Genetically Modified Organisms Screening Research Articles

Electroactive nanocarbon materials as signaling tags for electrochemical PCR

Electrochemical polymerase chain reaction (PCR) represents a valid alternative to the optical-based PCR due to reduced costs of signaling labels, use of simpler instrumentation, and possibility of miniaturization and portability of the systems, which can facilitate decentralized detection. The high intrinsic electroactivity and strong linear relationship between the material concentration and its redox signal suggest a possible use of oxidized nanocarbon materials as electroactive tags for PCR. Herein, we compared three different nanographene oxide materials namely nGO-1, nGO-2 and nGO-3 as signaling tags for the detection of genetically modified organisms (GMO) by electrochemical PCR. The three materials differ in size, chemical composition as well as type and amount of oxygen functionalities verified by extensive characterization with X-ray photoelectron spectroscopy (XPS), attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR), transmission electron microscopy (TEM) and electrochemical methods. A sense primer sequence belonging to the Cauliflower Mosaic Virus 35S promoter (a common genetic marker for GMO screening) was used to conjugate to the nanocarbon materials by carbodiimide chemistry before PCR amplification with a biotinylated antisense strand. Finally, the amplified electroactive PCR product was detected, where the reduction signal derived from the electrochemically reducible oxygenated functionalities on the nanocarbon material surface was directly correlated to the presence of GMO. Overall, we were able to correlate the different material characteristics with their performance as electroactive labels and identify the nanocarbon material that exhibits the highest potential to be used as innovative electroactive label for PCR in the amplification and detection of the selected target sequence.

Detection of soybean transgenic event GTS-40-3-2 using electric field-induced release and measurement (EFIRM).

Polymerase chain reaction (PCR) technology has become a standard technique for the detection of genetically modified organisms (GMOs). However, this method requires a PCR amplification process which is both expensive and time-consuming. Herein, we propose electric field-induced release and measurement (EFIRM) technology as an alternative method for GMO screening. The specificity and sensitivity of the EFIRM assay were proven to be comparable to those of the real-time PCR method for detecting genetically modified soybeans. After all the parameters had been evaluated, the actual evaluation of soybean samples from soybean cargoes was performed. An actual EFIRM screening was performed on 157 soybean cargo samples, which had 102 transgenic soybean samples containing the GTS-40-3-2 gene, through a blind trial at the Dalian port of China. Our results showed that 101 transgenic soybean samples were correctly detected, with only one false-negative case, and 55 non-transgenic soybean samples were detected as negative; this demonstrates that the EFIRM assay is an effective, accurate, simple, and economical novel method for detecting transgenic products, which may have a positive impact on the development of rapid on-site GMO monitoring platforms.

Two FAST multiplex real-time PCR reactions to assess the presence of genetically modified organisms in food

Methods to detect the presence of genetically modified organisms (GMOs) are evolving constantly to comply with legislation and include new transgenic traits developed by biotechnology companies. Since traditional screening methods target only a limited number of markers, not all GM-events can be detected easily. To cover a broader range, a new GMO screening method was developed, based on two real-time PCR reactions, targeting i) six major GM-markers and ii) six GM-events that do not contain these markers. This method used the FAST PCR technology and allowed a further reduction in time-to-result. Using a wide array of reference materials and proficiency test samples, the method showed a broad screening capacity and the absolute limit of detection was consistently below 20 copies, thereby demonstrating the method is fit-for-purpose.

Inter-laboratory validation of visual loop-mediated isothermal amplification assays for GM contents screening

Loop-mediated isothermal amplification (LAMP) has been widely used in many fields of molecular diagnostics, including detection of genetically modified organisms (GMOs). Herein, we report a collaborative ring trial validation of three established visual LAMP assays targeting three common GM elements, namely CaMV35S promoter, FMV35S promoter and NOS terminator, respectively. The high specificity of each assay was confirmed in different GM events analyses, and the sensitivity of each was determined to be 10, 10, and 50 haploid genome equivalents (HGEs) for CaMV35S promoter, FMV35S promoter, and NOS terminator, respectively. The probability of detection was also determined based on specificity and sensitivity data from 10 participating laboratories that returned correct results for the practical sample tests. These results demonstrate that the three visual LAMP assays are sensitive and time-saving, with high application potential for on-spot testing and routine screening of GMOs.

