Universitaria San Martino, IST Istituto Nazionale per la Ricerca sul Cancro, Genova, Italy
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Implementation of a companion diagnostic in the clinical laboratory: the BRAF example in melanoma. Clin Chim Acta 2014; 439:128-36. [PMID: 25454717 DOI: 10.1016/j.cca.2014.10.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2014] [Revised: 09/19/2014] [Accepted: 10/13/2014] [Indexed: 01/09/2023]
Abstract
A companion diagnostic test provides information that is essential for the safe and effective use of a corresponding therapeutic product as indicated in the drug instructions. The implementation of a companion diagnostic follows the rules of a molecular test for somatic mutations in a routine clinical laboratory environment and needs guidance on practical aspects, including the choice of the proper analytical method and the procedures for internal and external quality controls. Selection of the appropriate assay for detection of genetic alterations depends on several factors: the type of mutation under study, the sample to be assayed and its preparation procedure. In addition, the results of a molecular assay require a complex interpretation process of the analytical data as the patient's genotype, the translation of the identified variant into a predicted phenotype and knowledge on restrictions of the method used. In relation to these aspects herein we report an opinion paper of the Working Group Personalized Laboratory Medicine jointly constituted by the European Federation of Laboratory Medicine (EFLM) and by the European Society of Pharmacogenomics and Theranostics (ESPT) using, as an example, the BRAF genotype analysis in tumor tissue samples for identification of melanoma patients that can benefit treatment with BRAF inhibitors. The manuscript is focused on the following aspects: i) medical rationale, ii) methodologies of analysis, iii) laboratory performance evaluation and iv) the laboratory specific report for the clinicians. The critical evaluation of these aspects would be useful for the implementation of a companion diagnostic in the clinical laboratory.
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KRAS mutations: analytical considerations. Clin Chim Acta 2014; 431:211-20. [PMID: 24534449 DOI: 10.1016/j.cca.2014.01.049] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/20/2014] [Accepted: 01/22/2014] [Indexed: 12/27/2022]
Abstract
Colorectal cancer (CRC) is the third most common cancer and the second most common cause of cancer death globally. Significant improvements in survival have been made in patients with metastasis by new therapies. For example, Cetuximab and Panitumumab are monoclonal antibodies that inhibit the epidermal growth receptor (EGFR). KRAS mutations in codon 12 and 13 are the recognized biomarkers that are analyzed in clinics before the administration of anti-EGFR therapy. Genetic analyses have revealed that mutations in KRAS predict a lack of response to Panitumumab and Cetuximab in patients with metastatic CRC (mCRC). Notably, it is estimated that 35-45% of CRC patients harbor KRAS mutations. Therefore, KRAS mutation testing should be performed in all individuals with the advanced CRC in order to identify the patients who will not respond to the monoclonal EGFR antibody inhibitors. New techniques for KRAS testing have arisen rapidly, and each technique has advantages and disadvantages. Herein, we review the latest published literature specific to KRAS mutation testing techniques. Since reliability and feasibility are important issues in clinical analyses. Therefore, this review also summarizes the effectiveness and limitations of numerous KRAS mutation testing techniques.
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Tougeron D, Lecomte T, Pagès JC, Villalva C, Collin C, Ferru A, Tourani JM, Silvain C, Levillain P, Karayan-Tapon L. Effect of low-frequency KRAS mutations on the response to anti-EGFR therapy in metastatic colorectal cancer. Ann Oncol 2013; 24:1267-73. [PMID: 23293113 DOI: 10.1093/annonc/mds620] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Only patients with wild-type (WT) KRAS tumors benefit from anti-epidermal growth factor receptor (EGFR) monoclonal antibodies (Mabs) in metastatic colorectal cancer (mCRC). Pyrosequencing is now widely used for the determination of KRAS mutation burden and a conservative cut-off point of 10% has been defined. Up until now, the impact of low-frequency KRAS mutations (<10%) on the response to anti-EGFR Mabs has yet to be evaluated. PATIENTS AND METHODS Tumors from patients receiving anti-EGFR Mabs based on a WT genotype for KRAS, as determined using direct sequencing, have been retrospectively analyzed by pyrosequencing. Patients were categorized as WT (no KRAS mutation) or low-frequency mutation when KRAS mutation was <10% (KRAS low MT). RESULTS A total of 168 patients treated by anti-EGFR Mabs for mCRC were analyzed. According to pyrosequencing, 138 tumors remained KRAS WT, while 30 tumors were KRAS low MT. In the KRAS low MT and KRAS WT groups, the response rates were 6.7% and 37.0%, respectively, while stabilization amounted to 23.3% versus 32.6% and progression to 70% versus 29% (P < 0.01). Progression-free survival (PFS) was 2.7 ± 0.5 months for KRAS low MT and was 6.0 ± 0.3 months for KRAS WT (P < 0.01). CONCLUSIONS These results appear to validate consideration of low-frequency KRAS mutation tumors as positive, and justify a large-scale prospective study.
