New Multiplexing Tools for Reliable GMO Detection

Among the available methods for GMO detection, enforcement and routine laboratories use in practice PCR, based on the detection of transgenic DNA. The cost required for GMO analysis is constantly increasing due to the progress of GMO commercialization, with inclusion of higher diversity of species, traits and introduced genetic elements. Thus, analytical technologies must evolve towards high throughput GMO diagnostics. This chapter describes different strategies recently developed tosimultaneously detect/identify many GMOs. The combination of two or more PCR assays into one single tube is known as multiplexing. Multiplex PCRs combining a limited number of targets are available for GMO analysis. In some cases, several of these reactions can be performed in parallel and the resulting products mixed and detected together by capillary electrophoresis or array hybridization. Non PCR-based approaches (e.g. NAIMA) have also been explored for higher multiplexing potential. Simultaneous detection of very high numbers of targetsis possible bya SNPlex method based on single nucleotide polymorphisms and the Padlock ligation microarray system, relying on a first ligation that only occurs after hybridization to the target, followed by PCR and detection by array. Multiplex assays are most often qualitative, andif necessary, they can be coupled to specific simplex assays for quantification.Nevertheless, we discuss some strategies developed to achieve quantitative results with a multiplex approach.

[1]  Hans-Ulrich Waiblinger,et al.  A practical approach to screen for authorised and unauthorised genetically modified plants , 2010, Analytical and bioanalytical chemistry.

[2]  Arne Holst-Jensen,et al.  Testing for genetically modified organisms (GMOs): Past, present and future perspectives. , 2009, Biotechnology advances.

[3]  A. Holck,et al.  Quantitative, multiplex ligation-dependent probe amplification for the determination of eight genetically modified maize events , 2009 .

[4]  Hermann Broll,et al.  Real-Time PCR-Based Ready-to-Use Multi-Target Analytical System for GMO Detection , 2009 .

[5]  M. Pla,et al.  Multiplex polymerase chain reaction-capillary gel electrophoresis: a promising tool for GMO screening--assay for simultaneous detection of five genetically modified cotton events and species. , 2009, Journal of AOAC International.

[6]  J. Mano,et al.  Simultaneous detection of recombinant DNA segments introduced into genetically modified crops with multiplex ligase chain reaction coupled with multiplex polymerase chain reaction. , 2009, Journal of agricultural and food chemistry.

[7]  Myriam Sneyers,et al.  A PCR-microarray method for the screening of genetically modified organisms , 2009 .

[8]  J. Mano,et al.  Real-time PCR array as a universal platform for the detection of genetically modified crops and its application in identifying unapproved genetically modified crops in Japan. , 2009, Journal of agricultural and food chemistry.

[9]  Marleen M. Voorhuijzen,et al.  Optimised padlock probe ligation and microarray detection of multiple (non-authorised) GMOs in a single reaction , 2008, BMC Genomics.

[10]  V. Laval,et al.  A high-throughput multiplex method adapted for GMO detection. , 2008, Journal of agricultural and food chemistry.

[11]  T. Demeke,et al.  Multiplex qualitative PCR assay for identification of genetically modified canola events and real-time event-specific PCR assay for quantification of the GT73 canola event , 2008 .

[12]  A. Cifuentes,et al.  Simultaneous confirmatory analysis of different transgenic maize (zea mays) lines using multiplex polymerase chain reaction-restriction analysis and capillary gel electrophoresis with laser induced fluorescence detection. , 2008, Journal of agricultural and food chemistry.

[13]  K. Gruden,et al.  NAIMA: target amplification strategy allowing quantitative on-chip detection of GMOs , 2008, Nucleic acids research.

[14]  A. Holst-Jensen.  GMO testing—trade, labeling or safety first? , 2008, Nature Biotechnology.

[15]  K. Engel,et al.  Development of a modular system for detection of genetically modified organisms in food based on ligation-dependent probe amplification , 2008 .

[16]  Litao Yang,et al.  Development of one novel multiple-target plasmid for duplex quantitative PCR analysis of roundup ready soybean. , 2008, Journal of agricultural and food chemistry.

[17]  Wei Dong,et al.  GMDD: a database of GMO detection methods , 2008, BMC Bioinformatics.

[18]  A. Holck,et al.  Detection of five novel GMO maize events by qualitative, multiplex PCR and fluorescence capillary gel electrophoresis , 2008 .

[19]  Yves Bertheau,et al.  Validation of the performance of a GMO multiplex screening assay based on microarray detection , 2008 .

[20]  K. Gruden,et al.  Detection of nonauthorized genetically modified organisms using differential quantitative polymerase chain reaction: application to 35S in maize. , 2008, Analytical biochemistry.

[21]  K. Gruden,et al.  Alternative DNA amplification methods to PCR and their application in GMO detection: a review , 2008 .

