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Wang D, Fei Y, Niu C, Lu S, Chen X, Wu Y, He P, Zhang X, Chen H, Wang H, Gao Y. Proficiency testing for event-specific quantification of genetically modified maize MON87427: Performance assessment based on the metrologically traceable reference values as assigned values. Food Chem 2024; 453:139668. [PMID: 38805943 DOI: 10.1016/j.foodchem.2024.139668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 04/08/2024] [Accepted: 05/12/2024] [Indexed: 05/30/2024]
Abstract
The Asia Pacific Metrology Program and the Accreditation Cooperation joint Proficiency Testing (PT) program for the quantification of genetically modified maize MON87427 was organized by the National Institute of Metrology, China, to enhance the measurement accuracy and metrological traceability in the region. Certified reference materials were employed as test samples; metrologically traceable certified reference values served as PT reference values (PTRVs) for evaluating the participants results. The consensus values obtained from the participants were higher than the assigned values, potentially due to the systematic effects of DNA extraction process. The participants' relatively poor overall performance by the ζ-score compared with z-score demonstrates their need to thoroughly investigate quantification bias to elevate the measurement capability of genetically modified (GM) content and deepen their understanding of uncertainty estimation. This program confirmed the importance of using metrologically traceable reference values instead of consensus values as PTRV for reliable performance assessment.
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Affiliation(s)
- Di Wang
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Yue Fei
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Chunyan Niu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Song Lu
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Xian Chen
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China
| | - Yuhua Wu
- Key Laboratory of Agricultural Genetically Modified Organisms Traceability of the Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Ping He
- Specialized Standards Accreditation Department (SSAD), China National Accreditation Service for Conformity Assessment (CNAS), Beijing 100062, China
| | - Xiujie Zhang
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs (MARA), Beijing 100176, China
| | - Hong Chen
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs (MARA), Beijing 100176, China
| | - Haoqian Wang
- Development Center for Science and Technology, Ministry of Agriculture and Rural Affairs (MARA), Beijing 100176, China
| | - Yunhua Gao
- Center for Advanced Measurement Science, National Institute of Metrology, Beijing 100029, China.
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2
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Cleveland MH, He HJ, Milavec M, Bae YK, Vallone PM, Huggett JF. Digital PCR for the characterization of reference materials. Mol Aspects Med 2024; 96:101256. [PMID: 38359699 DOI: 10.1016/j.mam.2024.101256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/17/2024]
Abstract
Well-characterized reference materials support harmonization and accuracy when conducting nucleic acid-based tests (such as qPCR); digital PCR (dPCR) can measure the absolute concentration of a specific nucleic acid sequence in a background of non-target sequences, making it ideal for the characterization of nucleic acid-based reference materials. National Metrology Institutes are increasingly using dPCR to characterize and certify their reference materials, as it offers several advantages over indirect methods, such as UV-spectroscopy. While dPCR is gaining widespread adoption, it requires optimization and has certain limitations and considerations that users should be aware of when characterizing reference materials. This review highlights the technical considerations of dPCR, as well as its role when developing and characterizing nucleic acid-based reference materials.
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Affiliation(s)
- Megan H Cleveland
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA.
| | - Hua-Jun He
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna Pot 111, 1000, Ljubljana, Slovenia
| | - Young-Kyung Bae
- Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | - Peter M Vallone
- Material Measurement Laboratory, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Jim F Huggett
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK; School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
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3
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Tan LL, Loganathan N, Agarwalla S, Yang C, Yuan W, Zeng J, Wu R, Wang W, Duraiswamy S. Current commercial dPCR platforms: technology and market review. Crit Rev Biotechnol 2022; 43:433-464. [PMID: 35291902 DOI: 10.1080/07388551.2022.2037503] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Digital polymerase chain reaction (dPCR) technology has provided a new technique for molecular diagnostics, with superior advantages, such as higher sensitivity, precision, and specificity over quantitative real-time PCRs (qPCR). Eight companies have offered commercial dPCR instruments: Fluidigm Corporation, Bio-Rad, RainDance Technologies, Life Technologies, Qiagen, JN MedSys Clarity, Optolane, and Stilla Technologies Naica. This paper discusses the working principle of each offered dPCR device and compares the associated: technical aspects, usability, costs, and current applications of each dPCR device. Lastly, up-and-coming dPCR technologies are also presented, as anticipation of how the dPCR device landscape may likely morph in the next few years.
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Affiliation(s)
- Li Ling Tan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore.,Materials Science and Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Nitin Loganathan
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Sushama Agarwalla
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
| | - Chun Yang
- Mechanical and Aerospace Engineering School, Nanyang Technological University, Singapore, Singapore
| | - Weiyong Yuan
- Faculty of Materials & Energy, Institute for Clean Energy and Advanced Materials, Southwest University, Chongqing, China.,Chongqing Key Laboratory for Advanced Materials and Technologies of Clean Energies, Chongqing, China
| | - Jasmine Zeng
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Ruige Wu
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Wei Wang
- Singapore Institute of Manufacturing Technology, Singapore, Singapore
| | - Suhanya Duraiswamy
- Department of Chemical Engineering, Indian Institute of Technology Hyderabad, Hyderabad, India
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4
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A New Reference Plasmid “pGMT27” Provides an Efficient Transgenic Detection Method for Flue-Cured Tobacco. J FOOD QUALITY 2021. [DOI: 10.1155/2021/3220013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Owing to the economic value of its foliage, tobacco (Nicotiana tabacum) is cultivated all across the world. For the detection of genetically modified (GM) tobacco, there is a lack of universal standard material which ultimately limits the detection methods because the accuracy and comparability of the results cannot be ensured. Here, we prepared a reference plasmid “pGMT27” for the detection of GM tobacco, which was 18,296 bp in length harboring two of the tobacco endogenous and seven exogenous genes. By using qualitative PCR test for the nine genes, 10 copies were used for plasmid sensitivity. In the quantitative real-time PCR (qPCR) assays with pGMT27 as a calibrator, the reaction efficiencies for P-35S and NR were 101.427% and 98.036%, respectively, whereas the limit of detection (LOD) and limit of quantification (LOQ) were 5 copies and 10 copies per reaction. For standard deviation (SD) and relative standard deviation (RSD) of the Ct values, the repeatability values were from 0.04 to 0.42 and from 0.18% to 1.29%, respectively; and the reproducibility values were from 0.04 to 0.39 and from 0.18% to 1.14%, respectively. For the unknown sample test, the average conversion factor (Cf) was 0.39, and the accuracy bias was from −15.55% to 1.93%; for precision, the SD values ranged from 0.02 to 0.62, while RSD values were from 1.34% to 10.6%. We concluded that using the pGMT27 plasmid as a calibrator provided a highly efficient transgenic detection method for flue-cured tobacco.