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Affiliation(s)
- D Tougeron
- Department of Gastroenterology, Poitiers University Hospital, 2 rue de la Milétrie, 86000 Poitiers Cedex, France.
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Colomba E, Hélias-Rodzewicz Z, Von Deimling A, Marin C, Terrones N, Pechaud D, Surel S, Côté JF, Peschaud F, Capper D, Blons H, Zimmermann U, Clerici T, Saiag P, Emile JF. Detection of BRAF p.V600E Mutations in Melanomas. J Mol Diagn 2013; 15:94-100. [DOI: 10.1016/j.jmoldx.2012.09.001] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 09/04/2012] [Accepted: 09/13/2012] [Indexed: 01/11/2023] Open
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Shackelford RE, Whitling NA, McNab P, Japa S, Coppola D. KRAS Testing: A Tool for the Implementation of Personalized Medicine. Genes Cancer 2012; 3:459-66. [PMID: 23264846 DOI: 10.1177/1947601912460547] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2012] [Accepted: 08/14/2012] [Indexed: 12/21/2022] Open
Abstract
Activating point mutations in codons 12, 13, and 61 of the KRAS proto-oncogene are common in colorectal, non-small cell lung, pancreatic, and thyroid cancers. Constitutively activated KRAS mutations are strongly associated with a resistance to anti-epidermal growth factor receptor (EGFR) therapies, such as panitumumab and cetuximab used for treating metastatic colorectal carcinoma and EGFR tyrosine inhibitors used for advanced non-small cell lung cancers. Since anti-EGFR therapies are costly and may exert deleterious effects on individuals without activating mutations, KRAS mutation testing is recommended prior to the initiation of anti-EGFR therapy for these malignancies. The goal of this review is to summarize the KRAS mutation testing methods. Testing is now routinely requested in the clinical practice to provide data to assign the most appropriate anticancer chemotherapy for each given patient. Review of the most relevant literature was performed. Several areas were considered: ordering of the test, selection of the sample to be tested, and review of the testing methodologies. We found that several different methods are used for clinical KRAS mutation testing. Each of the methodologies is described, and information is provided about their performance, cost, turnaround times, detection limits, sensitivities, and specificities. We also provided "tips" for the appropriate selection and preparation of the sample to be tested. This is an important aspect of KRAS testing for clinical use, as the results of the test will affect clinical decisions with consequences for the patient.
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Tan C, Du X. KRAS mutation testing in metastatic colorectal cancer. World J Gastroenterol 2012; 18:5171-80. [PMID: 23066310 PMCID: PMC3468848 DOI: 10.3748/wjg.v18.i37.5171] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2012] [Revised: 06/06/2012] [Accepted: 08/04/2012] [Indexed: 02/06/2023] Open
Abstract
The KRAS oncogene is mutated in approximately 35%-45% of colorectal cancers, and KRAS mutational status testing has been highlighted in recent years. The most frequent mutations in this gene, point substitutions in codons 12 and 13, were validated as negative predictors of response to anti-epidermal growth factor receptor antibodies. Therefore, determining the KRAS mutational status of tumor samples has become an essential tool for managing patients with colorectal cancers. Currently, a variety of detection methods have been established to analyze the mutation status in the key regions of the KRAS gene; however, several challenges remain related to standardized and uniform testing, including the selection of tumor samples, tumor sample processing and optimal testing methods. Moreover, new testing strategies, in combination with the mutation analysis of BRAF, PIK3CA and loss of PTEN proposed by many researchers and pathologists, should be promoted. In addition, we recommend that microsatellite instability, a prognostic factor, be added to the abovementioned concomitant analysis. This review provides an overview of KRAS biology and the recent advances in KRAS mutation testing. This review also addresses other aspects of status testing for determining the appropriate treatment and offers insight into the potential drawbacks of mutational testing.