NGS-based amplicon sequencing approach; towards a new era in GMO screening and detection

The development and commercialization of Genetically Modified Organisms (GMOs) and its related products have been increasing in the last two decades. This challenges the currently applied time-consuming and expensive qPCR screening procedure from a practical perspective, due to the necessity to develop and validate additional targets at a regular pace and the increasing number of targets included in a single screening. In this study we developed a next generation sequencing (NGS)-based GMO screening approach covering 96 GMO targets and compared it to the two-step qPCR GMO screening approach; the two approaches were evaluated with five feed samples known to contain GMOs. The amplicons obtained from the feed samples were analyzed using 150-bp Paired-End sequencing, Illumina HiSeq 4000 platform. A dedicated data analysis pipeline was developed, which allows automated identification of GMOs and associated genetic elements and constructs. The result of the NGS-based screening were compared with the qPCR approach, indicating that 92% of the targets were commonly identified between the qPCR and NGS-based screening. The remaining 8% of the targets had discrepancies in detection between the two methods. This was mainly observed for targets that were detected in qPCR with high Cq values (above 36), which could not be detected in NGS-based screening. Additionally, due to the more extensive screening in the NGS-based strategy, in total 43 additional GMOs and related targets were identified compared to the standard qPCR screening. From the commonly identified targets in both approaches, 8 targets could not be associated with the detected GMOs. These targets had late Cq values (above 36) and could indicate traces of unknown GMOs in the samples. The current study shows the applicability of NGS as a novel, broad and reliable screening strategy for GMOs and its potential to improve current screening methods.

Improved detection and quantification of cauliflower mosaic virus in food crops: assessing false positives in GMO screening based on the 35S promoter

The 35S promoter (P35S) of the cauliflower mosaic virus (CaMV) is frequently used in screening tests as a first step in detecting and quantifying genetically modified organisms (GMOs) in food and feed samples. However, PCR reactions targeting P35S do not distinguish between GMOs and naturally occurring CaMV introduced by infection or contamination, resulting in false positives. Initial attempts at specific CaMV detection were based on a limited number of CAMV sequences. To account for the broad variability in the viral genome, we designed a new real-time PCR assay based on the genomic sequences of 96 CaMV isolates collected worldwide. This system amplified a 112 bp fragment of ORFV in the double-stranded genome, with complete sequence homology to the primer and probe targets of the tested genomes. Tests on a CaMV isolate collection and GMOs revealed improved specificity compared to previously published methods as well as high sensitivity, with limits of detection (LOD) and quantification (LOQ) of three copies of CaMV.

Ultrasensitive Single Fluorescence-Labeled Probe-Mediated Single Universal Primer-Multiplex-Droplet Digital Polymerase Chain Reaction for High-Throughput Genetically Modified Organism Screening.

As genetically modified (GM) technology develops and genetically modified organisms (GMOs) become more available, GMOs face increasing regulations and pressure to adhere to strict labeling guidelines. A singleplex detection method cannot perform the high-throughput analysis necessary for optimal GMO detection. Combining the advantages of multiplex detection and droplet digital polymerase chain reaction (ddPCR), a single universal primer-multiplex-ddPCR (SUP-M-ddPCR) strategy was proposed for accurate broad-spectrum screening and quantification. The SUP increases efficiency of the primers in PCR and plays an important role in establishing a high-throughput, multiplex detection method. Emerging ddPCR technology has been used for accurate quantification of nucleic acid molecules without a standard curve. Using maize as a reference point, four heterologous sequences ( 35S, NOS, NPTII, and PAT) were selected to evaluate the feasibility and applicability of this strategy. Surprisingly, these four genes cover more than 93% of the transgenic maize lines and serve as preliminary screening sequences. All screening probes were labeled with FAM fluorescence, which allows the signals from the samples with GMO content and those without to be easily differentiated. This fiveplex screening method is a new development in GMO screening. Utilizing an optimal amplification assay, the specificity, limit of detection (LOD), and limit of quantitation (LOQ) were validated. The LOD and LOQ of this GMO screening method were 0.1% and 0.01%, respectively, with a relative standard deviation (RSD) < 25%. This method could serve as an important tool for the detection of GM maize from different processed, commercially available products. Further, this screening method could be applied to other fields that require reliable and sensitive detection of DNA targets.