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Milavec M, Cleveland MH, Bae YK, Wielgosz RI, Vonsky M, Huggett JF. Metrological framework to support accurate, reliable, and reproducible nucleic acid measurements. Anal Bioanal Chem 2021; 414:791-806. [PMID: 34738220 PMCID: PMC8568362 DOI: 10.1007/s00216-021-03712-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Revised: 09/05/2021] [Accepted: 10/01/2021] [Indexed: 11/29/2022]
Abstract
Nucleic acid analysis is used in many areas of life sciences such as medicine, food safety, and environmental monitoring. Accurate, reliable measurements of nucleic acids are crucial for maximum impact, yet users are often unaware of the global metrological infrastructure that exists to support these measurements. In this work, we describe international efforts to improve nucleic acid analysis, with a focus on the Nucleic Acid Analysis Working Group (NAWG) of the Consultative Committee for Amount of Substance: Metrology in Chemistry and Biology (CCQM). The NAWG is an international group dedicated to improving the global comparability of nucleic acid measurements; its primary focus is to support the development and maintenance of measurement capabilities and the dissemination of measurement services from its members: the National Metrology Institutes (NMIs) and Designated Institutes (DIs). These NMIs and DIs provide DNA and RNA measurement services developed in response to the needs of their stakeholders. The NAWG members have conducted cutting edge work over the last 20 years, demonstrating the ability to support the reliability, comparability, and traceability of nucleic acid measurement results in a variety of sectors.
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Affiliation(s)
- Mojca Milavec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
| | - Megan H Cleveland
- National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, MD, 20899, USA
| | - Young-Kyung Bae
- Korea Research Institute of Standards and Science (KRISS), Daejeon, Republic of Korea
| | - Robert I Wielgosz
- Bureau International Des Poids Et Mesures (BIPM), Pavillon de Breteuil, 92312, Sèvres Cedex, France
| | - Maxim Vonsky
- D.I. Mendeleev Institute for Metrology, Moskovsky pr., 19, Saint-Petersburg, 190005, Russian Federation
| | - Jim F Huggett
- National Measurement Laboratory (NML), LGC, Queens Road, Teddington, TW11 0LY, Middlesex, UK.,School of Biosciences & Medicine, Faculty of Health & Medical Science, University of Surrey, Guildford, UK
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6
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Development and assessment of a duplex droplet digital PCR method for quantification of GM rice Kemingdao. Anal Bioanal Chem 2021; 413:4341-4351. [PMID: 34023912 DOI: 10.1007/s00216-021-03390-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 10/21/2022]
Abstract
The implementation of genetically modified organism (GMO) labeling policies requires accurate quantitative methods to measure the GMO content in test samples. A Kemingdao/phospholipase D (KMD/PLD) duplex ddPCR method was established with rice genomic DNA (gDNA) of homozygous KMD as template by optimizing the annealing temperature and cycle number. Duplex ddPCR showed a linear response over the dynamic range from 68 to 175,000 copies, covering four orders of magnitude. The limit of detection (LOD) and limit of quantification (LOQ) for duplex ddPCR were determined to be 9 copies and 34 copies of the rice haploid genome, respectively. A very high dilution factor would result in unacceptable bias and coefficients of variation for determining copy number of the gDNA solution, and more than 1000 copies of the DNA template in one reaction is preferred to obtain accurate quantitative results by duplex PCR. Five blinded DNA samples with copy number ratio of 10%, 5%, 1%, 0.1%, and 0.05%, and three blinded real-life matrix samples with mass fraction of 5%, 1%, and 0.5% were quantified by duplex ddPCR, simplex ddPCR, and qPCR. These three methods all gave comparable GMO content and copy numbers within the required precision, but the duplex ddPCR showed the narrowest uncertainty interval and provided the highest precision in comparison to simplex ddPCR and qPCR. The ddPCR is a more appealing and reliable technology for the accurate quantification of GMO content than simplex ddPCR and qPCR considering the uncertainty and precision of quantitative results, the time consumption of generating droplets, and the cost of ddPCR reagents.
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Abstract
Droplet digital polymerase chain reaction (ddPCR) is a method used to detect and quantify nucleic acids even when present in exceptionally low numbers. While it has proven to be valuable for clinical studies, it has failed to be widely adopted for environmental studies but despite some limitations, ddPCR may represent a better option than classical qPCR for environmental samples. Due to the complexity of the chemical and biological composition of environmental samples, protocols tailored to clinical studies are not appropriate, and results are difficult to interpret. We used environmental DNA samples originating from field studies to determine a protocol for environmental samples. Samples included field soils which had been inoculated with the soil fungus Rhizophagus irregularis (environmental positive control), field soils that had not been inoculated and the targeted fungus was not naturally present (environmental negative control), and root samples from both field categories. To control for the effect of soil inhibitors, we also included DNA samples of an organismal control extracted from pure fungal spores (organismal positive control). Finally, we included a no-template control consisting only of the PCR reaction reagents and nuclease free water instead of template DNA. Using original data, we examined which factors contribute to poor resolution in root and soil samples and propose best practices to ensure accuracy and repeatability. Furthermore, we evaluated manual and automatic threshold determination methods and we propose a novel protocol based on multiple controls that is more appropriate for environmental samples.
