Within the European Union (EU) and several other jurisdictions, import, use or release of genetically modified (GM) organism (GMO) derived material is illegal without prior authorisation. Field trials are used to assess the performance of GMOs prior to authorisation, but may result in low level contamination of neighbouring fields. Birds or rodents may spread grains or seeds and incomplete sanitation or other human error may lead to unintended spread of unauthorised GM material. Finally, intended distribution into the environment or food/feed chain can not be complete ruled out. Neither validated detection methods nor reference materials are usually available in these cases.

Presently the majority of GMOs commercialised globally are herbicide resistant and/or insect tolerant. The trait genes inserted are usually well known and belong to a few groups: pat / bar , epsps and various cry -genes. Genetic elements associated with the genes to facilitate and regulate their expression are also with few exceptions well known and belong to a few groups, e.g. the Cauliflower Mosaic Virus (CaMV) 35S promoter and terminator (P35S and T35S) or the Agrobacterium tumefaciens nos terminator (3'-nos).

For GMO detection it is necessary to use methods specific to particular genetic markers such as regulatory elements or trait genes (screening methods), fusion motifs between regulatory elements and trait genes (construct specific methods) or fusion motifs between inserted DNA and the recipient DNA (event specific markers). The number of GMOs that may be detected with the methods depend on the targeted genetic marker, and the analyst may need to balance broadspectered screening against ability to specifically identify the GMOs that may be detected. Detection of unauthorised GMOs may often be achievable with screening methods. However, with these methods only, it may be quite difficult to determine that the detected GMO material is coming from an unauthorised GMO. On the other hand, the absence of specific detection methods and reference materials for most unauthorised GMOs leaves few options for identification.

The availability of novel trait genes and regulatory elements is increasing rapidly, and some GMOs do not contain any of the commonly used elements (e.g. DP-305423 soybean). Commercial or other interests may prevent relevant information from being disseminated to stakeholders such as competent authorities and laboratories performing GMO detection.

GMOs that can not be detected with the commonly used screening methods because the introduced DNA sequences or genetic elements are unusual (novel) may be classified as unknown GMOs. These are particularly difficult to detect and identify. Presence of non-declared ingredients (e.g. “botanical impurity”) may further complicate the analytical work.

Any presence of unauthorised or unknown GMO or derived material in the food/feed supply chain in the EU is by definition illegal, and may pose a risk to society and economy, the environment and/or human and animal health. Ability to detect, identify and characterise unauthorised or unknown GMOs is therefore necessary to be able to define, delimit, prevent and remove problems.

Traceability facilitates the identification of the origin of material, and global information networks, databases, etc. may provide information about developments of new GMOs, novel genetic elements that are potentially exploitable and authorisations outside the stakeholder's own jurisdiction. This type of information can be used by stakeholders to improve their ability to detect, identify and characterise unauthorised or unknown GMOs, as well as to prioritise developments and applications of particular analytical methods.

Development of analytical methods and strategies for detection, identification and characterisation of unauthorised and unknown GMOs is a major priority exemplified with the EU-funded Co-Extra project.