Droplet digital PCR for routine analysis of genetically modified foods (GMO) – A comparison with real-time quantitative PCR

Duplicated Copy Number Variant of the Maize 9-Lipoxygenase ZmLOX5 Improves 9,10-KODA-Mediated Resistance to Fall Armyworms

Extensive genome structure variations, such as copy number variations (CNVs) and presence/absence variations, are the basis for the remarkable genetic diversity of maize; however, the effect of CNVs on maize herbivory defense remains largely underexplored. Here, we report that the naturally occurring duplication of the maize 9-lipoxygenase gene ZmLOX5 leads to increased resistance of maize to herbivory by fall armyworms (FAWs). Previously, we showed that ZmLOX5-derived oxylipins are required for defense against chewing insect herbivores and identified several inbred lines, including Yu796, that contained duplicated CNVs of ZmLOX5, referred to as Yu796-2×LOX5. To test whether introgression of the Yu796-2×LOX5 locus into a herbivore-susceptible B73 background that contains a single ZmLOX5 gene is a feasible approach to increase resistance, we generated a series of near-isogenic lines that contained either two, one, or zero copies of the Yu796-2×LOX5 locus in the B73 background via six backcrosses (BC6). Droplet digital PCR (ddPCR) confirmed the successful introgression of the Yu796-2×LOX5 locus in B73. The resulting B73-2×LOX5 inbred line displayed increased resistance against FAW, associated with increased expression of ZmLOX5, increased wound-induced production of its primary oxylipin product, the α-ketol, 9-hydroxy-10-oxo-12(Z),15(Z)-octadecadienoic acid (9,10-KODA), and the downstream defense hormones regulated by this molecule, 12-oxo-phytodienoic acid (12-OPDA) and abscisic acid (ABA). Surprisingly, wound-induced JA-Ile production was not increased in B73-2×LOX5, resulting from the increased JA catabolism. Furthermore, B73-2×LOX5 displayed reduced water loss in response to drought stress, likely due to increased ABA and 12-OPDA content. Taken together, this study revealed that the duplicated CNV of ZmLOX5 quantitively contributes to maize antiherbivore defense and presents proof-of-concept evidence that the introgression of naturally occurring duplicated CNVs of a defensive gene into productive but susceptible crop varieties is a feasible breeding approach for enhancing plant resistance to herbivory and tolerance to abiotic stress.

Fast and Accurate Multiplex Identification and Quantification of Seven Genetically Modified Soybean Lines Using Six-Color Digital PCR

The proliferation of genetically modified organisms (GMOs) presents challenges to GMO testing laboratories and policymakers. Traditional methods, like quantitative real-time PCR (qPCR), face limitations in quantifying the increasing number of GMOs in a single sample. Digital PCR (dPCR), specifically multiplexing, offers a solution by enabling simultaneous quantification of multiple GMO targets. This study explores the use of the Naica six-color Crystal dPCR platform for quantifying five GM soybean lines within a single six-plex assay. Two four-color assays were also developed for added flexibility. These assays demonstrated high specificity, sensitivity (limit of detection or LOD < 25 copies per reaction) and precision (bias to an estimated copy number concentration <15%). Additionally, two approaches for the optimization of data analysis were implemented. By applying a limit-of-blank (LOB) correction, the limit of quantification (LOQ) and LOD could be more precisely determined. Pooling of reactions additionally lowered the LOD, with a two- to eight-fold increase in sensitivity. Real-life samples from routine testing were used to confirm the assays' applicability for quantifying GM soybean lines in complex samples. This study showcases the potential of the six-color Crystal dPCR platform to revolutionize GMO testing, facilitating comprehensive analysis of GMOs in complex samples.

