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Naoumi N, Araya-Farias M, Megariti M, Alexandre L, Papadakis G, Descroix S, Gizeli E. Acoustic detection of a mutation-specific Ligase Chain Reaction based on liposome amplification. Analyst 2024; 149:3537-3546. [PMID: 38758167 DOI: 10.1039/d3an02142d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Single nucleotide variants (SNVs) play a crucial role in understanding genetic diseases, cancer development, and personalized medicine. However, existing ligase-based amplification and detection techniques, such as Rolling Circle Amplification and Ligase Detection Reaction, suffer from low efficiency and difficulties in product detection. To address these limitations, we propose a novel approach that combines Ligase Chain Reaction (LCR) with acoustic detection using highly dissipative liposomes. In our study, we are using LCR combined with biotin- and cholesterol-tagged primers to produce amplicons also modified at each end with a biotin and cholesterol molecule. We then apply the LCR mix without any purification directly on a neutravidin modified QCM device Au-surface, where the produced amplicons can bind specifically through the biotin end. To improve sensitivity, we finally introduce liposomes as signal enhancers. For demonstration, we used the detection of the BRAF V600E point mutation versus the wild-type allele, achieving an impressive detection limit of 220 aM of the mutant target in the presence of the same amount of the wild type. Finally, we combined the assay with a microfluidic fluidized bed DNA extraction technology, offering the potential for semi-automated detection of SNVs in patients' crude samples. Overall, our LCR/acoustic method outperforms other LCR-based approaches and surface ligation biosensing techniques in terms of detection efficiency and time. It effectively overcomes challenges related to DNA detection, making it applicable in diverse fields, including genetic disease and pathogen detection.
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Affiliation(s)
- Nikoletta Naoumi
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion, 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Monica Araya-Farias
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - Maria Megariti
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Lucile Alexandre
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - George Papadakis
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
| | - Stephanie Descroix
- Laboratoire Physico-Chimie Curie, CNRS UMR 168, Institut Curie, PSL Research University, Paris, France
- Institut Pierre-Gilles de Gennes for Microfluidic (IPGG), Paris, France
| | - Electra Gizeli
- Department of Biology, University of Crete, Vassilika Vouton, Heraklion, 70013, Greece
- Institute of Molecular Biology and Biotechnology-FORTH, 100 N. Plastira Str., Heraklion 70013, Greece.
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Jiang H, Xi H, Juhas M, Zhang Y. Biosensors for Point Mutation Detection. Front Bioeng Biotechnol 2021; 9:797831. [PMID: 34976987 PMCID: PMC8714947 DOI: 10.3389/fbioe.2021.797831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 11/17/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Hanlin Jiang
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Hui Xi
- College of Science, Harbin Institute of Technology, Shenzhen, China
| | - Mario Juhas
- Medical and Molecular Microbiology Unit, Department of Medicine, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Yang Zhang
- College of Science, Harbin Institute of Technology, Shenzhen, China
- *Correspondence: Yang Zhang,
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Gibriel AA, Adel O. Advances in ligase chain reaction and ligation-based amplifications for genotyping assays: Detection and applications. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2017; 773:66-90. [PMID: 28927538 PMCID: PMC7108312 DOI: 10.1016/j.mrrev.2017.05.001] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 04/24/2017] [Accepted: 05/01/2017] [Indexed: 02/07/2023]
Abstract
Genetic variants have been reported to cause several genetic diseases. Various genotyping assays have been developed for diagnostic and screening purposes but with certain limitations in sensitivity, specificity, cost effectiveness and/or time savings. Since the discovery of ligase chain reaction (LCR) in the late nineties, it became one of the most favored platforms for detecting these variants and also for genotyping low abundant contaminants. Recent and powerful modifications with the integration of various detection strategies such as electrochemical and magnetic biosensors, nanoparticles (NPs), quantum dots, quartz crystal and leaky surface acoustic surface biosensors, DNAzyme, rolling circle amplification (RCA), strand displacement amplification (SDA), surface enhanced raman scattering (SERS), chemiluminescence and fluorescence resonance energy transfer have been introduced to both LCR and ligation based amplifications to enable high-throughput and inexpensive multiplex genotyping with improved robustness, simplicity, sensitivity and specificity. In this article, classical and up to date modifications in LCR and ligation based amplifications are critically evaluated and compared with emphasis on points of strength and weakness, sensitivity, cost, running time, equipment needed, applications and multiplexing potential. Versatile genotyping applications such as genetic diseases detection, bacterial and viral pathogens detection are also detailed. Ligation based gold NPs biosensor, ligation based RCA and ligation mediated SDA assays enhanced detection limit tremendously with a discrimination power approaching 1.5aM, 2aM and 0.1fM respectively. MLPA (multiplexed ligation dependent probe amplification) and SNPlex assays have been commercialized for multiplex detection of at least 48 SNPs at a time. MOL-PCR (multiplex oligonucleotide ligation) has high-throughput capability with multiplex detection of 50 SNPs/well in a 96 well plate. Ligase detection reaction (LDR) is one of the most widely used LCR versions that have been successfully integrated with several detection strategies with improved sensitivity down to 0.4fM.
