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Abstract
Quantitative real-time PCR (qPCR) is a widely adopted technique used for scientific, clinical, diagnostic, or quality control purposes. One of the main applications of qPCR is gene expression analysis, although mutation detection, genotyping, DNA detection, and quantification (from pathogens or genetically modified organisms) are also investigated using this technique.Although nonspecific detection based on DNA-binding dyes (including SYBR Green I) offers versatility in qPCR assays, detection of the PCR product using fluorescent probes confers higher specificity and sensitivity to assays, justifying the use of fluorescent probes as a detection method.This chapter seeks to propose a procedure for the design of qPCR assays using fluorescent hydrolysis probe technology. Particular attention will be paid to explaining the steps necessary to ensure the specificity of the oligonucleotides used as primers or fluorescent probes.
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Affiliation(s)
- Florent Busi
- Unité de Biologie Fonctionnelle et Adaptative, Université de Paris, CNRS UMR 8251, Paris, France.
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2
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Sousa JB, Ramos-Jesus J, Silva LC, Pereira C, de-Los-Santos-Álvarez N, Fonseca RAS, Miranda-Castro R, Delerue-Matos C, Santos Júnior JR, Barroso MF. Fe 3O 4@Au nanoparticles-based magnetoplatform for the HMGA maize endogenous gene electrochemical genosensing. Talanta 2019; 206:120220. [PMID: 31514891 DOI: 10.1016/j.talanta.2019.120220] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 07/29/2019] [Accepted: 08/02/2019] [Indexed: 11/25/2022]
Abstract
This work addresses a technological advance applied to the construction of a magnetogenoassay with electrochemical transduction for the maize taxon-specific (HMGA gene) detection using gold-coated magnetic nanoparticles as nanosized platform. Superparamagnetic core-shell Fe3O4@Au nanoparticles (10.4 ± 1.7 nm) were used to assemble the genoassay through the covalent immobilization of HMGA DNA probes onto carboxylated self-assembled monolayers at the nanoparticles surface. A hybridization reaction using sandwich format was selected to prevent inefficient hybridization connected with stable secondary DNA structures using also fluorescein isothiocyanate as DNA signaling tag. The labelling of the hybridization reaction with enzymes allowed the chronoamperometric measurement of the peroxidase activity linked to the nanoplatform located on gold surface. Using this electrochemical magnetogenoassay a linear concentration range from 0.5 to 5 nM and a LOD of 90 pM with a RSD <1.2% was calculated. Certified maize was evaluated without further purification after PCR amplification. This work highlights the efficacy of the electrochemical magnetogenoassay for the HMGA detection, showing its potential as alternative procedure for the verification of the compliance of the legislation.
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Affiliation(s)
- Juliana Beatriz Sousa
- Programa de Pós-graduação em Biotecnologia - RENORBIO, Pró-reitoria de pesquisa e pós-graduação, Universidade Federal do Piauí - UFPI, Teresina, Brasil; REQUIMTE/LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Porto, Portugal
| | - Joilson Ramos-Jesus
- Núcleo de Pesquisa em Biodiversidade e Biotecnologia, UFPI, Parnaíba, Brazil
| | - L C Silva
- Instituto de Ciências Biológicas - ICB/UPE, Recife, Brazil
| | - C Pereira
- REQUIMTE/LAQV, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | | | | | - R Miranda-Castro
- Dpto. Química Física y Analítica, Universidad de Oviedo, Oviedo, Spain
| | - C Delerue-Matos
- REQUIMTE/LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Porto, Portugal
| | - J Ribeiro Santos Júnior
- Programa de Pós-graduação em Biotecnologia - RENORBIO, Pró-reitoria de pesquisa e pós-graduação, Universidade Federal do Piauí - UFPI, Teresina, Brasil
| | - M Fátima Barroso
- REQUIMTE/LAQV, Instituto Superior de Engenharia do Porto, Instituto Politécnico do Porto, Porto, Portugal.