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Sha J, Liang G, Pan J, Xuan H, Ping P, Li D, Bo J, Liu D, Shen W, Liu W, Huang Y. Application of pyrosequencing technique for improved detection of K-Ras mutation in formalin-fixed and paraffin-embedded prostate carcinoma tissues in Chinese patients. Clin Chim Acta 2012; 413:1532-5. [DOI: 10.1016/j.cca.2012.06.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 06/03/2012] [Indexed: 10/28/2022]
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Fadhil W, Ibrahem S, Seth R, AbuAli G, Ragunath K, Kaye P, Ilyas M. The utility of diagnostic biopsy specimens for predictive molecular testing in colorectal cancer. Histopathology 2012; 61:1117-24. [PMID: 22882224 DOI: 10.1111/j.1365-2559.2012.04321.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
AIMS If stratified medicine is to be applied in the neoadjuvant setting, predictive testing will have to be undertaken on preoperative diagnostic biopsy specimens. The aim of this study was to evaluate whether a diagnostic biopsy was adequately representative of the main tumour in colorectal cancer. METHODS AND RESULTS Thirty cases of paired biopsy and subsequent resection specimens were randomly selected. Samples were screened for mutation in KRAS (codons 12/13, 61, and 146), BRAF (codon 600 and exon 11), PIK3CA (exons 1, 9, and 20), TP53 (exons 5-8), and microsatellite instability, using the quick multiplex consensus or standard polymerase chain reaction (PCR) protocols followed by high-resolution melting analysis. A total of 570 paired PCR tests were performed for mutation detection, and identical results were obtained in both biopsy and resection specimens in 569 tests (>99% concordance). Four cases (13%) showed microsatellite instability, and, in all four cases, instability was seen at identical mononucleotide markers in both biopsy and matched resection specimens. CONCLUSIONS This is the first study to show that diagnostic biopsy specimens, even though they are a tiny sample of the tumour, are sufficiently representative for use in predictive testing for early driver mutations in colorectal cancer.
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Affiliation(s)
- Wakkas Fadhil
- Division of Pathology, School of Molecular Medical Sciences, University of Nottingham, Nottingham, UK
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Azuara D, Ginesta MM, Gausachs M, Rodriguez-Moranta F, Fabregat J, Busquets J, Pelaez N, Boadas J, Galter S, Moreno V, Costa J, de Oca J, Capellá G. Nanofluidic digital PCR for KRAS mutation detection and quantification in gastrointestinal cancer. Clin Chem 2012; 58:1332-41. [PMID: 22745110 DOI: 10.1373/clinchem.2012.186577] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
BACKGROUND Concomitant quantification of multiple mutant KRAS (v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog) alleles may provide information in addition to that provided by standard mutation-detection procedures. We assessed the feasibility of a nanofluidic digital PCR array platform to detect and quantify KRAS mutations simultaneously in clinically relevant samples. METHODS We assessed 2 groups of patients (colorectal and pancreatic disease): Group 1 consisted of 27 patients with colorectal carcinomas, 14 patients with adenomas, and 5 control individuals; group 2 consisted of 42 patients with pancreatic carcinoma, 4 with adenocarcinomas of the ampulla, and 6 with chronic pancreatitis). Digital PCR was performed with the Digital Array Chip (Fluidigm). RESULTS Nanofluidic digital PCR detected mutant alleles at 0.05% to 0.1%, depending on the variant analyzed. For the colorectal disease group, conventional PCR detected 9 (64%) of 14 adenomas that were positive for KRAS mutants, whereas digital PCR increased this number to 11 (79%) of 14. Sixteen (59%) of 27 carcinomas showed KRAS mutation with conventional PCR. Two additional cases were detected with digital PCR. In 5 cases (3 adenomas, 2 carcinomas), the total number of mutant alleles changed. For the pancreatic disease group, digital PCR increased the number of positive cases from 26 to 34 (81%) and identified ≥ 2 mutant alleles in 25 cases, compared with conventional PCR, which identified multiple KRAS mutant alleles in only 12 cases. A good correlation was observed between results obtained with tumor biopsies and those obtained with pancreatic juice. CONCLUSIONS Digital PCR provides a robust, quantitative measure of the proportion of KRAS mutant alleles in routinely obtained samples. It also allows a better classification of tumors, with potential clinical relevance.