Detection of SARS-CoV-2 and Other Viruses in Wastewater: Optimization and Automation of an Aluminum Hydroxide Adsorption-Precipitation Method for Virus Concentration

This study aimed to provide a low-cost technique for virus detection in wastewater by improving an aluminum hydroxide adsorption-precipitation method. The releasing efficiency of viruses trapped by the aluminum hydroxide precipitates was improved by adding ethylenediaminetetraacetic acid disodium salt (EDTA-2Na) to dissolve the precipitates at a Na2EDTA·2H2O:AlCl3 molar ratio of 1.8-3.6. The recovery rates of the improved method for seven viruses, including SARS-CoV-2-abEN pseudovirus and six animal viruses, were 5.9-22.3% in tap water and 4.9-35.1% in wastewater. Rotavirus A (9.0-4.5 × 103 copies/mL), porcine circovirus type 2 (5.8-6.4 × 105 copies/mL), and porcine parvovirus (5.6-2.7 × 104 copies/mL) were detected in China's pig farm wastewater, while rotavirus A (2.0 × 103 copies/mL) was detected in hospital wastewater. SARS-CoV-2 was detected in hospital wastewater (8.4 × 102 to 1.4 × 104 copies/mL), sewage (6.4 × 10 to 2.3 × 103 copies/mL), and river water (6.6 × 10 to 9.3 × 10 copies/mL) in Nepal. The method was automized, with a rate of recovery of 4.8 ± 1.4% at a virus concentration of 102 copies/mL. Thus, the established method could be used for wastewater-based epidemiology with sufficient sensitivity in coping with the COVID-19 epidemic and other virus epidemics.

Expression of GM content in mass fraction from digital PCR data

Nowadays the quantification of the content of genetically modified (GM) constituents in food or feed products is performed by using either quantitative real-time PCR (qPCR) or digital PCR (dPCR). The latter is increasingly used. Therefore, experimental protocols for the quantification of 52 GM events authorised in the EU have been converted into a digital format and minimum performance characteristics for dPCR methods are detailed. Because of the need to harmonise the transformation of PCR results between two different measurement scales, 50 conversion factors for Certified Reference Materials (CF_CRM) have been experimentally determined by three and sometimes four independent expert laboratories. The uncertainty of each CF_CRM has been estimated to express dPCR results in mass fraction with a consistent uncertainty contribution. In 38 out of 58 cases, the validated qPCR methods (for 52 event-specific and 6 taxon-specific measurements) could easily be transferred into dPCR methods by using the same oligo sequences, final oligo concentration or annealing temperatures for the dPCR procedure. Laboratories have nevertheless used different strategies to improve the resolution or to reduce the so-called rain in their dPCR outcome. Those modifications were needed for PCR procedures that could not be converted without changes into a digital format. Therefore, exclusion/quality criteria such as the maximum rate of partitions with intermediate fluorescence “rain”, the minimum resolution and repeatability are suggested for dPCR methods. The CF_CRM determined in this study were generally in agreement with the declared zygosity of the GM parental donor for hemizygous maize events. In a limited number of GM events the CF_CRM values were significantly different when measured with different maize-specific (ZmAdh1 or hmgA) genes.

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Digital PCR protocols for the quantification of 52 GM events

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Minimum performance criteria for digital PCR results

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Conversion factors to express GM content determined by digital PCR in mass fraction

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Harmonised measurement system for official GMO controls in the EU

Increasing the Efficiency of Canola and Soybean GMO Detection and Quantification Using Multiplex Droplet Digital PCR

Simple Summary

Digital PCR (dPCR) technology has been used for absolute quantification of genetically modified (GM) events. Duplex dPCR consisting of a target gene and a reference gene is mostly used for absolute quantification of GM events. We investigated the feasibility of absolute quantification of two, three, and four GM canola and soybean events at the same time using the QX200 Droplet Digital PCR (ddPCR) system. Adjustments of the probe concentrations and labels for some of the assays were needed for successful multiplex ddPCR. Absolute quantification of GM canola and soybean events was achieved for duplex, triplex, and tetraplex ddPCR at 0.1%, 1%, and 5% concentrations.

