Workpackage 6: Technical Challenges Of GMO Detection

Workpackage leader

Arne Holst-Jensen
National Veterinary Institute
Oslo, Norway

The general objective of this workpackage is to overcome major technical challenges in relation to analytical GMO traceability. These challenges include resource availability (time, cost, equipment and reagents), target description and reference material availability, and assessments of analyte reliability.
The research activities planned should result in availability of more cost effective methods and technologies, allowing for rationalised GMO testing both with respect to the time it takes to obtain the analytical results needed to take decisions regarding materials tested, the costs associated with testing (money, manpower, consumables, etc.), and use and availability of limited resources (particular reference materials, expensive and special equipment).
Limited availability of descriptions of (potential) target analytes should be overcome through the use of profiling techniques in combination with comprehensive profile databases, sophisticated stepwise theoretical and experimental approaches for subtraction of potential sources of false analytical results, and extensive testing against properly selected and/or designed controls. This is foreseen to involve the use of model systems for feasibility assessments as a first step.
Target analyte reliability must be ensured, and sources of error in analytical estimates must be identified. Potential sources of biased instability of target analytes under various conditions will be assessed. This will result in appropriate guidelines for the interpretation and reporting of analytical results and associated measurement uncertainties.
Data and developed methods will be communicated to other workpackages to ensure integration of results into appropriate guidelines, recommendations, position documents, and, if feasible, decision support tools.

The final output of this workpackage should be:

  • Multiplex screening methods to determine if samples contain GMO derived materials or not, to identify the GMO from which the material is derived and to identify the species from which ingredients in the sample are derived.
  • Methods to determine if samples contain unknown GMOs, and to successively characterise and trace the unknown GMOs.
  • Multiplex quantitative methods to assess if a sample exceeds legally defined thresholds or not, including identification of samples that should be subject to refined quantitative analysis such as single-event real-time quantitative PCRs.
  • Guidelines and recommendations for design of rational GMO testing schemes on the basis of multiplex methods.
  • Assessment of the possibility to identify target analytes for commercial gene stacked events (cGS), and to develop corresponding analytical methods.
  • Assessment of the possibility to establish an alternative to PCR technologies for comprehensive GMO testing, and propose and develop corresponding methods.
  • Assessment on a range of target analytes if particular bias in stability can be observed relative to:
    • Analyte and analyte structure (e.g. DNA vs. protein, AT:GC bias in DNA, domains in protein folding structure)
    • Type of locus (coding/non-coding, mobile element, functional domain)
    • Organism (e.g. plants and their endo- and epiphytes and -parasites (e.g. particular bacteria, virus' and fungi), and naturally occurring donors of genes targeted by GMO detection methods, but also plants with different nutritional composition (protein-, starch- or fat-rich))
    • Tissue (e.g. fruits vs. leaves, seeds, etc.)
    • Product of processing (e.g. dry milled vs. wet milled, heated vs. air dried, etc.)
    • Analyte extraction method (e.g. CTAB vs. SDS or guanidine based DNA extraction methods)
    • Specific analytical detection method (e.g. PCR vs. low temperature hybridisation or isothermal amplification)
    • Contributions to guidelines regarding rational testing schemes, method validation and domains of application of analytical methods on the basis of target analyte instability bias.
  • Communicate with stakeholders to identify and incorporate their needs in the planning of the research activities, and to disseminate achievements that stakeholders may implement.