The International Life Sciences Institute Health and Environmental Sciences Institute
Protein Allergenicity Technical Committee hosted an international workshop November
16-17, 2009, in Paris, France, with over 60 participants from academia, government,
and industry to review and discuss the potential utility of "-omics" technologies
for assessing the variability in plant gene, protein, and metabolite expression. The
goal of the workshop was to illustrate how a plant's constituent makeup and phenotypic
processes can be surveyed analytically. Presentations on the "-omics" techniques (i.e.,
genomics, proteomics, and metabolomics) highlighted the workshop, and summaries of
these presentations are published separately in this supplemental issue. This paper
summarizes key messages, as well as the consensus points reached, in a roundtable
discussion on eight specific questions posed during the final session of the workshop.
The workshop established some common, though not unique, challenges for all "-omics"
techniques, and include (a) standardization of separation/extraction and analytical
techniques; (b) difficulty in associating environmental impacts (e.g., planting, soil
texture, location, climate, stress) with potential alterations in plants at genomic,
proteomic, and metabolomic levels; (c) many independent analytical measurements, but
few replicates/subjects--poorly defined accuracy and precision; and (d) bias--a lack
of hypothesis-driven science. Information on natural plant variation is critical in
establishing the utility of new technologies due to the variability in specific analytes
that may result from genetic differences (crop genotype), different crop management
practices (conventional high input, low input, organic), interaction between genotype
and environment, and the use of different breeding methods. For example, variations
of several classes of proteins were reported among different soybean, rice, or wheat
varieties or varieties grown at different locations. Data on the variability of allergenic
proteins are important in defining the risk of potential allergenicity. Once established
as a standardized assay, survey approaches such as the "-omics" techniques can be
considered in a hypothesis-driven analysis of plants, such as determining unintended
effects in genetically modified (GM) crops. However, the analysis should include both
the GM and control varieties that have the same breeding history and exposure to the
same environmental conditions. Importantly, the biological relevance and safety significance
of changes in "-omic" data are still unknown. Furthermore, the current compositional
assessment for evaluating the substantial equivalence of GM crops is robust, comprehensive,
and a good tool for food safety assessments. The overall consensus of the workshop
participants was that many "-omics" techniques are extremely useful in the discovery
and research phases of biotechnology, and are valuable for hypothesis generation.
However, there are many methodological shortcomings identified with "-omics" approaches,
a paucity of reference materials, and a lack of focused strategy for their use that
currently make them not conducive for the safety assessment of GM crops.
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