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Affiliation(s)
- Daniel Azuara
- Translational Research Laboratory, Catalan Institute of Oncology-ICO-IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
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Shen S, Qin D. Pyrosequencing data analysis software: a useful tool for EGFR, KRAS, and BRAF mutation analysis. Diagn Pathol 2012; 7:56. [PMID: 22640803 PMCID: PMC3433338 DOI: 10.1186/1746-1596-7-56] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Accepted: 05/28/2012] [Indexed: 01/02/2023] Open
Abstract
Background Pyrosequencing is a new technology and can be used for mutation tests. However, its data analysis is a manual process and involves sophisticated algorithms. During this process, human errors may occur. A better way of analyzing pyrosequencing data is needed in clinical diagnostic laboratory. Computer software is potentially useful for pyrosequencing data analysis. We have developed such software, which is able to perform pyrosequencing mutation data analysis for epidermal growth factor receptor, Kirsten rat sarcoma viral oncogene homolog and v-raf murine sarcoma viral oncogene homolog B1. The input data for analysis includes the targeted nucleotide sequence, common mutations in the targeted sequence, pyrosequencing dispensing order, pyrogram peak order and peak heights. The output includes mutation type and percentage of mutant gene in the specimen. Results The data from 1375 pyrosequencing test results were analyzed using the software in parallel with manual analysis. The software was able to generate correct results for all 1375 cases. Conclusion The software developed is a useful molecular diagnostic tool for pyrosequencing mutation data analysis. This software can increase laboratory data analysis efficiency and reduce data analysis error rate. Virtual slides The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/1348911657684292.
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Affiliation(s)
- Shanxiang Shen
- Department of Pathology, Moffitt Cancer Center, 12902 USF Magnolia Drive, Tampa, Florida 33612, USA
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Concordance in KRAS and BRAF mutations in endoscopic biopsy samples and resection specimens of colorectal adenocarcinoma. Eur J Cancer 2012; 48:1108-15. [PMID: 22446020 DOI: 10.1016/j.ejca.2012.02.054] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 01/26/2012] [Accepted: 02/21/2012] [Indexed: 02/06/2023]
Abstract
BACKGROUND KRAS testing is mandatory if anti-EGFR therapy is considered in patients with metastatic colorectal cancer (CRC). In addition, BRAF mutations seem to be an important negative prognostic factor. The aim of this study is to establish the concordance of KRAS and BRAF mutational status in paired biopsy and resection specimens of primary CRC using several analytic methods. METHODS DNA was extracted from paraffin blocks of 126 CRC patients. KRAS codon 12/13 and BRAF V600E mutational status was assessed using high resolution melting (HRM), direct sequencing (DS) of the HRM polymerase chain reaction (PCR) product. In addition, the Therascreen Amplification Refractory Mutation System (ARMS)-Scorpion KRAS assay and BRAF pyrosequencing were employed; both assays claim to require less tumour cells in comparison with DS. RESULTS KRAS and BRAF were found to be mutually exclusive. Mutation frequencies were 33.9% for KRAS, and for BRAF 19.0%, respectively. Concordance of KRAS mutational status between biopsy and resection specimens was 97.4% (ARMS), 98.4% (DS) and 99.2% (HRM), respectively. For BRAF concordance was 98.4% (Pyro, DS) and 99.2% (HRM). CONCLUSIONS KRAS and BRAF mutational status of endoscopic biopsies and resection specimens of CRC showed a >95% concordance. Endoscopic biopsies can be confidently used for molecular analysis.
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Jeong D, Jeong Y, Lee S, Lee H, Lee W, Kim H, Park D, Park S, Mu W, Cho HD, Oh MH, Lee SS, Yang SH, Kim CJ. Detection of BRAF(V600E) Mutations in Papillary Thyroid Carcinomas by Peptide Nucleic Acid Clamp Real-Time PCR: A Comparison with Direct Sequencing. KOREAN JOURNAL OF PATHOLOGY 2012; 46:61-7. [PMID: 23109980 PMCID: PMC3479705 DOI: 10.4132/koreanjpathol.2012.46.1.61] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Revised: 12/29/2011] [Accepted: 01/10/2012] [Indexed: 12/19/2022]
Abstract
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.