Abstract

The number of genetically modified (GM) events for canola, maize, and soybean has been steadily increasing. Real-time PCR is widely used for the detection and quantification of individual GM events. Digital PCR (dPCR) has also been used for absolute quantification of GM events. A duplex dPCR assay consisting of one reference gene and one GM event has been carried out in most cases. The detection of more than one GM event in a single assay will increase the efficiency of dPCR. The feasibility of detection and quantification of two, three, and four GM canola and soybean events at the same time was investigated at 0.1%, 1%, and 5% levels using the QX200 Droplet Digital PCR (ddPCR) system. The reference gene assay was carried out on the same plate but in different wells. For some of the assays, optimization of the probe concentrations and labels was needed for successful ddPCR. Results close to the expected result were achieved for duplex, triplex, and tetraplex ddPCR assays for GM canola events. Similar ddPCR results were also achieved for some GM soybean events with some exceptions. Overall, absolute quantification of up to four GM events at the same time improves the efficiency of GM detection.

Applicability of a General Analytical Approach for Detection of Genetically Modified Organisms: Collaborative Trial

BACKGROUND

With the commercialization of genetically modified organisms (GMOs) in the market, laboratories have undergone a significantly increased workload. A universal analytical approach was designed to achieve cost-efficient and high-throughput GMOs screening with high specificity and accuracy. The approach provides accurate qualification of authorized and unauthorized GMOs.

OBJECTIVE

This paper describes the assessment of this analytical approach developed to detect majority of commercialized GMOs over the world.

METHODS

Seven elements and three events were detected by qPCR in a single laboratory to detect 59 commercialized GMOs. Certificated reference materials and food/feed samples from Chinese market were also evaluated for the specificity, conformity and robustness of this approach and were challenged in the inter-laboratory study.

RESULTS

The results showed that elements and events selected can best detect GMO presence with good specificity and sensitivity. The results showed a concordance between 97.5% and 99.56% and the variance between 0.65% and 12.88%, which is in line with the minimum requirement of analytical methods of GMO testing.

CONCLUSION

The approach validated here can be used to manipulate GMO presence in food and feed and showed the capacity to manipulate GMOs trace in the trade and domestic agriculture grocery in China.

HIGHLIGHTS

A universal analytical approach used to track GMO presence was evaluated for its specificity, sensitivity and robustness.

Integrated approach for the molecular characterization of edited plants obtained via Agrobacterium tumefaciens-mediated gene transfer

Agrobacterium tumefaciens-mediated gene transfer—actually the most used method to engineer plants—may lead to integration of multiple copies of T-DNA in the plant genome, as well as to chimeric tissues composed of modified cells and wild type cells. A molecular characterization of the transformed lines is thus a good practice to select the best ones for further investigation. Nowadays, several quantitative and semi-quantitative techniques are available to estimate the copy number (CN) of the T-DNA in genetically modified plants. In this study, we compared three methods based on (1) real-time polymerase chain reaction (qPCR), (2) droplet digital PCR (ddPCR), and (3) next generation sequencing (NGS), to carry out a molecular characterization of grapevine edited lines. These lines contain a knock-out mutation, obtained via CRISPR/Cas9 technology, in genes involved in plant susceptibility to two important mildew diseases of grapevine. According to our results, qPCR and ddPCR outputs are largely in agreement in terms of accuracy, especially for low CN values, while ddPCR resulted more precise than qPCR. With regard to the NGS analysis, the CNs detected with this method were often not consistent with those calculated by qPCR and ddPCR, and NGS was not able to discriminate the integration points in three out of ten lines. Nevertheless, the NGS method can positively identify T-DNA truncations or the presence of tandem/inverted repeats, providing distinct and relevant information about the transgene integration asset. Moreover, the expression analysis of Cas9 and single guide RNA (sgRNA), and the sequencing of the target site added new information to be related to CN data. This work, by reporting a practical case-study on grapevine edited lines, explores pros and cons of the most advanced diagnostic techniques available for the precocious selection of the proper transgenic material. The results may be of interest both to scientists developing new transgenic lines, and to laboratories in charge of GMO control.

qPCR and qRT-PCR analysis: Regulatory points to consider when conducting biodistribution and vector shedding studies