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Huang D, Qian J, Shi Z, Zhao J, Fang M, Xu Z. CRISPR-Cas12a-Assisted Multicolor Biosensor for Semiquantitative Point-of-Use Testing of the Nopaline Synthase Terminator in Genetically Modified Crops by Unaided Eyes. ACS Synth Biol 2020; 9:3114-3123. [PMID: 33047952 DOI: 10.1021/acssynbio.0c00365] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Existing methods of detecting foreign genes and their expression products from genetically modified organisms (GMOs) suffer from the requirement of professional equipment and skillful operators. The same problem stays for the CRISPR-Cas12a system, although it has been emerging as a powerful tool for nucleic acid detection due to its remarkable sensitivity and specificity. In this report, a portable platform for the visible detection of GMOs based on CRISPR-Cas12a was established, which relies on a color change of gold nanorods (GNRs) caused by the invertase-glucose oxidase cascade reaction and the Fenton reaction for signal readout. A nopaline synthase (NOS) terminator was employed as a model target commonly existing in foreign genes of GMOs. With the help of recombinase-aided amplification, this platform achieved comparable sensitivity of DNA targets (1 aM) with that of a fluorescence reporting assay. As low as 0.1 wt % genetically modified (GM) content in Bt-11 maize was visually observed by unaided eyes, and the semiquantitation of GM ingredients can be obtained within the range of 0.1 to 40 wt % through the absorption measurement of GNRs. Furthermore, five real samples were tested by our method, and the results indicated that the GM ingredient percentages of GMO samples were 2.24 and 24.08 wt %, respectively, while the other three samples were GMO-free. With the advantages of a simple procedure, no need for large or professional instruments, high sensitivity, and selectivity, this platform is expected to provide reasonable technical support for the safe supervision of GMOs.
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Affiliation(s)
- Di Huang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiajie Qian
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhuwei Shi
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Jiarun Zhao
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Mengjun Fang
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
| | - Zhinan Xu
- Key Laboratory of Biomass Chemical Engineering (Education Ministry), College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
- Institute of Biological Engineering, College of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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9
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Alarcon CM, Shan G, Layton DT, Bell TA, Whipkey S, Shillito RD. Application of DNA- and Protein-Based Detection Methods in Agricultural Biotechnology. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:1019-1028. [PMID: 30560659 DOI: 10.1021/acs.jafc.8b05157] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
DNA- and protein-based detection methods are widely used tools for monitoring biotechnology-derived crops and their products globally. Agricultural biotechnology companies, food/feed suppliers and supply chains, diagnostic testing companies, and regulatory authorities heavily rely on these two technologies for product development, seed production, compliance, and contractual needs. The primary use of DNA- and protein-based detection methods is either to verify the presence or absence of genetically engineered (GE) materials or to quantify the amount of GE material present in a product. This review describes key parameters of DNA- and protein-based detection methods, and thorough assessment of their applications and their advantage and limitations in agricultural biotechnology are discussed in detail. The review highlights the principle and considerations of detection method selection, which will equip users to choose suitable technology and obtain reliable test results. The review also compares the compatibility of the two technologies in GE product testing using a case study.
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Affiliation(s)
- Clara M Alarcon
- Corteva Agriscience, Agricultural Division of DowDuPont , 8305 Northwest 62nd Avenue , Johnston , Iowa 50131 , United States
| | - Guomin Shan
- Corteva Agriscience, Agricultural Division of DowDuPont , 9330 Zionsville Road , Indianapolis , Indiana 46268 , United States
| | - Dean T Layton
- EnviroLogix, Incorporated , 11 Leamington Lane , Hilton Head Island , South Carolina 29928 , United States
| | - Tandace A Bell
- Grain Inspection, Packers, and Stockyards Administration , United States Department of Agriculture (USDA) , 10383 North Ambassador Drive , Kansas City , Missouri 64153 , United States
| | - Susan Whipkey
- EnviroLogix, Incorporated , 500 Riverside Industrial Parkway , Portland Maine 04103 , United States
| | - Raymond D Shillito
- BASF , 407 Davis Drive , Tech 3, Morrisville , North Carolina 27560 , United States
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10
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Andrew CI, Paul CO, Opeolu OO. Detection of genetically modified DNA in processed maize and soybean products in Nigeria. ACTA ACUST UNITED AC 2018. [DOI: 10.5897/ajb2018.16479] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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Dobnik D, Gruden K, Žel J, Bertheau Y, Holst-Jensen A, Bohanec M. Decision Support for the Comparative Evaluation and Selection of Analytical Methods: Detection of Genetically Modified Organisms as an Example. FOOD ANAL METHOD 2018. [DOI: 10.1007/s12161-018-1194-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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12
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Demeke T, Dobnik D. Critical assessment of digital PCR for the detection and quantification of genetically modified organisms. Anal Bioanal Chem 2018; 410:4039-4050. [PMID: 29574561 PMCID: PMC6010488 DOI: 10.1007/s00216-018-1010-1] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 03/06/2018] [Accepted: 03/08/2018] [Indexed: 12/21/2022]
Abstract
The number of genetically modified organisms (GMOs) on the market is steadily increasing. Because of regulation of cultivation and trade of GMOs in several countries, there is pressure for their accurate detection and quantification. Today, DNA-based approaches are more popular for this purpose than protein-based methods, and real-time quantitative PCR (qPCR) is still the gold standard in GMO analytics. However, digital PCR (dPCR) offers several advantages over qPCR, making this new technique appealing also for GMO analysis. This critical review focuses on the use of dPCR for the purpose of GMO quantification and addresses parameters which are important for achieving accurate and reliable results, such as the quality and purity of DNA and reaction optimization. Three critical factors are explored and discussed in more depth: correct classification of partitions as positive, correctly determined partition volume, and dilution factor. This review could serve as a guide for all laboratories implementing dPCR. Most of the parameters discussed are applicable to fields other than purely GMO testing. Graphical abstract There are generally three different options for absolute quantification of genetically modified organisms (GMOs) using digital PCR: droplet- or chamber-based and droplets in chambers. All have in common the distribution of reaction mixture into several partitions, which are all subjected to PCR and scored at the end-point as positive or negative. Based on these results GMO content can be calculated.
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Affiliation(s)
- Tigst Demeke
- Canadian Grain Commission, Grain Research Laboratory, 1404-303 Main Street, Winnipeg, MB, R3C3G8, Canada
| | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia.