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Affiliation(s)
- Dongjun Jeong
- Department of Pathology, Soonchunhyang University College of Medicine, Cheonan, Korea
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Wu HM, Li L, Yuan XW, Zhou YQ, Xiao QZ, Liu WY, Zhou WJ, Xu XM. Rapid, accurate detection of TMPRSS6 gene causative mutations with a high-resolution melting assay. Blood Cells Mol Dis 2011; 47:198-204. [DOI: 10.1016/j.bcmd.2011.06.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/31/2011] [Accepted: 06/13/2011] [Indexed: 01/23/2023]
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Yeo MK, Liang ZL, Oh T, Moon Y, An S, Kim MK, Kim KS, Shong M, Kim JM, Jo YS. Pyrosequencing cut-off value identifying BRAFV600E mutation in fine needle aspiration samples of thyroid nodules. Clin Endocrinol (Oxf) 2011; 75:555-60. [PMID: 21609347 DOI: 10.1111/j.1365-2265.2011.04115.x] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
CONTEXT Recently, tremendous efforts have been made towards the development of sensitive techniques to detect the BRAF(V600E) mutation in fine needle aspiration biopsy (FNAB) samples. However, newly developed quantitative and semi-quantitative methods, such as dual-priming oligonucleotide (DPO)-based multiplex polymerase chain reaction (PCR), have the potential to generate false-positive (FP) results. OBJECTIVES To eliminate the possibility of FP results, we generated a receiver operating characteristic (ROC) curve to investigate the diagnostic accuracy of pyrosequencing using quantitative data. DESIGN Cytological diagnoses of 983 thyroid nodules were made according to the Bethesda System 2007. The BRAF(V600E) mutation was analysed by pyrosequencing, and statistical analyses were performed. RESULTS Of the 983 nodules, 902 were adopted to evaluate the diagnostic value of pyrosequencing. The number of pathologically confirmed malignancies was 192, of which 182 were papillary thyroid cancer (PTC). By generating an ROC curve, we defined the optimal cut-off value of the mutant allele peak as 5·95% (area under the curve, 0·849; sensitivity, 0·55; 1-specificity, 0). When we applied this selective cut-off value, the number of PTCs positive for BRAF(V600E) was 99 (54·4% of the total number of PTCs). With cytology alone, the diagnostic sensitivity and specificity of detecting malignancy were 71·2% and 100%, respectively. Pyrosequencing improved the diagnostic sensitivity from 71·2% to 78·5% (McNemar's test, P < 0·001), without any change in the diagnostic specificity. When 'suspicious for malignancy' was considered a positive cytological outcome, pyrosequencing increased the diagnostic sensitivity of cytology from 95·8% to 96·9%; however, this improvement did not show statistical significance (McNemar's test, P > 0·05). CONCLUSIONS Pyrosequencing is an effective method for detecting the BRAF(V600E) mutation in FNAB samples. By allowing the optimal cut-off value to be determined, pyrosequencing improves the diagnostic sensitivity while eliminating the possibility of FP results.
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Affiliation(s)
- Min-Kyung Yeo
- Department of Pathology, Chungnam National University School of Medicine, Daejeon, South Korea
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Chen Y, Wilde HD. Mutation scanning of peach floral genes. BMC PLANT BIOLOGY 2011; 11:96. [PMID: 21605436 PMCID: PMC3120741 DOI: 10.1186/1471-2229-11-96] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2011] [Accepted: 05/23/2011] [Indexed: 05/30/2023]
Abstract
BACKGROUND Mutation scanning technology has been used to develop crop species with improved traits. Modifications that improve screening throughput and sensitivity would facilitate the targeted mutation breeding of crops. Technical innovations for high-resolution melting (HRM) analysis are enabling the clinic-based screening for human disease gene polymorphism. We examined the application of two HRM modifications, COLD-PCR and QMC-PCR, to the mutation scanning of genes in peach, Prunus persica. The targeted genes were the putative floral regulators PpAGAMOUS and PpTERMINAL FLOWER I. RESULTS HRM analysis of PpAG and PpTFL1 coding regions in 36 peach cultivars found one polymorphic site in each gene. PpTFL1 and PpAG SNPs were used to examine approaches to increase HRM throughput. Cultivars with SNPs could be reliably detected in pools of twelve genotypes. COLD-PCR was found to increase the sensitivity of HRM analysis of pooled samples, but worked best with small amplicons. Examination of QMC-PCR demonstrated that primary PCR products for further analysis could be produced from variable levels of genomic DNA. CONCLUSIONS Natural SNPs in exons of target peach genes were discovered by HRM analysis of cultivars from a southeastern US breeding program. For detecting natural or induced SNPs in larger populations, HRM efficiency can be improved by increasing sample pooling and template production through approaches such as COLD-PCR and QMC-PCR. Technical advances developed to improve clinical diagnostics can play a role in the targeted mutation breeding of crops.