Development of a multiplex fluorescence quantitative PCR for detection of genetically modified organisms

The commercially available genetically modified plants authorized worldwide and therefore the target sequences for molecular detection of genetically modified organisms (GMOs) are ever-increasing. The European Union has implemented a set of very strict procedures for approval to grow, import and/or utilize GMOs as food or food ingredients. As a result, GMO laboratories and food production industry currently are forced to apply different methods to test raw material and complex processed food products. Three exogenous genes (the 35 s promoter of the cauliflower mosaic virus (35 s), nos terminator from Agrobacterium tumefaciens (nos), and the neomycin phosphotransferase II (nptII) gene) are commonly used in GMO detection. In this paper, a multiplex quantitative real-time PCR (qPCR) system was developed which allows simultaneously detection of the three exogenous genes in one reaction tube. The determined limits for the multiplex qPCR assays were 4 copies/reaction in maize samples. The specificity of the assays was demonstrated to be 100% according to the detection results of 23 genetically modified (GM) crops and 97 complex processed food products. The validation data show the individual PCR efficiency was accredited with negligible impacts between three detection channels in 7500 fluorescence quantitative PCR machine. These results indicate that this high-throughput multiplex qPCR method which combined with a reference gene is feasible for screening of GMOs, even for the processed food.

Semiautomated TaqMan PCR screening of GMO labelled samples for (unauthorised) GMOs

In most countries, systems are in place to analyse food products for the potential presence of genetically modified organisms (GMOs), to enforce labelling requirements and to screen for the potential presence of unauthorised GMOs. With the growing number of GMOs on the world market, a larger diversity of methods is required for informative analyses. In this paper, the specificity of an extended screening set consisting of 32 screening methods to identify different crop species (endogenous genes) and GMO elements was verified against 59 different GMO reference materials. In addition, a cost- and time-efficient strategy for DNA isolation, screening and identification is presented. A module for semiautomated analysis of the screening results and planning of subsequent event-specific tests for identification has been developed. The Excel-based module contains information on the experimentally verified specificity of the element methods and of the EU authorisation status of the GMO events. If a detected GMO element cannot be explained by any of the events as identified in the same sample, this may indicate the presence of an unknown unauthorised GMO that may not yet have been assessed for its safety for humans, animals or the environment.

A temperature-tolerant multiplex elements and genes screening system for genetically modified organisms based on dual priming oligonucleotide primers and capillary electrophoresis.

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.

Development of a qualitative real-time PCR method to detect 19 targets for identification of genetically modified organisms.

As the amount of commercially available genetically modified organisms (GMOs) grows recent years, the diversity of target sequences for molecular detection techniques are eagerly needed. Considered as the gold standard for GMO analysis, the real-time PCR technology was optimized to produce a high-throughput GMO screening method. With this method we can detect 19 transgenic targets. The specificity of the assays was demonstrated to be 100 % by the specific amplification of DNA derived from reference material from 20 genetically modified crops and 4 non modified crops. Furthermore, most assays showed a very sensitive detection, reaching the limit of ten copies. The 19 assays are the most frequently used genetic elements present in GM crops and theoretically enable the screening of the known GMO described in Chinese markets. Easy to use, fast and cost efficient, this method approach fits the purpose of GMO testing laboratories.

Aflatoxin and Genetically Modified Organisms Analysis in Turkish Corn

Genetically Modified Organisms (GMOs) are plants, animals or microorganisms that have been altered using genetic insertion or deletion via technology (also called genetic engineering or GE). Corn is one of the main inputs of both food and feed production. Also it is a major commodity of which many transgenic varieties are commercially available. In this study, the aflatoxin and GMO analyses of corn were made in two different years (2013 and 2014). Corn samples were collected between August and October in 2013 and 2014 around Turkey from non-neighboring fields representing each 10 thousand tons production and blending. After the analyses, which were performed by using LC-MS/MS technique, 38 of 538 corn samples (7.06%) were found to contain aflatoxin in 2013. 17 of these were collected from the first harvest, 21 were from the second harvest period. Aflatoxin limits were exceeded in samples from only 2 regions in 2014. This study also reports results of GMO screening tests with 0.05% detection limit in two marketing years. 35D promoter, NOS terminator and FMV promoter are sought with the tests. None of the samples shows positive results, that is, samples do not contain GMO.

New multiplex PCR methods for rapid screening of genetically modified organisms in foods

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.