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Sanchiz Á, Ballesteros I, Marqués E, Dieguez MC, Rueda J, Cuadrado C, Linacero R. Evaluation of locked nucleic acid and TaqMan probes for specific detection of cashew nut in processed food by real time PCR. Food Control 2018. [DOI: 10.1016/j.foodcont.2018.02.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Cao G, Kong J, Xing Z, Tang Y, Zhang X, Xu X, Kang Z, Fang X, Guan M. Rapid detection of CALR type 1 and type 2 mutations using PNA-LNA clamping loop-mediated isothermal amplification on a CD-like microfluidic chip. Anal Chim Acta 2018; 1024:123-135. [PMID: 29776538 DOI: 10.1016/j.aca.2018.04.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 01/18/2023]
Abstract
Bleeding and thrombosis represent common complications in myeloproliferative neoplasms (MPN) and significantly contribute to morbidity and mortality. Molecular markers, including CALR mutations, were considered not only as diagnostic markers, but also as risk factors for bleeding and thrombosis associated with MPN, especially for patients in remote primary hospitals. We sought to develop an easy-to-use assay for the rapid detection of CALR type 1 (CALR-1) and type 2 (CALR-2) mutations in Philadelphia chromosome-negative MPN patients. Peptide nucleic acid-locked nucleic acid (PNA-LNA) clamping loop-mediated isothermal amplification (LAMP) assays were established, which were integrated into a centrifugal compact disc (CD) microfluidic platform. A total of 158 clinical blood samples were tested simultaneously by this microfluidic platform and an in-house real time PCR assay. The detection performance of the LAMP arrays was validated and conflicting results were identified by Sanger sequencing. The results suggested that the LAMP methods we developed exhibited good sensitivity, specificity, and precision. By real time fluorescence assay the detection limit for CALR-1 and CALR-2 mutations could reach as low as 1% and 0.5% respectively, and 10% and 5% respectively by visual method. There were no nonspecific background amplifications among different detection systems. For the CALR-1 and CALR-2 LAMP detection systems, intra-batch CV values of 1% mutated plasmid were 10.56% and 10.51% respectively, and the inter-batch CV values were 19.55% and 18.39%, respectively. The products were all analyzed by melting curve analysis and electrophoresis followed by Sanger sequencing analysis, which were consistent with the database sequences. The microfluidic platform could complete rapid detection of CALR-1/2 mutations within 60 min. The results of clinical samples detected by our CD-like microfluidic chipLAMP assay and rtPCR assay suggested that 133 samples were CALR wild type, 15 were CALR-1 mutation type, and 9 were CALR-2 mutation type. The correlation coefficient value (Kendall's tau_b) of the two assays was 0.99. Interestingly, by the newly established detection platform, we were surprised to find that one patient of Chinese origin harbored both CALR-1 and CALR-2 mutations. This result was verified by Sanger sequencing analysis. The LAMP detection systems developed herein displayed good sensitivity, specificity, and stability. Additionally, the detection results could be directly judged by color changes of the reaction systems without any auxiliary equipment. Thus, the platform we developed has the potential of being widely used in remote and economically undeveloped areas in the future.
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Affiliation(s)
- Guojun Cao
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China
| | - Jilie Kong
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China; Shanghai Suxin Co. Ltd., PR China
| | - Zhifang Xing
- Department of Blood Transfusion, Minhang Hospital, Fudan University, Shanghai 201199, PR China
| | - Yigui Tang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China
| | - Xinju Zhang
- Center of Laboratory, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China
| | - Xiao Xu
- Center of Laboratory, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China
| | - Zhihua Kang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China
| | - Xueen Fang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, PR China; Shanghai Suxin Co. Ltd., PR China.
| | - Ming Guan
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai 200040, PR China.
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5
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Detection of pistachio allergen coding sequences in food products: A comparison of two real time PCR approaches. Food Control 2017. [DOI: 10.1016/j.foodcont.2016.12.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Abstract
Advances and applications of synthetic genetic polymers (xeno-nucleic acids) are reviewed in this article. The types of synthetic genetic polymers are summarized. The basic properties of them are elaborated and their technical applications are presented. Challenges and prospects of synthetic genetic polymers are discussed.