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Affiliation(s)
- Abdullah A Gibriel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt.
| | - Ola Adel
- Biochemistry & Molecular Biology Department, Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt; Center for Drug Research & Development (CDRD), Faculty of Pharmacy, The British University in Egypt (BUE), Cairo, Egypt
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Pergolizzi G, Wagner GK, Bowater RP. Biochemical and Structural Characterisation of DNA Ligases from Bacteria and Archaea. Biosci Rep 2016; 36:00391. [PMID: 27582505 PMCID: PMC5052709 DOI: 10.1042/bsr20160003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Revised: 08/28/2016] [Accepted: 08/30/2016] [Indexed: 12/13/2022] Open
Abstract
DNA ligases are enzymes that seal breaks in the backbones of DNA, leading to them being essential for the survival of all organisms. DNA ligases have been studied from many different types of cells and organisms and shown to have diverse sizes and sequences, with well conserved specific sequences that are required for enzymatic activity. A significant number of DNA ligases have been isolated or prepared in recombinant forms and, here, we review their biochemical and structural characterisation. All DNA ligases contain an essential lysine that transfers an adenylate group from a co-factor to the 5'-phosphate of the DNA end that will ultimately be joined to the 3'-hydroxyl of the neighbouring DNA strand. The essential DNA ligases in bacteria use nicotinamide adenine dinucleotide ( β -NAD+) as their co-factor whereas those that are essential in other cells use adenosine-5'-triphosphate (ATP) as their co-factor. This observation suggests that the essential bacterial enzyme could be targeted by novel antibiotics and the complex molecular structure of β -NAD+ affords multiple opportunities for chemical modification. Several recent studies have synthesised novel derivatives and their biological activity against a range of DNA ligases has been evaluated as inhibitors for drug discovery and/or non-natural substrates for biochemical applications. Here, we review the recent advances that herald new opportunities to alter the biochemical activities of these important enzymes. The recent development of modified derivatives of nucleotides highlights that the continued combination of structural, biochemical and biophysical techniques will be useful in targeting these essential cellular enzymes.
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Affiliation(s)
- Giulia Pergolizzi
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, N/A, United Kingdom
| | - Gerd K Wagner
- Department of Chemistry, King's College London, Faculty of Natural & Mathematical Sciences, Britannia House, 7 Trinity Street, London, N/A, United Kingdom
| | - Richard Peter Bowater
- School of Biological Sciences, University of East Anglia, Norwich, N/A, NR4 7TJ, United Kingdom
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Bowater RP, Cobb AM, Pivonkova H, Havran L, Fojta M. Biophysical and electrochemical studies of protein–nucleic acid interactions. MONATSHEFTE FUR CHEMIE 2015. [DOI: 10.1007/s00706-014-1405-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Jiaul Haque AM, Kim J, Dutta G, Kim S, Yang H. Redox cycling-amplified enzymatic Ag deposition and its application in the highly sensitive detection of creatine kinase-MB. Chem Commun (Camb) 2015; 51:14493-6. [DOI: 10.1039/c5cc06117b] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This communication reports a novel enzymatic Ag-deposition scheme combined with chemical–chemical redox cycling by reduced β-nicotinamide adenine dinucleotide.