[22]  Arne Holst-Jensen,et al.  A statistical approach for evaluation of PCR results to improve the practical limit of quantification (LOQ) of GMO analyses (SIMQUANT) , 2008 .

[23]  M. Querci,et al.  Innovative Application of Fluorescent Microsphere Based Assay for Multiple GMO Detection , 2008 .

[24]  Arne Holst-Jensen,et al.  Microarray-based method for detection of unknown genetic modifications , 2007, BMC biotechnology.

[25]  Heng-Wei Cheng.  Animal welfare: should we change housing to better accommodate the animal or change the animal to accommodate the housing? , 2007 .

[26]  Lijuan Xie,et al.  Quantification of chlorophyll content and classification of nontransgenic and transgenic tomato leaves using visible/near-infrared diffuse reflectance spectroscopy. , 2007, Journal of agricultural and food chemistry.

[27]  José Luis La Paz,et al.  Comparison of real-time PCR detection chemistries and cycling modes using Mon810 event-specific assays as model. , 2007, Journal of agricultural and food chemistry.

[28]  Yves Bertheau,et al.  EU regulations on the traceability and detection of GMOs: difficulties in interpretation, implementation and compliance , 2007 .

[29]  N. Harris,et al.  Investigation of the use of rolling circle amplification for the detection of GM food , 2007 .

[30]  Monica Ermolli,et al.  First application of a microsphere-based immunoassay to the detection of genetically modified organisms (GMOs): quantification of Cry1Ab protein in genetically modified maize. , 2007, Journal of agricultural and food chemistry.

[31]  G. Berben,et al.  Physical degradation of genomic DNA of soybean flours does not impair relative quantification of its transgenic content , 2007 .

[32]  José Luis La Paz,et al.  A new PCR‐CGE (size and color) method for simultaneous detection of genetically modified maize events , 2006, Electrophoresis.

[33]  H. Akiyama,et al.  Detection method for genetically modified papaya using duplex PCR. , 2006, Shokuhin eiseigaku zasshi. Journal of the Food Hygienic Society of Japan.

[34]  E. Timmermans,et al.  Real-time nucleic acid sequence-based amplification assay to quantify changes in mitochondrial DNA concentrations in cell cultures and blood cells from HIV-infected patients receiving antiviral therapy. , 2006, Clinical chemistry.

[35]  Patrick Philipp,et al.  A Microarray-based Detection System for Genetically Modified (GM) Food Ingredients , 2006, Plant Molecular Biology.

[36]  K. Engel,et al.  Ligation-dependent probe amplification for the simultaneous event-specific detection and relative quantification of DNA from two genetically modified organisms , 2006 .

[37]  K. G. Berdal,et al.  Novel reference gene, PKABA1, used in a duplex real-time polymerase chain reaction for detection and quantitation of wheat- and barley-derived DNA. , 2006, Journal of agricultural and food chemistry.

[38]  Akihiro Hino,et al.  Development of a multiplex polymerase chain reaction method for simultaneous detection of eight events of genetically modified maize. , 2005, Journal of agricultural and food chemistry.

[39]  C. Peano,et al.  Multiplex polymerase chain reaction and ligation detection reaction/universal array technology for the traceability of genetically modified organisms in foods. , 2005, Analytical biochemistry.

[40]  K. Rudi,et al.  Differentiation of important and closely related cereal plant species (Poaceae) in food by hybridization to an oligonucleotide array. , 2005, Journal of agricultural and food chemistry.

[41]  Kaoru Wakabayashi,et al.  Quantitative detection system for maize sample containing combined-trait genetically modified maize. , 2005, Analytical chemistry.

[42]  Heng Zhao,et al.  Rapid and reliable detection and identification of GM events using multiplex PCR coupled with oligonucleotide microarray. , 2005, Journal of agricultural and food chemistry.

[43]  Marc De Loose,et al.  Event-specific plasmid standards and real-time PCR methods for transgenic Bt11, Bt176, and GA21 maize and transgenic GT73 canola. , 2005, Journal of agricultural and food chemistry.

[44]  A. Kobilinsky,et al.  Minimum cost acceptance sampling plans for grain control, with application to GMO detection , 2005 .

[45]  R. Marchelli,et al.  A microarray platform for parallel detection of five transgenic events in foods: a combined polymerase chain reaction-ligation detection reaction-universal array method. , 2005, Journal of agricultural and food chemistry.

[46]  Nelson Marmiroli,et al.  Qualitative and quantitative evaluation of the genomic DNA extracted from GMO and non-GMO foodstuffs with four different extraction methods. , 2004, Journal of agricultural and food chemistry.

[47]  A. Cifuentes,et al.  Sensitive and simultaneous analysis of five transgenic maizes using multiplex polymerase chain reaction, capillary gel electrophoresis, and laser‐induced fluorescence , 2004, Electrophoresis.