Gene and cell therapy fields have experienced remarkable growth during the past decade. Demands for preclinical and clinical safety assessments of these cell and gene therapy test articles (TAs) have effectively increased the necessity for regulated biodistribution, vector shedding, gene expression, and/or pharmacokinetics bioanalysis studies. Guidance documents issued from numerous international regulatory authorities recommend the use of quantitative polymerase chain reaction (qPCR) and/or quantitative reverse transcriptase PCR (qRT-PCR) assays due to their highly sensitive and robust target-specific detection. However, only preclinical biodistribution assay sensitivity is specified in these documents. Criteria such as accuracy, precision, and repeatability are not yet defined. This guidance void has resulted in several conflicting institutional interpretations of essential parameters necessary for the development and validation of robust assays to support safety assessments of gene and cell therapy TAs. There is an urgent need for an ongoing discussion among bioanalytical scientists in this field to generate a "best practice" consensus around preclinical and clinical qPCR/qRT-PCR assay design. With regard to this need, we offer critical points to consider when developing, validating, running sample analysis, and reporting qPCR/qRT-PCR assays.

Universal LNA Probe-Mediated Multiplex Droplet Digital Polymerase Chain Reaction for Ultrasensitive and Accurate Quantitative Analysis of Genetically Modified Organisms

Multiplex and high-throughput assays are becoming the main trends in the development of new nucleic acid detection and quantification methods, such as those for genetically modified organism (GMO) analysis. Here, we report a novel universal LNA probe-mediated droplet digital polymerase chain reaction (PCR) method (ULNA-ddPCR) for multiple DNA target quantification in GMOs. In ULNA-ddPCR, only one universal LNA probe is used for multiple DNA targets instead of using one to one TaqMan probe. The specificity, sensitivity, dynamic range, and accuracy of the ULNA-ddPCR method are determined by employing GM rice analysis as an example. Simplex and triplex ULNA-ddPCR assays for three GM rice events, T2A-1, T1C-19, and G6H1, are established and evaluated. All results indicate that the developed simplex and triplex ULNA-ddPCR assays are suitable for quantitative analysis of GM rice events with high sensitivity, accuracy, and low cost. The ULNA-ddPCR method also has the potential for multiple DNA target quantification in other research fields.

Digital PCR: What Relevance to Plant Studies?

Simple Summary

Digital PCR is a third-generation technology based on the subdivision of the analytical sample into numerous partitions that are amplified individually. This review presents the major applications of digital PCR (dPCR) technology developed so far in the field of plant science. In greater detail, dPCR assays have been developed to trace genetically modified plant components, pathogenic and non-pathogenic microorganisms, and plant species. Other applications have concerned the study of the aspects of structural and functional genetics.

Abstract

Digital PCR (dPCR) is a breakthrough technology that able to provide sensitive and absolute nucleic acid quantification. It is a third-generation technology in the field of nucleic acid amplification. A unique feature of the technique is that of dividing the sample into numerous separate compartments, in each of which an independent amplification reaction takes place. Several instrumental platforms have been developed for this purpose, and different statistical approaches are available for reading the digital output data. The dPCR assays developed so far in the plant science sector were identified in the literature, and the major applications, advantages, disadvantages, and applicative perspectives of the technique are presented and discussed in this review.

Reliable and robust droplet digital PCR (ddPCR) and RT-ddPCR protocols for mouse studies

Droplet digital PCR (ddPCR) is a recent method developed for the quantification of nucleic acids sequences. It is an evolution of PCR methodology incorporating two principal differences: a PCR reaction is performed in thousands of water-oil emulsion droplets and fluorescence is measured at the end of PCR amplification. It leads to the precise and reproducible quantification of DNA and RNA sequences. Here, we present quantitative methods for DNA and RNA analysis using Bio-Rad QX100 or QX200 systems, respectively. The aim of these methods is to provide useful molecular tools for validating genetically altered animal models such as those subject to CRISPR/Cas9 genome editing, as well for expression or CNV studies. A standard procedure for simultaneous DNA and RNA extraction adapted for mouse organs is also described. These methods were initially designed for mouse studies but also work for samples from other species like rat or human. In our lab, thousands of samples and hundreds of target genes from genetically altered lines were examined using these methods. This large dataset was analyzed to evaluate technical optimizations and limitations. Finally, we propose additional recommendations to be included in dMIQE (Minimum information for publication of quantitative digital PCR experiments) guidelines when using ddPCR instruments.

