The present document has been produced and adopted by the bodies identified above as author(s). This task has been carried out exclusively by the author(s) in the context of a contract between the European Food Safety Authority and the author(s), awarded following a tender procedure. The present document is published complying with the transparency principle to which the Authority is subject. It may not be considered as an output adopted by the Authority. The European food Safety Authority reserves its rights, view and position as regards the issues addressed and the conclusions reached in the present document, without prejudice to the rights of the authors.
Whilst omics technologies may have major implications for EFSA’s scientific activities, it is not clear to what extent they can be integrated in risk assessment. The main objectives of this project included a review of the state of the art of omics technologies (Report 1) and a foresight investigation on the future developments of these technologies in risk assessment (Report 2, starting from page 85). The review gives a description of the different types of omics technologies with respect to recent progresses made on the application of these techniques in chemical and microbiological risk assessment, and their added value and limitations as compared to classical risk assessment. Case studies for chemical hazards, nutrition and plant health showed current applications related to a search for biomarkers of exposure and discovering mode of actions. In general, statistical issues concern the many different approaches for omics data analysis which makes it difficult to compare different study results. The most relevant application of omics data to early detection of emerging microbiological hazards lies in the combination of genomics and epidemiology. Genetic analysis of both pathogens that are related to sporadic disease cases and to outbreak events can be used to reduce public health risks through the detection of virulence factors, resistance genes and genetic diversity. Whole genome sequencing is the most promising relevant technique for its application in risk assessment, source attribution and in detecting (diffuse) outbreaks. The availability of (easily accessible) databases with genomic information that can predict the behaviour of a strain remains a challenge.