[48]  C. Consolandi,et al.  Detection and quantitation of genetically modified maize (Bt-176 transgenic maize) by applying ligation detection reaction and universal array technology. , 2004, Journal of agricultural and food chemistry.

[49]  Marc Loose,et al.  Cloned plasmid DNA fragments as calibrators for controlling GMOs: different real-time duplex quantitative PCR methods , 2004, Analytical and bioanalytical chemistry.

[50]  S. Prat,et al.  Development of melting temperature-based SYBR Green I polymerase chain reaction methods for multiplex genetically modified organism detection. , 2003, Analytical biochemistry.

[51]  U. Landegren,et al.  Parallel gene analysis with allele-specific padlock probes and tag microarrays. , 2003, Nucleic acids research.

[52]  Knut Rudi,et al.  A novel multiplex quantitative DNA array based PCR (MQDA-PCR) for quantification of transgenic maize in food and feed. , 2003, Nucleic acids research.

[53]  Ronald W. Davis,et al.  Multiplexed genotyping with sequence-tagged molecular inversion probes , 2003, Nature Biotechnology.

[54]  C. Consolandi,et al.  Ligation detection reaction and universal array for detection and identification of genetically modified organisms (GMOs) , 2002 .

[55]  H. Permingeat,et al.  Detection and quantification of transgenes in grains by multiplex and real-time PCR. , 2002, Journal of agricultural and food chemistry.

[56]  R. Meyer,et al.  Real-time multiplex PCR: An accurate method for the detection and quantification of 35S-CaMV promoter in genetically modified maize-containing food , 2002 .

[57]  M. Gautier,et al.  Comparison of simplex and duplex real-time PCR for the quantification of GMO in maize and soybean , 2002 .

[58]  Farid E Ahmed,et al.  Detection of genetically modified organisms in foods. , 2002, Trends in biotechnology.

[59]  B. Deiman,et al.  Characteristics and applications of nucleic acid sequence-based amplification (NASBA) , 2002, Molecular biotechnology.

[60]  C. N. Gundry,et al.  Real-time multiplex PCR assays. , 2001, Methods.

[61]  Charles R. Hurburgh,et al.  Detection of Roundup Ready™ Soybeans by Near-Infrared Spectroscopy , 2001 .

[62]  M Toyoda,et al.  A multiplex PCR method of detecting recombinant DNAs from five lines of genetically modified maize. , 2001, Shokuhin eiseigaku zasshi. Journal of the Food Hygienic Society of Japan.

[63]  U Landegren,et al.  PCR-generated padlock probes detect single nucleotide variation in genomic DNA. , 2000, Nucleic acids research.

[64]  M Vaïtilingom,et al.  Real-time quantitative PCR detection of genetically modified Maximizer maize and Roundup Ready soybean in some representative foods. , 1999, Journal of agricultural and food chemistry.

[65]  N. Gerry,et al.  Universal DNA microarray method for multiplex detection of low abundance point mutations. , 1999, Journal of molecular biology.

[66]  U. Landegren,et al.  Signal amplification of padlock probes by rolling circle replication. , 1998, Nucleic acids research.

[67]  K. Livak,et al.  Real time quantitative PCR. , 1996, Genome research.

[68]  F. Kramer,et al.  Novel, ligation-dependent PCR assay for detection of hepatitis C in serum , 1996, Journal of clinical microbiology.

[69]  F. Barany,et al.  Detection of steroid 21-hydroxylase alleles using gene-specific PCR and a multiplexed ligation detection reaction. , 1995, Genomics.

[70]  U Landegren,et al.  Padlock probes: circularizing oligonucleotides for localized DNA detection. , 1994, Science.

[71]  B. Pulendran,et al.  Ligation-anchored PCR: a simple amplification technique with single-sided specificity. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[72]  J. Compton,et al.  Nucleic acid sequence-based amplification , 1991, Nature.

[73]  R A Gibbs,et al.  Deletion screening of the Duchenne muscular dystrophy locus via multiplex DNA amplification. , 1988, Nucleic acids research.

[74]  U Landegren,et al.  A ligase-mediated gene detection technique. , 1988, Science.

[75]  Van Den Eede Guy,et al.  Microarray Method for the Screening of EU Approved GMOs by Identification of their Genetic Elements , 2007 .

[76]  R. Onori,et al.  Real-time PCR multiplex method for the quantification of Roundup Ready soybean in raw material and processed food , 2006 .

[77]  A. Cifuentes,et al.  Recent advances in the application of capillary electromigration methods for food analysis , 2006, Electrophoresis.

[78]  N. Siafakas,et al.  Multiplex polymerase chain reaction: A practical approach , 2002, Journal of clinical laboratory analysis.

[79]  F. Barany.  Genetic disease detection and DNA amplification using cloned thermostable ligase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.