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Affiliation(s)
- Qian Ma
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Danence Lee
- Department of Chemistry
- National University of Singapore
- Singapore 117543
| | - Yong Quan Tan
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Garrett Wong
- Department of Biochemistry
- National University of Singapore
- Singapore 117597
| | - Zhiqiang Gao
- Department of Chemistry
- National University of Singapore
- Singapore 117543
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7
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Zhao Y, Li G, Sun C, Li C, Wang X, Liu H, Zhang P, Zhao X, Wang X, Jiang Y, Yang R, Wan K, Zhou L. Locked Nucleic Acid Probe-Based Real-Time PCR Assay for the Rapid Detection of Rifampin-Resistant Mycobacterium tuberculosis. PLoS One 2015; 10:e0143444. [PMID: 26599667 PMCID: PMC4657947 DOI: 10.1371/journal.pone.0143444] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Accepted: 11/04/2015] [Indexed: 02/07/2023] Open
Abstract
Drug-resistant Mycobacterium tuberculosis can be rapidly diagnosed through nucleic acid amplification techniques by analyzing the variations in the associated gene sequences. In the present study, a locked nucleic acid (LNA) probe-based real-time PCR assay was developed to identify the mutations in the rpoB gene associated with rifampin (RFP) resistance in M. tuberculosis. Six LNA probes with the discrimination capability of one-base mismatch were designed to monitor the 23 most frequent rpoB mutations. The target mutations were identified using the probes in a “probe dropout” manner (quantification cycle = 0); thus, the proposed technique exhibited superiority in mutation detection. The LNA probe-based real-time PCR assay was developed in a two-tube format with three LNA probes and one internal amplification control probe in each tube. The assay showed excellent specificity to M. tuberculosis with or without RFP resistance by evaluating 12 strains of common non-tuberculosis mycobacteria. The limit of detection of M. tuberculosis was 10 genomic equivalents (GE)/reaction by further introducing a nested PCR method. In a blind validation of 154 clinical mycobacterium isolates, 142/142 (100%) were correctly detected through the assay. Of these isolates, 88/88 (100%) were determined as RFP susceptible and 52/54 (96.3%) were characterized as RFP resistant. Two unrecognized RFP-resistant strains were sequenced and were found to contain mutations outside the range of the 23 mutation targets. In conclusion, this study established a sensitive, accurate, and low-cost LNA probe-based assay suitable for a four-multiplexing real-time PCR instrument. The proposed method can be used to diagnose RFP-resistant tuberculosis in clinical laboratories.
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Affiliation(s)
- Yong Zhao
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
| | - Guilian Li
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Chongyun Sun
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
- Department of Clinical Laboratory, Chinese People’s Liberation Army General Hospital, Beijing 100853, P. R. China
| | - Chao Li
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Xiaochen Wang
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, P. R. China
| | - Haican Liu
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Pingping Zhang
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Xinrui Wang
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
- Institute for Plague Prevention and Control of Hebei Province, Zhangjiakou 075000, P. R. China
| | - Yi Jiang
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
| | - Ruifu Yang
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
| | - Kanglin Wan
- State Key Laboratory for Infectious Diseases Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, P. R. China
- * E-mail: (LZ); (KW)
| | - Lei Zhou
- Laboratory of Analytical Microbiology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing 100071, P. R. China
- Beijing Key Laboratory of POCT for Bioemergency and Clinic (No. BZ0329), Beijing 100071, P. R. China
- * E-mail: (LZ); (KW)
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Fátima Barroso M, Freitas M, Oliveira MBP, de-los-Santos-Álvarez N, Lobo-Castañón MJ, Delerue-Matos C. 3D-nanostructured Au electrodes for the event-specific detection of MON810 transgenic maize. Talanta 2015; 134:158-164. [DOI: 10.1016/j.talanta.2014.10.017] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Revised: 10/06/2014] [Accepted: 10/12/2014] [Indexed: 10/24/2022]
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Abstract
This viewpoint briefly reviews the impact of Locked Nucleic Acid (LNA) oligonucleotides, first described in a ChemComm paper in 1998. A number of unique applications in oligonucleotide biotechnology have been made possible by the high binding affinity and specificity of LNA, and these provide the main focus of the viewpoint.
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Affiliation(s)
- Jonathan K Watts
- Department of Chemistry and Institute for Life Sciences, University of Southampton, SO17 1BJ, UK.