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13
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Sánchez-Paniagua López M, Manzanares-Palenzuela CL, López-Ruiz B. Biosensors for GMO Testing: Nearly 25 Years of Research. Crit Rev Anal Chem 2018; 48:391-405. [DOI: 10.1080/10408347.2018.1442708] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Marta Sánchez-Paniagua López
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
| | | | - Beatriz López-Ruiz
- Sección Departamental de Química Analítica, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
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14
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Santos RB, Pires AS, Abranches R. Addition of a histone deacetylase inhibitor increases recombinant protein expression in Medicago truncatula cell cultures. Sci Rep 2017; 7:16756. [PMID: 29196720 PMCID: PMC5711867 DOI: 10.1038/s41598-017-17006-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/20/2017] [Indexed: 01/02/2023] Open
Abstract
Plant cell cultures are an attractive platform for the production of recombinant proteins. A major drawback, hindering the establishment of plant cell suspensions as an industrial platform, is the low product yield obtained thus far. Histone acetylation is associated with increased transcription levels, therefore it is expected that the use of histone deacetylase inhibitors would result in an increase in mRNA and protein levels. Here, this hypothesis was tested by adding a histone deacetylase inhibitor, suberanilohydroxamic acid (SAHA), to a cell line of the model legume Medicago truncatula expressing a recombinant human protein. Histone deacetylase inhibition by SAHA and histone acetylation levels were studied, and the effect of SAHA on gene expression and recombinant protein levels was assessed by digital PCR. SAHA addition effectively inhibited histone deacetylase activity resulting in increased histone acetylation. Higher levels of transgene expression and accumulation of the associated protein were observed. This is the first report describing histone deacetylase inhibitors as inducers of recombinant protein expression in plant cell suspensions as well as the use of digital PCR in these biological systems. This study paves the way for employing epigenetic strategies to improve the final yields of recombinant proteins produced by plant cell cultures.
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Affiliation(s)
- Rita B Santos
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av República, 2780-157, Oeiras, Portugal
| | - Ana Sofia Pires
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av República, 2780-157, Oeiras, Portugal
| | - Rita Abranches
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av República, 2780-157, Oeiras, Portugal.
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15
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Grelewska-Nowotko K, Żurawska-Zajfert M, Żmijewska E, Sowa S. Optimization and Verification of Droplet Digital PCR Even-Specific Methods for the Quantification of GM Maize DAS1507 and NK603. Appl Biochem Biotechnol 2017; 185:207-220. [PMID: 29110175 DOI: 10.1007/s12010-017-2634-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/16/2017] [Indexed: 12/21/2022]
Abstract
In recent years, digital polymerase chain reaction (dPCR), a new molecular biology technique, has been gaining in popularity. Among many other applications, this technique can also be used for the detection and quantification of genetically modified organisms (GMOs) in food and feed. It might replace the currently widely used real-time PCR method (qPCR), by overcoming problems related to the PCR inhibition and the requirement of certified reference materials to be used as a calibrant. In theory, validated qPCR methods can be easily transferred to the dPCR platform. However, optimization of the PCR conditions might be necessary. In this study, we report the transfer of two validated qPCR methods for quantification of maize DAS1507 and NK603 events to the droplet dPCR (ddPCR) platform. After some optimization, both methods have been verified according to the guidance of the European Network of GMO Laboratories (ENGL) on analytical method verification (ENGL working group on "Method Verification." (2011) Verification of Analytical Methods for GMO Testing When Implementing Interlaboratory Validated Methods). Digital PCR methods performed equally or better than the qPCR methods. Optimized ddPCR methods confirm their suitability for GMO determination in food and feed.
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Affiliation(s)
- Katarzyna Grelewska-Nowotko
- GMO Controlling Laboratory, Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland.
| | - Magdalena Żurawska-Zajfert
- GMO Controlling Laboratory, Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Ewelina Żmijewska
- GMO Controlling Laboratory, Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
| | - Sławomir Sowa
- GMO Controlling Laboratory, Department of Plant Biotechnology and Cytogenetics, Plant Breeding and Acclimatization Institute - National Research Institute, Radzikow, 05-870, Blonie, Poland
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Salisu IB, Shahid AA, Yaqoob A, Ali Q, Bajwa KS, Rao AQ, Husnain T. Molecular Approaches for High Throughput Detection and Quantification of Genetically Modified Crops: A Review. FRONTIERS IN PLANT SCIENCE 2017; 8:1670. [PMID: 29085378 PMCID: PMC5650622 DOI: 10.3389/fpls.2017.01670] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 09/11/2017] [Indexed: 06/01/2023]
Abstract
As long as the genetically modified crops are gaining attention globally, their proper approval and commercialization need accurate and reliable diagnostic methods for the transgenic content. These diagnostic techniques are mainly divided into two major groups, i.e., identification of transgenic (1) DNA and (2) proteins from GMOs and their products. Conventional methods such as PCR (polymerase chain reaction) and enzyme-linked immunosorbent assay (ELISA) were routinely employed for DNA and protein based quantification respectively. Although, these Techniques (PCR and ELISA) are considered as significantly convenient and productive, but there is need for more advance technologies that allow for high throughput detection and the quantification of GM event as the production of more complex GMO is increasing day by day. Therefore, recent approaches like microarray, capillary gel electrophoresis, digital PCR and next generation sequencing are more promising due to their accuracy and precise detection of transgenic contents. The present article is a brief comparative study of all such detection techniques on the basis of their advent, feasibility, accuracy, and cost effectiveness. However, these emerging technologies have a lot to do with detection of a specific event, contamination of different events and determination of fusion as well as stacked gene protein are the critical issues to be addressed in future.
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Affiliation(s)
- Ibrahim B. Salisu
- Department of Animal Science, Faculty of Agriculture, Federal University Dutse, Jigawa, Nigeria
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ahmad A. Shahid
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Amina Yaqoob
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
- Institute of Molecular Biology and Biotechnology, University of Lahore, Lahore, Pakistan
| | - Kamran S. Bajwa
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Abdul Q. Rao
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Tayyab Husnain
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
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17
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Li Z, Li X, Wang C, Song G, Pi L, Zheng L, Zhang D, Yang L. One Novel Multiple-Target Plasmid Reference Molecule Targeting Eight Genetically Modified Canola Events for Genetically Modified Canola Detection. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2017; 65:8489-8500. [PMID: 28844131 DOI: 10.1021/acs.jafc.7b02453] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Multiple-target plasmid DNA reference materials have been generated and utilized as good substitutes of matrix-based reference materials in the analysis of genetically modified organisms (GMOs). Herein, we report the construction of one multiple-target plasmid reference molecule, pCAN, which harbors eight GM canola event-specific sequences (RF1, RF2, MS1, MS8, Topas 19/2, Oxy235, RT73, and T45) and a partial sequence of the canola endogenous reference gene PEP. The applicability of this plasmid reference material in qualitative and quantitative PCR assays of the eight GM canola events was evaluated, including the analysis of specificity, limit of detection (LOD), limit of quantification (LOQ), and performance of pCAN in the analysis of various canola samples, etc. The LODs are 15 copies for RF2, MS1, and RT73 assays using pCAN as the calibrator and 10 genome copies for the other events. The LOQ in each event-specific real-time PCR assay is 20 copies. In quantitative real-time PCR analysis, the PCR efficiencies of all event-specific and PEP assays are between 91% and 97%, and the squared regression coefficients (R2) are all higher than 0.99. The quantification bias values varied from 0.47% to 20.68% with relative standard deviation (RSD) from 1.06% to 24.61% in the quantification of simulated samples. Furthermore, 10 practical canola samples sampled from imported shipments in the port of Shanghai, China, were analyzed employing pCAN as the calibrator, and the results were comparable with those assays using commercial certified materials as the calibrator. Concluding from these results, we believe that this newly developed pCAN plasmid is one good candidate for being a plasmid DNA reference material in the detection and quantification of the eight GM canola events in routine analysis.