New qualitative trait-specific SYBR®Green qPCR methods to expand the panel of GMO screening methods used in the CoSYPS

Since 2011, a new Commission Regulation (EU/619/2011) defines that laboratories testing for genetically modified organisms (GMO) need to be able to detect also genetically modified (GM) events pending for authorisation. This, in addition to the fact that the number of GM events authorised in the European Union (EU) that need to be identified multiplies rapidly and that the detection of unauthorised GMO becomes more important, led to the development of a time and cost-effective screening approach. Moreover, the GM elements that are utilised in the transgenic inserts also become increasingly diverse. Consequently, the screening approaches have to be updated to enable full coverage and better discrimination of all these events. To respond to this need, two new qualitative SYBR®Green real-time PCR (qPCR) methods were developed and in-house validated: one method is element-specific and targets the Cry3Bb trait, and the other one is a construct-specific method detecting the gat-tpinII junction. Method acceptance parameters such as the sensitivity, specificity and repeatability were assessed as well as the robustness of the methods. Additionally, the reproducibility was evaluated by transferring the methods to a second laboratory. Both methods allow a specific, sensitive and repeatable detection of the respective targets in food and feed samples and can be easily applied in a routine laboratory. Moreover, they can be used together with previously validated SYBR®Green qPCR methods to expand the panel of screening methods. This allows an extended coverage of the GM events authorised in the EU and adds discriminative power to the screening phase.

Multiplex electrochemical DNA platform for femtomolar-level quantification of genetically modified soybean

Current EU regulations on the mandatory labeling of genetically modified organisms (GMOs) with a minimum content of 0.9% would benefit from the availability of reliable and rapid methods to detect and quantify DNA sequences specific for GMOs. Different genosensors have been developed to this aim, mainly intended for GMO screening. A remaining challenge, however, is the development of genosensing platforms for GMO quantification, which should be expressed as the number of event-specific DNA sequences per taxon-specific sequences. Here we report a simple and sensitive multiplexed electrochemical approach for the quantification of Roundup-Ready Soybean (RRS). Two DNA sequences, taxon (lectin) and event-specific (RR), are targeted via hybridization onto magnetic beads. Both sequences are simultaneously detected by performing the immobilization, hybridization and labeling steps in a single tube and parallel electrochemical readout. Hybridization is performed in a sandwich format using signaling probes labeled with fluorescein isothiocyanate (FITC) or digoxigenin (Dig), followed by dual enzymatic labeling using Fab fragments of anti-Dig and anti-FITC conjugated to peroxidase or alkaline phosphatase, respectively. Electrochemical measurement of the enzyme activity is finally performed on screen-printed carbon electrodes. The assay gave a linear range of 2–250pM for both targets, with LOD values of 650fM (160amol) and 190fM (50amol) for the event-specific and the taxon-specific targets, respectively. Results indicate that the method could be applied for GMO quantification below the European labeling threshold level (0.9%), offering a general approach for the rapid quantification of specific GMO events in foods.

JRC GMO-Matrix: a web application to support Genetically Modified Organisms detection strategies.

BackgroundThe polymerase chain reaction (PCR) is the current state of the art technique for DNA-based detection of Genetically Modified Organisms (GMOs). A typical control strategy starts by analyzing a sample for the presence of target sequences (GM-elements) known to be present in many GMOs. Positive findings from this “screening” are then confirmed with GM (event) specific test methods. A reliable knowledge of which GMOs are detected by combinations of GM-detection methods is thus crucial to minimize the verification efforts.DescriptionIn this article, we describe a novel platform that links the information of two unique databases built and maintained by the European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF) at the Joint Research Centre (JRC) of the European Commission, one containing the sequence information of known GM-events and the other validated PCR-based detection and identification methods. The new platform compiles in silico determinations of the detection of a wide range of GMOs by the available detection methods using existing scripts that simulate PCR amplification and, when present, probe binding. The correctness of the information has been verified by comparing the in silico conclusions to experimental results for a subset of forty-nine GM events and six methods.ConclusionsThe JRC GMO-Matrix is unique for its reliance on DNA sequence data and its flexibility in integrating novel GMOs and new detection methods. Users can mine the database using a set of web interfaces that thus provide a valuable support to GMO control laboratories in planning and evaluating their GMO screening strategies. The platform is accessible at http://gmo-crl.jrc.ec.europa.eu/jrcgmomatrix/.

DNA extraction techniques compared for accurate detection of genetically modified organisms (GMOs) in maize food and feed products.

In this paper, DNA extraction methods have been evaluated to detect the presence of genetically modified organisms (GMOs) in maize food and feed products commercialised in Turkey. All the extraction methods tested performed well for the majority of maize foods and feed products analysed. However, the highest DNA content was achieved by the Wizard, Genespin or the CTAB method, all of which produced optimal DNA yield and purity for different maize food and feed products. The samples were then screened for the presence of GM elements, along with certified reference materials. Of the food and feed samples, 8% tested positive for the presence of one GM element (NOS terminator), of which half (4% of the total) also contained a second element (the Cauliflower Mosaic Virus 35S promoter). The results obtained herein clearly demonstrate the presence of GM maize in the Turkish market, and that the Foodproof GMO Screening Kit provides reliable screening of maize food and feed products.