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10
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Matveeva TV, Bogomaz DI, Pavlova OA, Nester EW, Lutova LA. Horizontal gene transfer from genus agrobacterium to the plant linaria in nature. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2012; 25:1542-51. [PMID: 23134518 DOI: 10.1094/mpmi-07-12-0169-r] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Genes can be transferred horizontally between prokaryotes and eukaryotes in nature. The best-studied examples occur between Agrobacterium rhizogenes and certain Nicotiana spp. To investigate possible additional cases of horizontal gene transfer in nature between Agrobacterium and plants, a real-time polymerase chain reaction-based approach was employed to screen 127 plant species, belonging to 38 families of Dicotyledones, for the presence of oncogenes homologous to the transfer DNA fragments (T-DNA) from both A. tumefaciens and A. rhizogenes. Among all of the analyzed plant species, we found that only Linaria vulgaris contained sequences homologous to the T-DNA of A. rhizogenes. All screened L. vulgaris plants from various parts of Russia contained the same homologous sequences, including rolB, rolC, ORF13, ORF14, and mis genes. The same opine gene is found in the species of Nicotiana which contain genes of A. rhizogenes. In L. vulgaris, there are two copies of T-DNA organized as a single tandem imperfect direct repeat. The plant DNA sequence of the site of integration shows similarity to a retrotransposon. This site is most likely silent, suggesting that the T-DNA is not expressed. Attempts to demonstrate expression of the T-DNA genes were negative. Our study indicates that the frequency of gene transfer and fixation in the germline from Agrobacterium to plant hosts is rare in the natural environment.
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Affiliation(s)
- Tatiana V Matveeva
- Department of Genetics, St. Petersburg State University, St. Petersburg, Russia.
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Alderborn A, Sundström J, Soeria-Atmadja D, Sandberg M, Andersson HC, Hammerling U. Genetically modified plants for non-food or non-feed purposes: straightforward screening for their appearance in food and feed. Food Chem Toxicol 2009; 48:453-64. [PMID: 20004226 DOI: 10.1016/j.fct.2009.10.049] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2009] [Revised: 10/06/2009] [Accepted: 10/30/2009] [Indexed: 01/17/2023]
Abstract
Genetically modified (GM) plants aimed at producing food/feed are part of regular agriculture in many areas of the World. Commodity plants have also found application as bioreactors, designated non-food/non-feed GM (NFGM) plants, thereby making raw material for further refinement to industrial, diagnostic or pharmaceutical preparations. Many among them may pose health challenge to consumers or livestock animals, if occurring in food/feed. NFGM plants are typically released into the environment, but are grown under special oversight and any among several containment practices, none of which provide full protection against accidental dispersal. Adventitious admixture with food or feed can occur either through distributional mismanagement or as a consequence of gene flow to plant relatives. To facilitate NFGM surveillance we propose a new mandatory tagging of essentially all such plants, prior to cultivation or marketing in the European Union. The suggested tag--Plant-Made Industrial or Pharmaceutical Products Tag (PMIP-T)--is envisaged to occur as a transgenic silent DNA identifier in host plants and designed to enable technically simple identification and characterisation of any NFGM. Implementation of PMIP-T would permit inexpensive, reliable and high-throughput screening for NFGM specifically. The paper outlines key NFGM prospects and challenges as well as the PMIP-T concept.
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Affiliation(s)
- A Alderborn
- Dept. of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden
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Development of a qualitative, multiplex real-time PCR kit for screening of genetically modified organisms (GMOs). Anal Bioanal Chem 2009; 396:2043-54. [DOI: 10.1007/s00216-009-3149-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Revised: 09/09/2009] [Accepted: 09/09/2009] [Indexed: 11/30/2022]
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Holst-Jensen A. Testing for genetically modified organisms (GMOs): Past, present and future perspectives. Biotechnol Adv 2009; 27:1071-1082. [PMID: 19477261 DOI: 10.1016/j.biotechadv.2009.05.025] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
This paper presents an overview of GMO testing methodologies and how these have evolved and may evolve in the next decade. Challenges and limitations for the application of the test methods as well as to the interpretation of results produced with the methods are highlighted and discussed, bearing in mind the various interests and competences of the involved stakeholders. To better understand the suitability and limitations of detection methodologies the evolution of transformation processes for creation of GMOs is briefly reviewed.
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Affiliation(s)
- Arne Holst-Jensen
- Department of Feed and Food Safety, National Veterinary Institute, Ullevaalsveien 68, P.O. Box 750 Sentrum, 0106 Oslo, Norway.
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