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Affiliation(s)
- Yihua Chen
- Horticulture Department, University of Georgia, Athens, GA 30602, USA
| | - H Dayton Wilde
- Horticulture Department, University of Georgia, Athens, GA 30602, USA
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Solassol J, Ramos J, Crapez E, Saifi M, Mangé A, Vianès E, Lamy PJ, Costes V, Maudelonde T. KRAS mutation detection in paired frozen and Formalin-Fixed Paraffin-Embedded (FFPE) colorectal cancer tissues. Int J Mol Sci 2011; 12:3191-204. [PMID: 21686179 PMCID: PMC3116185 DOI: 10.3390/ijms12053191] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2011] [Revised: 04/11/2011] [Accepted: 05/05/2011] [Indexed: 01/05/2023] Open
Abstract
KRAS mutation has been unambiguously identified as a marker of resistance to cetuximab-based treatment in metastatic colorectal cancer (mCRC) patients. However, most studies of KRAS mutation analysis have been performed using homogenously archived CRC specimens, and studies that compare freshly frozen specimens and formalin-fixed paraffin-embedded (FFPE) specimens of CRC are lacking. The aim of the present study was to evaluate the impact of tissue preservation on the determination of KRAS mutational status. A series of 131 mCRC fresh-frozen tissues were first analyzed using both high-resolution melting (HRM) and direct sequencing. KRAS mutations were found in 47/131 (35.8%) using both approaches. Out of the 47 samples that were positive for KRAS mutations, 33 had available matched FFPE specimens. Using HRM, 2/33 (6%) demonstrated suboptimal template amplification, and 2/33 (6%) expressed an erroneous wild-type KRAS profile. Using direct sequencing, 6/33 (18.1%) displayed a wild-type KRAS status, and 3/33 (9.1%) showed discordant mutations. Finally, the detection of KRAS mutations was lower among the FFPE samples compared with the freshly frozen samples, demonstrating that tissue processing clearly impacts the accuracy of KRAS genotyping.
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Affiliation(s)
- Jérome Solassol
- Department of Cellular Biology, Center Hospital University, Montpellier 34000, France; E-Mails: (A.M.); (E.V.); (T.M.)
- University of Montpellier I, Montpellier 34000, France; E-Mails: (J.R.); (V.C.)
- Author to whom correspondence should be addressed; E-Mail: ; Tel.: +33-467612412; Fax: +33-467339590
| | - Jeanne Ramos
- University of Montpellier I, Montpellier 34000, France; E-Mails: (J.R.); (V.C.)
- Department of Pathology, Center Hospital University, Montpellier 34000, France; E-Mail:
| | - Evelyne Crapez
- Department of Biology, Centre Lutte Contre Cancer Val d’Aurelle, Montpellier 34000, France; E-Mails: (E.C.); (P.-J.L.)
| | - Majda Saifi
- Department of Pathology, Center Hospital University, Montpellier 34000, France; E-Mail:
| | - Alain Mangé
- Department of Cellular Biology, Center Hospital University, Montpellier 34000, France; E-Mails: (A.M.); (E.V.); (T.M.)
- University of Montpellier I, Montpellier 34000, France; E-Mails: (J.R.); (V.C.)
| | - Evelyne Vianès
- Department of Cellular Biology, Center Hospital University, Montpellier 34000, France; E-Mails: (A.M.); (E.V.); (T.M.)
| | - Pierre-Jean Lamy
- Department of Biology, Centre Lutte Contre Cancer Val d’Aurelle, Montpellier 34000, France; E-Mails: (E.C.); (P.-J.L.)
| | - Valérie Costes
- University of Montpellier I, Montpellier 34000, France; E-Mails: (J.R.); (V.C.)
- Department of Pathology, Center Hospital University, Montpellier 34000, France; E-Mail:
| | - Thierry Maudelonde
- Department of Cellular Biology, Center Hospital University, Montpellier 34000, France; E-Mails: (A.M.); (E.V.); (T.M.)
- University of Montpellier I, Montpellier 34000, France; E-Mails: (J.R.); (V.C.)
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