GMOseek: a user friendly tool for optimized GMO testing.

BackgroundWith the increasing pace of new Genetically Modified Organisms (GMOs) authorized or in pipeline for commercialization worldwide, the task of the laboratories in charge to test the compliance of food, feed or seed samples with their relevant regulations became difficult and costly. Many of them have already adopted the so called "matrix approach" to rationalize the resources and efforts used to increase their efficiency within a limited budget. Most of the time, the "matrix approach" is implemented using limited information and some proprietary (if any) computational tool to efficiently use the available data.ResultsThe developed GMOseek software is designed to support decision making in all the phases of routine GMO laboratory testing, including the interpretation of wet-lab results. The tool makes use of a tabulated matrix of GM events and their genetic elements, of the laboratory analysis history and the available information about the sample at hand. The tool uses an optimization approach to suggest the most suited screening assays for the given sample. The practical GMOseek user interface allows the user to customize the search for a cost-efficient combination of screening assays to be employed on a given sample. It further guides the user to select appropriate analyses to determine the presence of individual GM events in the analyzed sample, and it helps taking a final decision regarding the GMO composition in the sample. GMOseek can also be used to evaluate new, previously unused GMO screening targets and to estimate the profitability of developing new GMO screening methods.ConclusionThe presented freely available software tool offers the GMO testing laboratories the possibility to select combinations of assays (e.g. quantitative real-time PCR tests) needed for their task, by allowing the expert to express his/her preferences in terms of multiplexing and cost. The utility of GMOseek is exemplified by analyzing selected food, feed and seed samples from a national reference laboratory for GMO testing and by comparing its performance to existing tools which use the matrix approach. GMOseek proves superior when tested on real samples in terms of GMO coverage and cost efficiency of its screening strategies, including its capacity of simple interpretation of the testing results.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2105-15-258) contains supplementary material, which is available to authorized users.

Inter-laboratory Testing of GMO Detection by Combinatory SYBR®Green PCR Screening (CoSYPS)

Combinatory SYBR®Green real-time PCR Screening (CoSYPS) is an efficient, sensitive approach for detecting complex targets such as genetically modified organisms (GMOs) in food and feed products. GMO analysis for legal purposes has become increasingly complex and costly due to the diversity in recombinant targets present in the different GMOs. For this reason, screening for the presence of GMOs is in general the first step in the detection of GM material in a product. CoSYPS allows detecting the large majority of globally commercial GMOs using SYBR®Green real-time PCR methods for six GM targets (P35S, Tnos, CryIAb, CP4-EPSPS, PAT and BAR) combined with species-specific PCR methods (e.g., maize, soy, rapeseed). Here, the results of an inter-laboratory trial on seven samples with different GMO mixtures at different levels are presented. In total, 13 laboratories participated in the trial and the currently most frequently used PCR analysis platforms are represented. The inter-laboratory study clearly demonstrates that PCR methods used in CoSYPS form a very robust GMO screening system. Sensitivity, specificity, positive and negative predictive values are for all PCR methods higher than 95 % for all samples. Together, these results show that the SYBR®Green real-time PCR methods used in CoSYPS are effectively applicable to different PCR platforms and amendable to configuration into a sensitive high-throughput GMO screening and decision support tool.

Loop-Mediated Isothermal Amplification: Rapid Visual and Real-Time Methods for Detection of Genetically Modified Crops

A rapid, reliable, and sensitive loop-mediated isothermal amplification (LAMP) system was developed for screening of genetically modified organisms (GMOs). The optimized LAMP assays using designed primers target commonly employed promoters, i.e., Cauliflower Mosaic Virus 35S (P-35S) and Figwort Mosaic Virus promoter (P-FMV), and marker genes, i.e., aminoglycoside 3'-adenyltransferase (aadA), neomycin phosphotransferase II (nptII), and β-glucuronidase (uidA). The specificity and performance of the end-point and real-time LAMP assays were confirmed using eight genetically modified (GM) cotton events on four detection systems, employing two chemistries. LAMP assays on the isothermal real-time system were found to be most sensitive, detecting up to four target copies, within 35 min. The LAMP assays herein presented using alternate detection systems can be effectively utilized for rapid and cost-effective screening of the GM status of a sample, irrespective of the crop species or GM trait. These assays coupled with a fast and simple DNA extraction method may further facilitate on-site GMO screening.