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Affiliation(s)
- Al-Monsur Jiaul Haque
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 609-735
- Korea
| | - Jihye Kim
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 609-735
- Korea
| | - Gorachand Dutta
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 609-735
- Korea
| | - Sinyoung Kim
- Department of Laboratory Medicine
- Yonsei University College of Medicine
- Seoul 135-720
- Korea
| | - Haesik Yang
- Department of Chemistry and Chemistry Institute for Functional Materials
- Pusan National University
- Busan 609-735
- Korea
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Li Y, Yan Y, Lei Y, Zhao D, Yuan T, Zhang D, Cheng W, Ding S. Surface plasmon resonance biosensor for label-free and highly sensitive detection of point mutation using polymerization extension reaction. Colloids Surf B Biointerfaces 2014; 120:15-20. [DOI: 10.1016/j.colsurfb.2014.04.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 04/09/2014] [Accepted: 04/14/2014] [Indexed: 11/16/2022]
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Stejskalová E, Horáková P, Vacek J, Bowater RP, Fojta M. Enzyme-linked electrochemical DNA ligation assay using magnetic beads. Anal Bioanal Chem 2014; 406:4129-36. [PMID: 24820061 DOI: 10.1007/s00216-014-7811-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2014] [Revised: 03/23/2014] [Accepted: 04/03/2014] [Indexed: 01/19/2023]
Abstract
DNA ligases are essential enzymes in all cells and have been proposed as targets for novel antibiotics. Efficient DNA ligase activity assays are thus required for applications in biomedical research. Here we present an enzyme-linked electrochemical assay based on two terminally tagged probes forming a nicked junction upon hybridization with a template DNA. Nicked DNA bearing a 5' biotin tag is immobilized on the surface of streptavidin-coated magnetic beads, and ligated product is detected via a 3' digoxigenin tag recognized by monoclonal antibody-alkaline phosphatase conjugate. Enzymatic conversion of napht-1-yl phosphate to napht-1-ol enables sensitive detection of the voltammetric signal on a pyrolytic graphite electrode. The technique was tested under optimal conditions and various situations limiting or precluding the ligation reaction (such as DNA substrates lacking 5'-phosphate or containing a base mismatch at the nick junction, or application of incompatible cofactor), and utilized for the analysis of the nick-joining activity of a range of recombinant Escherichia coli DNA ligase constructs. The novel technique provides a fast, versatile, specific, and sensitive electrochemical assay of DNA ligase activity.
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Affiliation(s)
- Eva Stejskalová
- Institute of Biophysics, v.v.i., Academy of Sciences of the Czech Republic, Královopolská 135, 612 65, Brno, Czech Republic
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9
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Development of a ligase detection reaction/CGE method using a LIF dual-channel detection system for direct identification of allelic composition of mutated DNA in a mixed population of excess wild-type DNA. Electrophoresis 2013; 34:1415-22. [DOI: 10.1002/elps.201200671] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2012] [Revised: 02/09/2013] [Accepted: 02/16/2013] [Indexed: 11/07/2022]
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Yi Z, Li XY, Gao Q, Tang LJ, Chu X. Aptamer-aided target capturing with biocatalytic metal deposition: an electrochemical platform for sensitive detection of cancer cells. Analyst 2013; 138:2032-7. [PMID: 23420020 DOI: 10.1039/c3an36474g] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel aptamer biosensor for cancer cell assay has been reported on the basis of ultrasensitive electrochemical detection. Cancer cell capturing is first accomplished via aptamer-aided recognition, and the cell-aptamer binding events then mediate an alkaline phosphatase-catalyzed silver deposition reaction which can be probed by electrochemical detection. Following biocatalytic silver deposition, an efficient amplification approach for sensitive electrochemical measurements is demonstrated, for cell detection with high sensitivity. Ramos cell are used as a model case, a typical biomarker of the acute blood cell cancer, Burkitt's lymphoma. The results reveal that the developed technique displays desirable selectivity in Ramos cell discrimination, and linear response range from 10 to 10(6) cells with a detection limit as low as 10 cells. Due to the simple procedures, label-free and electrochemistry based detection format, this technique is simple and cost-effective, and exhibits excellent compatibility with miniaturization technologies. The electrochemical cell detection strategy may create an intrinsically specific and sensitive platform for cancer cell assay and associated studies.
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Affiliation(s)
- Zi Yi
- State Key Laboratory of Chemo/Bio-Sensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, 410082, PR China
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Highly sensitive and selective colorimetric genotyping of single-nucleotide polymorphisms based on enzyme-amplified ligation on magnetic beads. Biosens Bioelectron 2012; 36:89-94. [DOI: 10.1016/j.bios.2012.03.045] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2012] [Revised: 03/26/2012] [Accepted: 03/29/2012] [Indexed: 11/22/2022]
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12
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Detection of single-nucleotide polymorphisms with novel leaky surface acoustic wave biosensors, DNA ligation and enzymatic signal amplification. Biosens Bioelectron 2012; 33:274-8. [DOI: 10.1016/j.bios.2011.12.036] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2011] [Revised: 12/19/2011] [Accepted: 12/20/2011] [Indexed: 12/27/2022]
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13
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A graphene-based platform for single nucleotide polymorphism (SNP) genotyping. Biosens Bioelectron 2011; 26:4213-6. [DOI: 10.1016/j.bios.2011.03.023] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2011] [Revised: 03/20/2011] [Accepted: 03/27/2011] [Indexed: 01/17/2023]
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14
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Kim JM, Koo CM, Kim J. Voltammetric Discrimination of DNA Single Base-Pair Mismatches via Taq DNA Ligase-Based Mismatch Recognition. ELECTROANAL 2011. [DOI: 10.1002/elan.201100120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Shin S, Won BY, Jung C, Shin SC, Cho DY, Lee SS, Park HG. Electrochemical detection of DNA mutations on a PNA-modified electrode utilizing a single-stranded DNA specific endonuclease. Chem Commun (Camb) 2011; 47:6611-3. [PMID: 21573274 DOI: 10.1039/c1cc11476j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Utilizing a peptide nucleic acid (PNA)-modified electrode and a single-stranded DNA specific endonuclease, a novel electrochemical method to identify DNA mutations has been developed and represents a totally new strategy for the electrochemical diagnosis of human genetic mutations.