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Affiliation(s)
- Zhuqing Li
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Xiang Li
- Shanghai Entry-Exit Inspection and Quarantine Bureau, GMO Detection Laboratory , 1208 Minheng Road, Shanghai 200135, P. R. China
| | - Canhua Wang
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Guiwen Song
- Development Center of Science and Technology, Ministry of Agriculture of People's Republic of China , Beijing 100025, China
| | - Liqun Pi
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Lan Zheng
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
| | - Dabing Zhang
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
- Key Laboratory of Crop Marker-Assisted Breeding of Huaian Municipality, Jiangsu Collaborative Innovation Center of Regional Modern Agriculture and Environmental Protection , Huaian 223300, China
| | - Litao Yang
- National Center for the Molecular Characterization of Genetically Modified Organisms, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University , Shanghai 200240, China
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18
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Lian DS, Zeng HS. Capillary Electrophoresis Based on Nucleic Acid Detection as Used in Food Analysis. Compr Rev Food Sci Food Saf 2017; 16:1281-1295. [DOI: 10.1111/1541-4337.12297] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/14/2017] [Accepted: 07/19/2017] [Indexed: 12/21/2022]
Affiliation(s)
- Dong-Sheng Lian
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
| | - Hua-Song Zeng
- Guangzhou Women and Children's Medical Center of Guangzhou Medical University; NO. 9 at Jinsui Rd., Tianhe District Guangzhou Guangdong China
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19
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Fraiture MA, Herman P, De Loose M, Debode F, Roosens NH. How Can We Better Detect Unauthorized GMOs in Food and Feed Chains? Trends Biotechnol 2017; 35:508-517. [DOI: 10.1016/j.tibtech.2017.03.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 02/17/2017] [Accepted: 03/02/2017] [Indexed: 12/21/2022]
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20
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Abstract
A digital assay is one in which the sample is partitioned into many small containers such that each partition contains a discrete number of biological entities (0, 1, 2, 3, …). A powerful technique in the biologist's toolkit, digital assays bring a new level of precision in quantifying nucleic acids, measuring proteins and their enzymatic activity, and probing single-cell genotypes and phenotypes. Part I of this review begins with the benefits and Poisson statistics of partitioning, including sources of error. The remainder focuses on digital PCR (dPCR) for quantification of nucleic acids. We discuss five commercial instruments that partition samples into physically isolated chambers (cdPCR) or droplet emulsions (ddPCR). We compare the strengths of dPCR (absolute quantitation, precision, and ability to detect rare or mutant targets) with those of its predecessor, quantitative real-time PCR (dynamic range, larger sample volumes, and throughput). Lastly, we describe several promising applications of dPCR, including copy number variation, quantitation of circulating tumor DNA and viral load, RNA/miRNA quantitation with reverse transcription dPCR, and library preparation for next-generation sequencing. This review is intended to give a broad perspective to scientists interested in adopting digital assays into their workflows. Part II focuses on digital protein and cell assays.
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Affiliation(s)
- Amar S Basu
- 1 Department of Electrical and Computer Engineering, and Department of Biomedical Engineering, Wayne State University, Detroit, MI, USA
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21
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Jacobs BKM, Goetghebeur E, Vandesompele J, De Ganck A, Nijs N, Beckers A, Papazova N, Roosens NH, Clement L. Model-Based Classification for Digital PCR: Your Umbrella for Rain. Anal Chem 2017; 89:4461-4467. [PMID: 28350455 DOI: 10.1021/acs.analchem.6b04208] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Standard data analysis pipelines for digital PCR estimate the concentration of a target nucleic acid by digitizing the end-point fluorescence of the parallel micro-PCR reactions, using an automated hard threshold. While it is known that misclassification has a major impact on the concentration estimate and substantially reduces accuracy, the uncertainty of this classification is typically ignored. We introduce a model-based clustering method to estimate the probability that the target is present (absent) in a partition conditional on its observed fluorescence and the distributional shape in no-template control samples. This methodology acknowledges the inherent uncertainty of the classification and provides a natural measure of precision, both at individual partition level and at the level of the global concentration. We illustrate our method on genetically modified organism, inhibition, dynamic range, and mutation detection experiments. We show that our method provides concentration estimates of similar accuracy or better than the current standard, along with a more realistic measure of precision. The individual partition probabilities and diagnostic density plots further allow for some quality control. An R implementation of our method, called Umbrella, is available, providing a more objective and automated data analysis procedure for absolute dPCR quantification.
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Affiliation(s)
- Bart K M Jacobs
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University , Ghent, Belgium
| | - Els Goetghebeur
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University , Ghent, Belgium
| | - Jo Vandesompele
- Center for Medical Genetics Ghent (CMGG), Ghent University , Ghent, Belgium.,Biogazelle, Zwijnaarde, Belgium.,Bioinformatics Institute Ghent From Nucleotides to Networks (Big N2N), Ghent University , Ghent, Belgium
| | | | | | | | - Nina Papazova
- Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Nancy H Roosens
- Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Lieven Clement
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University , Ghent, Belgium.,Bioinformatics Institute Ghent From Nucleotides to Networks (Big N2N), Ghent University , Ghent, Belgium
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22
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Fu W, Wei S, Wang C, Du Z, Zhu P, Wu X, Wu G, Zhu S. A temperature-tolerant multiplex elements and genes screening system for genetically modified organisms based on dual priming oligonucleotide primers and capillary electrophoresis. Food Chem 2017; 229:396-402. [PMID: 28372191 DOI: 10.1016/j.foodchem.2017.02.088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Revised: 11/17/2016] [Accepted: 02/17/2017] [Indexed: 01/22/2023]
Abstract
High throughput screening systems are the preferred solution to meet the urgent requirement of increasing number of genetically modified organisms (GMOs). In this study, we have successfully developed a multiplex GMO element screening system with dual priming oligonucleotide (DPO) primers. This system can detect the cauliflower mosaic virus 35S (CaMV 35S), terminator of nopaline synthase gene (NOS), figwort mosaic virus 35S (FMV 35S) promoter, neomycin phosphotransferaseII (NPTII), Bt Cry 1Ab, phosphinothricin acetyltransferase genes (bar) and Streptomyces viridochromogenes (pat) simultaneously, which covers more than 90% of all authorized GMO species worldwide. This system exhibits a high tolerance to annealing temperatures, high specificity and a limit of detection equal to conventional PCR. A total of 214 samples from markets, national entry-exit agencies, the Institute for Reference Materials and Measurement (IRMM) and the American Oil Chemists' Society (AOCS) were also tested for applicability. This screening system is therefore suitable for GMO screening.