Safety Assessment of Genetically Modified Feed: Is There Any Difference From Food?

Food security is one of major concerns for the growing global population. Modern agricultural biotechnologies, such as genetic modification, are a possible solution through enabling an increase of production, more efficient use of natural resources, and reduced environmental impacts. However, new crop varieties with altered genetic materials may be subjected to safety assessments to fulfil the regulatory requirements, prior to marketing. The aim of the assessment is to evaluate the impact of products from the new crop variety on human, animal, and the environmental health. Although, many studies on the risk assessment of genetically modified (GM) food have been published, little consideration to GM feedstuff has been given, despite that between 70 to 90% of all GM crops and their biomass are used as animal feed. In addition, in some GM plants such as forages that are only used for animal feeds, the assessment of the genetic modification may be of relevance only to livestock feeding. In this article, the regulatory framework of GM crops intended for animal feed is reviewed using the available information on GM food as the baseline. Although, the majority of techniques used for the safety assessment of GM food can be used in GM feed, many plant parts used for livestock feeding are inedible to humans. Therefore, the concentration of novel proteins in different plant tissues and level of exposure to GM feedstuff in the diet of target animals should be considered. A further development of specific methodologies for the assessment of GM crops intended for animal consumption is required, in order to provide a more accurate and standardized assessment to the GM feed safety.

Performance assessment of digital PCR for the quantification of GM-maize and GM-soya events

Accurate quantitative methods are needed to determine the amount of transgenic material in ingredients and comply with labelling GMO thresholds. Quantitative real-time PCR methods are usually applied for GMO quantification, but since a few years, digital PCR (dPCR) has been described as a potential alternative by quantifying DNA molecules directly without any standard curves. In this study, the performance of dPCR to quantify 9 GM-soya events and 15 GM-maize events was assessed. Following GMO validation guidelines, the trueness and precision were determined on high, medium and low levels of transgenic content. Results showed biases below ± 25% and satisfactory precision data. Limits of quantification were determined for each GM-event and were between 12 and 31 target copies. The reliability of GMO quantification by dPCR was further confirmed by analysing several proficiency test samples. Overall, dPCR showed accurate and precise GMO quantification on all the tested GM-events, from high to low transgenic amount. With its ease-of-use, dPCR was found to be an appealing alternative technology for routine GMO testing laboratories. Graphical abstract.

Development and Application of Droplet Digital PCR Tools for the Detection of Transgenes in Pastures and Pasture-Based Products

Implementation of molecular biotechnology, such as transgenic technologies, in forage species can improve agricultural profitability through achievement of higher productivity, better use of resources such as soil nutrients, water, or light, and reduced environmental impact. Development of detection and quantification techniques for genetically modified plants are necessary to comply with traceability and labeling requirements prior to regulatory approval for release. Real-time PCR has been the standard method used for detection and quantification of genetically modified events, and droplet digital PCR is a recent alternative technology that offers a higher accuracy. Evaluation of both technologies was performed using a transgenic high-energy forage grass as a case study. Two methods for detection and quantification of the transgenic cassette, containing modified fructan biosynthesis genes, and a selectable marker gene, hygromycin B phosphotransferase used for transformation, were developed. Real-time PCR was assessed using two detection techniques, SYBR Green I and fluorescent probe-based methods. A range of different agricultural commodities were tested including fresh leaves, tillers, seeds, pollen, silage and hay, simulating a broad range of processed agricultural commodities that are relevant in the commercial use of genetically modified pastures. The real-time and droplet digital PCR methods were able to detect both exogenous constructs in all agricultural products. However, a higher sensitivity and repeatability in transgene detection was observed with the droplet digital PCR technology. Taking these results more broadly, it can be concluded that the droplet digital PCR technology provides the necessary resolution for quantitative analysis and detection, allowing absolute quantification of the target sequence at the required limits of detection across all jurisdictions globally. The information presented here provides guidance and resources for pasture-based biotechnology applications that are required to comply with traceability requirements.