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Affiliation(s)
- Sujeong Shin
- Department of Chemical and Biomolecular Engineering (BK21 Program), KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Republic of Korea
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Electrochemical biosensors for detection of point mutation based on surface ligation reaction and oligonucleotides modified gold nanoparticles. Anal Chim Acta 2011; 688:163-7. [PMID: 21334481 DOI: 10.1016/j.aca.2011.01.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2010] [Revised: 12/21/2010] [Accepted: 01/04/2011] [Indexed: 11/23/2022]
Abstract
An electrochemical method for point mutation detection based on surface ligation reaction and oligonucleotides (ODNs) modified gold nanoparticles (AuNPs) was demonstrated. Point mutation identification was achieved using Escherichia coli DNA ligase. This system for point mutation detection relied on a sandwich assay comprising capture ODN immobilized on Au electrodes, target ODN and ligation ODN. Because of the sequence-specific surface reactions of E. coli DNA ligase, the ligation ODN covalently linked to the capture ODN only in the presence of a perfectly complementary target ODN. The presence of ligation products on Au electrode was detected using chronocoulometry through hybridization with reporter ODN modified AuNPs. The use of AuNPs improved the sensitivity of chronocoulometry in this approach, a detection limit of 0.9 pM complementary ODN was obtained. For single base mismatched ODN (smODN), a negligible signal was observed. Even if the concentration ratio of complementary ODN to smODN was decreased to 1:1000, a detectable signal was observed. This work may provide a specific, sensitive and cost-efficient approach for point mutant detection.
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Zhu D, Xing D, Tang Y, Zhang L. A novel mutant allele specific amplification and electrochemiluminescence method for the detection of point mutation in clinical samples. Biosens Bioelectron 2009; 24:3306-10. [DOI: 10.1016/j.bios.2009.04.027] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Revised: 04/17/2009] [Accepted: 04/17/2009] [Indexed: 11/25/2022]
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18
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van Krieken JHJM, Jung A, Kirchner T, Carneiro F, Seruca R, Bosman FT, Quirke P, Fléjou JF, Plato Hansen T, de Hertogh G, Jares P, Langner C, Hoefler G, Ligtenberg M, Tiniakos D, Tejpar S, Bevilacqua G, Ensari A. KRAS mutation testing for predicting response to anti-EGFR therapy for colorectal carcinoma: proposal for an European quality assurance program. Virchows Arch 2008; 453:417-31. [PMID: 18802721 DOI: 10.1007/s00428-008-0665-y] [Citation(s) in RCA: 220] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2008] [Revised: 08/21/2008] [Accepted: 08/21/2008] [Indexed: 12/21/2022]
Abstract
Novel therapeutic agents targeting the epidermal growth factor receptor (EGFR) have improved outcomes for patients with colorectal carcinoma. However, these therapies are effective only in a subset of patients. Activating mutations in the KRAS gene are found in 30-40% of colorectal tumors and are associated with poor response to anti-EGFR therapies. Thus, KRAS mutation status can predict which patient may or may not benefit from anti-EGFR therapy. Although many diagnostic tools have been developed for KRAS mutation analysis, validated methods and standardized testing procedures are lacking. This poses a challenge for the optimal use of anti-EGFR therapies in the management of colorectal carcinoma. Here we review the molecular basis of EGFR-targeted therapies and the resistance to treatment conferred by KRAS mutations. We also present guideline recommendations and a proposal for a European quality assurance program to help ensure accuracy and proficiency in KRAS mutation testing across the European Union.
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Affiliation(s)
- J H J M van Krieken
- Department of Pathology, Radboud University Nijmegen Medical Centre, Nijmegen, 6500, HB, The Netherlands.
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