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Affiliation(s)
- Wei Fu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Shuang Wei
- Shantou Entry-exit Inspection and Quarantine Bureau, Shantou 515041, China
| | - Chenguang Wang
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China; College of Plant Protection, China Agricultural University, Beijing 100193, China
| | - Zhixin Du
- Guangxi Entry-exit Inspection and Quarantine Bureau, Nanning 530028, China
| | - Pengyu Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xiyang Wu
- Department of Food Science and Engineering, College of Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gang Wu
- Key Laboratory of Oil Crop Biology of the Ministry of Agriculture, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Shuifang Zhu
- Institute of Plant Quarantine, Chinese Academy of Inspection and Quarantine, Beijing 100176, China.
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23
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24
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Bevanda L, Žilić M, Ećimović B, Matković V. Public opinion toward GMOs and biotechnology in Bosnia and Herzegovina. IFMBE PROCEEDINGS 2017. [DOI: 10.1007/978-981-10-4166-2_70] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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25
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Mass Releases of Genetically Modified Insects in Area-Wide Pest Control Programs and Their Impact on Organic Farmers. SUSTAINABILITY 2017. [DOI: 10.3390/su9010059] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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26
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Garafutdinov RR, Galimova AA, Sakhabutdinova AR. Polymerase chain reaction with nearby primers. Anal Biochem 2016; 518:126-133. [PMID: 27908595 DOI: 10.1016/j.ab.2016.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 11/25/2016] [Accepted: 11/26/2016] [Indexed: 02/05/2023]
Abstract
DNA analysis of biological specimens containing degraded nucleic acids such as mortal remains, archaeological artefacts, forensic samples etc. has gained more attention in recent years. DNA extracted from these samples is often inapplicable for conventional polymerase chain reaction (PCR), so for its amplification the nearby primers are commonly used. Here we report the data that clarify the features of PCR with nearby and abutting primers. We have shown that the proximity of primers leads to significant reduction of the reaction time and ensures the successful performance of DNA amplification even in the presence of PCR inhibitors. The PCR with abutting primers is usually characterized by the absence of nonspecific amplification products that causes extreme sensitivity with limit of detection on single copy level. The feasibility of PCR with abutting primers was demonstrated on species identification of 100 years old rotten wood.
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Affiliation(s)
- Ravil R Garafutdinov
- Institute of Biochemistry and Genetics Ufa Science Centre Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
| | - Aizilya A Galimova
- Institute of Biochemistry and Genetics Ufa Science Centre Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
| | - Assol R Sakhabutdinova
- Institute of Biochemistry and Genetics Ufa Science Centre Russian Academy of Sciences, 450054, Prosp. Oktyabrya, 71, Ufa, Bashkortostan, Russia.
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27
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Köppel R, Peterseil V, Dagand E, Schütz E, Kolberg N, Milavec M, Moor D. Collaborative trial to assess the performance of digital PCR in the field of GMO analysis using an artificial sample material. Eur Food Res Technol 2016. [DOI: 10.1007/s00217-016-2824-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Gao H, Yu X, Deng T, Sun M, Xiao X, Huang X, Chen Y, Li R. Event-specific detection of transgenic potato AV43-6-G7 using real-time and digital PCR methods. BMC Biotechnol 2016; 16:74. [PMID: 27784303 PMCID: PMC5081928 DOI: 10.1186/s12896-016-0303-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 10/13/2016] [Indexed: 01/09/2023] Open
Abstract
Background The isolation of unknown DNA sequences flanked by known sequences is an important task in the event-specific detection of GMOs. None of event-specific detection method was developed based on the junction sequence of an exogenous integrant in the transgenic potato AV43-6-G7. Results The flanking sequence between the exogenous fragment and recombinant chromosome of this potato was successfully acquired through exogenous gene 5′-RACE. The event-specific primers and Taqman probe were designed to amplify fragments spanning the exogenous DNA and potato genomic DNA. The specific real-time PCR and digital PCR detection methods for AV43-6-G7 potato were established based on primers designed according to the flanking sequences. The detection limit of the qualitative PCR assay was 0.01 % for AV43-6-G7 potato in 100 ng of potato genomic DNA, corresponding to approximately 11.6 copies of the potato haploid genome. The ddPCR assays for Potato AV43-6-G7 achieved a limit of quantification of approximately 58 target copies, with RSD ≤ 25 %. The aLOQ of this system was approximately 1.2 copies. Conclusions These results indicated that these event-specific methods would be useful for the identification of potato AV43-6-G7. Electronic supplementary material The online version of this article (doi:10.1186/s12896-016-0303-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hongwei Gao
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China.
| | - Xiaofan Yu
- Qingdao University Medical College, Qingdao, China
| | - Tingting Deng
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Min Sun
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China
| | - Xizhi Xiao
- Shandong Entry-Exit Inspection and Quarantine Bureau of People's Republic of China, Qingdao, China
| | - Xin Huang
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Ying Chen
- Chinese Academy of Inspection and Quarantine Institute, Beijing, China
| | - Ronggui Li
- Qingdao University Medical College, Qingdao, China
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29
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Dobnik D, Štebih D, Blejec A, Morisset D, Žel J. Multiplex quantification of four DNA targets in one reaction with Bio-Rad droplet digital PCR system for GMO detection. Sci Rep 2016; 6:35451. [PMID: 27739510 PMCID: PMC5064307 DOI: 10.1038/srep35451] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 09/30/2016] [Indexed: 11/25/2022] Open
Abstract
The advantages of the digital PCR technology are already well documented until now. One way to achieve better cost efficiency of the technique is to use it in a multiplexing strategy. Droplet digital PCR platforms, which include two fluorescence filters, support at least duplex reactions and with some developments and optimization higher multiplexing is possible. The present study not only shows a development of multiplex assays in droplet digital PCR, but also presents a first thorough evaluation of several parameters in such multiplex digital PCR. Two 4-plex assays were developed for quantification of 8 different DNA targets (7 genetically modified maize events and maize endogene). Per assay, two of the targets were labelled with one fluorophore and two with another. As current analysis software does not support analysis of more than duplex, a new R- and Shiny-based web application analysis tool (http://bit.ly/ddPCRmulti) was developed that automates the analysis of 4-plex results. In conclusion, the two developed multiplex assays are suitable for quantification of GMO maize events and the same approach can be used in any other field with a need for accurate and reliable quantification of multiple DNA targets.