Identification of single target taxon-specific reference assays for the most commonly genetically transformed crops using digital droplet PCR

Knowledge of the number of DNA sequences targeted by the taxon-specific reference assays is essential for correct GM quantification and is key to the harmonisation of measurement results. In the present study droplet digital PCR (ddPCR) was used to determine the number of DNA target copies of taxon-specific assays validated for real-time PCR for the four main genetically modified (GM) crops. The transferability of experimental conditions from real-time PCR to ddPCR was also explored, as well as the effect of DNA digestion. The results of this study indicate that for each crop at least one taxon-specific assay can be identified as having a single DNA target. A short list of taxon-specific reference assays is proposed as best candidates for the relative quantification of GM events for soybean, maize, cotton and oilseed rape. The investigated assays could be in most cases transferred to ddPCR without further optimisation. The use of DNA digestion did not improve ddPCR characteristics such as rain and resolution at the conditions tested.

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.

Effect of endogenous reference genes on digital PCR assessment of genetically engineered canola events

Droplet digital PCR (ddPCR) has been used for absolute quantification of genetically engineered (GE) events. Absolute quantification of GE events by duplex ddPCR requires the use of appropriate primers and probes for target and reference gene sequences in order to accurately determine the amount of GE materials. Single copy reference genes are generally preferred for absolute quantification of GE events by ddPCR. Study has not been conducted on a comparison of reference genes for absolute quantification of GE canola events by ddPCR. The suitability of four endogenous reference sequences (HMG-I/Y, FatA(A), CruA and Ccf) for absolute quantification of GE canola events by ddPCR was investigated. The effect of DNA extraction methods and DNA quality on the assessment of reference gene copy numbers was also investigated. ddPCR results were affected by the use of single vs. two copy reference genes. The single copy, FatA(A), reference gene was found to be stable and suitable for absolute quantification of GE canola events by ddPCR. For the copy numbers measured, the HMG-I/Y reference gene was less consistent than FatA(A) reference gene. The expected ddPCR values were underestimated when CruA and Ccf (two copy endogenous Cruciferin sequences) were used because of high number of copies. It is important to make an adjustment if two copy reference genes are used for ddPCR in order to obtain accurate results. On the other hand, real-time quantitative PCR results were not affected by the use of single vs. two copy reference genes.

Critical assessment of digital PCR for the detection and quantification of genetically modified organisms

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.

Development and inter-laboratory assessment of droplet digital PCR assays for multiplex quantification of 15 genetically modified soybean lines

Quantification of genetically modified organisms (GMOs) in food and feed products is often required for their labelling or for tolerance thresholds. Standard-curve-based simplex quantitative polymerase chain reaction (qPCR) is the prevailing technology, which is often combined with screening analysis. With the rapidly growing number of GMOs on the world market, qPCR analysis becomes laborious and expensive. Innovative cost-effective approaches are therefore urgently needed. Here, we report the development and inter-laboratory assessment of multiplex assays to quantify GMO soybean using droplet digital PCR (ddPCR). The assays were developed to facilitate testing of foods and feed for compliance with current GMO regulations in the European Union (EU). Within the EU, the threshold for labelling is 0.9% for authorised GMOs per ingredient. Furthermore, the EU has set a technical zero tolerance limit of 0.1% for certain unauthorised GMOs. The novel multiplex ddPCR assays developed target 11 GMO soybean lines that are currently authorised, and four that are tolerated, pending authorisation in the EU. Potential significant improvements in cost efficiency are demonstrated. Performance was assessed for the critical parameters, including limits of detection and quantification, and trueness, repeatability, and robustness. Inter-laboratory performance was also determined on a number of proficiency programme and real-life samples.