In the EU, genetically modified organisms (GMOs) are subject to the authorization require-ments of Directive 2001/18/EC or Regulation (EC) No. 1829/2003. Application for authoriza-tion of a genetically modified plant requires description of identification and detection meth-ods. Those methods are used by control laboratories of the Member States to detect and identify genetically modified plants and to quantify their occurrence in food and feed. In its ruling of July 25, 2018 (C-528/16), the European Court of Justice determined that plants pro-duced with directed mutagenesis (genome editing) are covered by the regulations under Di-rective 2001/18/EC on the release and placing on the market of GMOs. For control laborato-ries this poses specific challenges for detection, identification and quantification of genome-edited plants.
Genome editing techniques allow targeted modifications at predefined sites in the genome of organisms. They belong to the "novel genomic techniques (NGT)", defined as “techniques capable to change the genetic material of an organism and that have emerged or have been developed since 2001”. The possible detection of genome-edited GMOs depends on the type of modification achieved and whether (transgenic) foreign DNA or genome-editing compo-nents may have been integrated into the plant genome. For detection, small mutations (point mutations) pose the greatest challenge. In this report, based on the currently used methods for the detection of classical GMOs, the existing possibilities and challenges for genome-edited plants are discussed.
Detection of even very small sequence differences, such as point mutations, is possible with the current technical equipment of a control laboratory. Optimization steps (primer/probe de-sign, thermal profiles) may be required to increase sensitivity. To transfer detection methods into routine operation, the methods have to be validated. A characteristic-unique modification or the combined detection of multiple modifications in a tested genome may allow the identi-fication of genome-edited plants. Quantification of these analytical results by currently avail-able methods is technically possible using certain approaches.
Accurate information on the modification made is the most important prerequisite for the de-velopment of methods for detection, identification and quantification of genome-edited GMOs. Such information could be gathered from publicly available sources. It is recom-mended combining information from different public documents, including scientific publica-tions, patents and regulatory documents from third countries. This information could be gath-ered in databases maintained by international organizations. Existing databases, such as the Biosafety Clearing House under the Cartagena Protocol on Biosafety or EUginius, could serve as a model for an international database for sharing information on globally marketed NGT products. It is recommended to establish such a database, maintained at the interna-tional level, to provide easy access for control laboratories to all relevant information.
In order to be able to establish the developed methods in the laboratory, and for control pur-poses, reference material is necessary (biological material and derived material; includes the genome-edited plant and/or the parental line/starting material). Upon application for food, feed, or cultivation purposes, the applicant shall provide reference material. For GMO without application, the availability of reference material can be ensured by a central body (e.g., the Joint Research Centre, JRC) in cooperation with the developers. If biological material is not available, plasmids with the corresponding DNA sequences can also be synthesized based on sequence information, if available, and serve as reference material.
Research is needed primarily in method development, characterization of genome editing applications (non-intended modifications, specificities, recognition sequences, etc.), and in the development of databases for pan-genomes to be used in control laboratories in the long term. It is recommended that this work be funded through European research funding pro-grammes and through mandates to JRC and EFSA.