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Affiliation(s)
- David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Dejan Štebih
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Andrej Blejec
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Dany Morisset
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Jana Žel
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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30
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Development and validation of the modular Feed-code method for qualitative and quantitative determination of feed botanical composition. Anal Bioanal Chem 2016; 408:8299-8316. [DOI: 10.1007/s00216-016-9943-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 09/05/2016] [Accepted: 09/13/2016] [Indexed: 10/20/2022]
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31
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Optimization of digital droplet polymerase chain reaction for quantification of genetically modified organisms. BIOMOLECULAR DETECTION AND QUANTIFICATION 2016; 7:9-20. [PMID: 27077048 PMCID: PMC4827695 DOI: 10.1016/j.bdq.2015.12.003] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/14/2015] [Accepted: 12/14/2015] [Indexed: 11/24/2022]
Abstract
Experience matrix condenses ddPCR performance parameters in graphical presentation. Assay separation value based on absolute fluorescence signal distance and variation. Separation value and experience matrix simplify choice of best assay parameters. Influence of oligonucleotide concentration and annealing/extension temperature.
Digital PCR in droplets (ddPCR) is an emerging method for more and more applications in DNA (and RNA) analysis. Special requirements when establishing ddPCR for analysis of genetically modified organisms (GMO) in a laboratory include the choice between validated official qPCR methods and the optimization of these assays for a ddPCR format. Differentiation between droplets with positive reaction and negative droplets, that is setting of an appropriate threshold, can be crucial for a correct measurement. This holds true in particular when independent transgene and plant-specific reference gene copy numbers have to be combined to determine the content of GM material in a sample. Droplets which show fluorescent units ranging between those of explicit positive and negative droplets are called ‘rain’. Signals of such droplets can hinder analysis and the correct setting of a threshold. In this manuscript, a computer-based algorithm has been carefully designed to evaluate assay performance and facilitate objective criteria for assay optimization. Optimized assays in return minimize the impact of rain on ddPCR analysis. We developed an Excel based ‘experience matrix’ that reflects the assay parameters of GMO ddPCR tests performed in our laboratory. Parameters considered include singleplex/duplex ddPCR, assay volume, thermal cycler, probe manufacturer, oligonucleotide concentration, annealing/elongation temperature, and a droplet separation evaluation. We additionally propose an objective droplet separation value which is based on both absolute fluorescence signal distance of positive and negative droplet populations and the variation within these droplet populations. The proposed performance classification in the experience matrix can be used for a rating of different assays for the same GMO target, thus enabling employment of the best suited assay parameters. Main optimization parameters include annealing/extension temperature and oligonucleotide concentrations. The droplet separation value allows for easy and reproducible assay performance evaluation. The combination of separation value with the experience matrix simplifies the choice of adequate assay parameters for a given GMO event.
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Key Words
- ABI, LifeTechnologies (formerly AppliedBiosystems)
- Bio, DNA Technology/Biosearch Technologies
- Cat. No., catalogue number
- DNA, deoxyribonucleic acid
- Droplet digital PCR (ddPCR)
- EC, European Commission
- ERM, Certified European Reference Material
- EU, European Union
- EURL-GMFF, European Reference Laboratory for GM Food and Feed
- Experience matrix
- Food/feed analysis
- GM, genetically modified
- GMO, genetically modified organism
- Genetically modified organism (GMO)
- HEX,H, hexachlorfluorescein
- L, liter
- Lec, lectin gene of soy
- MIQE, minimal information for publication of quantitative digital PCR experiments
- MRPL, minimum required performance limit
- MS, Microsoft
- MWG, Eurofins-MWG
- MeanSignal, mean fluorescence signal value
- PCR, polymerase chain reaction
- Quantification
- SD, standard deviation (of fluorescence signals)
- TAMRA,T, tetramethylrhodamin
- TIB, TIB Molbiol
- Tech, technician
- VBA, visual basic for applications
- VIC,V, fluorescent dye (LifeTechnologies)
- cp/cp, (gene) copy per (gene) copy
- dPCR, digital PCR
- ddPCR, droplet digital PCR
- fluorescein, FAM,F
- gDNA, genomic DNA
- qPCR, (quantitative) real-time PCR
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Wan J, Song L, Wu Y, Brzoska P, Keys D, Chen C, Valliyodan B, Shannon JG, Nguyen HT. Application of Digital PCR in the Analysis of Transgenic Soybean Plants. ACTA ACUST UNITED AC 2016. [DOI: 10.4236/abb.2016.710039] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Félix-Urquídez D, Pérez-Urquiza M, Valdez Torres JB, León-Félix J, García-Estrada R, Acatzi-Silva A. Development, Optimization, and Evaluation of a Duplex Droplet Digital PCR Assay To Quantify the T-nos/hmg Copy Number Ratio in Genetically Modified Maize. Anal Chem 2015; 88:812-9. [PMID: 26605751 PMCID: PMC4718530 DOI: 10.1021/acs.analchem.5b03238] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Certified
reference materials (CRMs) are required to guarantee
the reliability of analytical measurements. The CRMs available in
the field of genetically modified organisms (GMOs) are characterized
using real-time polymerase chain reaction (qPCR). This technology
has limited application, because of its dependence on a calibrant.
The objective of this study was to obtain a method with higher metrological
quality, to characterize the CRMs for their contents of T-nos/hmg copy number ratio in maize. A duplex droplet
digital PCR (ddPCR) assay was developed and optimized by a central
composite design. The developed method achieved an absolute limit
of detection (LOD) of 11 cP T-nos, a relative LOD
of 0.034%, a limit of quantification (LOQ) of 23 cP (relative LOQ
of 0.08%), and a dynamic range of 0.08%–100% T-nos/hmg ratio. The specificity and applicability of
the assay were established for the analysis of low T-nos concentrations (0.9%) in several corn varieties. The convenience
of DNA digestion to reduce measurement bias in the case of multiple-copy
binding was confirmed through an enzymatic restriction assay. Given
its overall performance, this method can be used to characterize CRM
candidates for their contents of T-nos/hmg ratio.
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Affiliation(s)
- Dalmira Félix-Urquídez
- Research Center for Food and Development, Culiacán, Sinaloa México.,National Metrology Center, El Marqués, Querétaro México
| | | | | | | | | | - Abraham Acatzi-Silva
- Reference National Center for Detection of Genetically Modified Organisms, Tecámac, Estado de México México
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Fraiture MA, Herman P, Taverniers I, De Loose M, Deforce D, Roosens NH. Current and new approaches in GMO detection: challenges and solutions. BIOMED RESEARCH INTERNATIONAL 2015; 2015:392872. [PMID: 26550567 PMCID: PMC4624882 DOI: 10.1155/2015/392872] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 09/07/2015] [Indexed: 11/17/2022]
Abstract
In many countries, genetically modified organisms (GMO) legislations have been established in order to guarantee the traceability of food/feed products on the market and to protect the consumer freedom of choice. Therefore, several GMO detection strategies, mainly based on DNA, have been developed to implement these legislations. Due to its numerous advantages, the quantitative PCR (qPCR) is the method of choice for the enforcement laboratories in GMO routine analysis. However, given the increasing number and diversity of GMO developed and put on the market around the world, some technical hurdles could be encountered with the qPCR technology, mainly owing to its inherent properties. To address these challenges, alternative GMO detection methods have been developed, allowing faster detections of single GM target (e.g., loop-mediated isothermal amplification), simultaneous detections of multiple GM targets (e.g., PCR capillary gel electrophoresis, microarray, and Luminex), more accurate quantification of GM targets (e.g., digital PCR), or characterization of partially known (e.g., DNA walking and Next Generation Sequencing (NGS)) or unknown (e.g., NGS) GMO. The benefits and drawbacks of these methods are discussed in this review.
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Affiliation(s)
- Marie-Alice Fraiture
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Philippe Herman
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
| | - Isabel Taverniers
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
| | - Marc De Loose
- Technology and Food Sciences Unit, Institute for Agricultural and Fisheries Research (ILVO), Burg. Van Gansberghelaan 115, Bus 1, 9820 Merelbeke, Belgium
- Department of Plant Biotechnology and Bioinformatics, Faculty of Sciences, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Dieter Deforce
- Laboratory of Pharmaceutical Biotechnology, Faculty of Pharmaceutical Sciences, Ghent University, Ottergemsesteenweg 460, 9000 Ghent, Belgium
| | - Nancy H. Roosens
- Platform of Biotechnology and Molecular Biology (PBB) and Biosafety and Biotechnology Unit (SBB), Scientific Institute of Public Health (WIV-ISP), J. Wytsmanstraat 14, 1050 Brussels, Belgium
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Dobnik D, Spilsberg B, Bogožalec Košir A, Holst-Jensen A, Žel J. Multiplex Quantification of 12 European Union Authorized Genetically Modified Maize Lines with Droplet Digital Polymerase Chain Reaction. Anal Chem 2015; 87:8218-26. [DOI: 10.1021/acs.analchem.5b01208] [Citation(s) in RCA: 77] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- David Dobnik
- Department
of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
| | - Bjørn Spilsberg
- Section
of Virology, Norwegian Veterinary Institute, P.O. Box 750, Sentrum, 0106 Oslo, Norway
| | - Alexandra Bogožalec Košir
- Department
of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
- Josef Stefan International Postgraduate School, Jamova 39, 1000 Ljubljana, Slovenia
| | - Arne Holst-Jensen
- Section
of Virology, Norwegian Veterinary Institute, P.O. Box 750, Sentrum, 0106 Oslo, Norway
| | - Jana Žel
- Department
of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000 Ljubljana, Slovenia
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Datukishvili N, Kutateladze T, Gabriadze I, Bitskinashvili K, Vishnepolsky B. New multiplex PCR methods for rapid screening of genetically modified organisms in foods. Front Microbiol 2015; 6:757. [PMID: 26257724 PMCID: PMC4513241 DOI: 10.3389/fmicb.2015.00757] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/10/2015] [Indexed: 12/15/2022] Open
Abstract
We present novel multiplex PCR methods for rapid and reliable screening of genetically modified organisms (GMOs). New designed PCR primers targeting four frequently used GMO specific sequences permitted identification of new DNA markers, in particular 141 bp fragment of cauliflower mosaic virus (CaMV) 35S promoter, 224 bp fragment of Agrobacterium tumefaciens nopaline synthase (NOS) terminator, 256 bp fragment of 5-enolppyruvylshikimate-phosphate synthase (epsps) gene and 258 bp fragment of Cry1Ab delta-endotoxin (cry1Ab) gene for GMO screening. The certified reference materials containing Roundup Ready soybean (RRS) and maize MON 810 were applied for the development and optimization of uniplex and multiplex PCR systems. Evaluation of amplification products by agarose gel electrophoresis using negative and positive controls confirmed high specificity and sensitivity at 0.1% GMO for both RRS and MON 810. The fourplex PCR was developed and optimized that allows simultaneous detection of three common transgenic elements, such as: CaMV 35S promoter, NOS terminator, epsps gene together with soybean-specific lectin gene. The triplex PCR developed enables simultaneous identification of transgenic elements, such as: 35S promoter and cry1Ab gene together with maize zein gene. The analysis of different processed foods demonstrated that multiplex PCR methods developed in this study are useful for accurate and fast screening of GM food products.
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Affiliation(s)
- Nelly Datukishvili
- Ivane Beritashvili Center of Experimental Biomedicine Tbilisi, Georgia ; Faculty of Natural Sciences and Engineering, Ilia State University Tbilisi, Georgia
| | | | - Inga Gabriadze
- Ivane Beritashvili Center of Experimental Biomedicine Tbilisi, Georgia
| | - Kakha Bitskinashvili
- Faculty of Natural Sciences and Engineering, Ilia State University Tbilisi, Georgia
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