Bioinformatics

Bioinformatics refers to the development and running of software tools and methods able to organise, store, retrieve and analyse large volumes of biological data.
At the JRC, we apply bioinformatics to genetic data, i.e. to DNA sequences, for the detection, identification and quantification of Genetically Modified Organisms (GMOs). Our expertise and the underlying infrastructure may also be applied to analyse other genetic information from plants, animals, bacteria, fungi and humans, which allows extending bioinformatics to other research fields like food fraud, medical diagnostics and environmental data analysis.

GMOs bioinformatics activities

JRC researchers have developed powerful databases and tools to verify the specificity of the analytical methods submitted by applicants requesting authorisation of a new GMO under Regulation (EC) No 1829/2003. The European Union Reference Laboratory for GM Food and Feed (EURL GMFF) is mandated to validate such methods, which includes assessing their specificity. This is done by comparing the DNA sequence targeted by the method to known DNA sequences stored in public sequence databases and in confidential databases hosted by the EURL GMFF (see below).  

Under Regulation (EU) 2017/625, the JRC is also designated as EURL GMFF for contributing to the improvement and harmonisation of analytical methods used by the official control laboratories of the EU Member States. In this context, the EURL GMFF assists the National Reference Laboratories (NRLs) in their control activities by providing several IT systems and a series of web applications for selecting the appropriate detection methods, designing screening strategies and interpreting the results obtained.

The databases and tools developed and managed by the EURL GMFF are the following: 

• The Central Core Sequence Information System (CCSIS) is a relational database including GMO sequences submitted by the applicants or retrieved from patents and publicly available sources, which are used for performing similarity searches and verify the specificity of the methods. Since the sequences submitted by the applicants are Sensitive Non Classified (SNC) information, access to CCSIS is strictly controlled.
• Processing considerable data volumes as large genomes in a short period requires very powerful computing equipment. A JRC High Performance Computing facility helps running the specificity analyses on public genomes and internal sequence data using ad-hoc bioinformatics pipelines and internal tools.
• GMOMETHODS: the European Union Database of Reference Methods contains complete descriptions of reference methods for GMO analysis. The assays are DNA-based detection methods, mainly polymerase chain reaction (PCR) assays validated by the EURL GMFF or by other laboratories according to the principles and requirements of international standards and meeting pre-defined performance criteria. The tool assists control laboratories in selecting the appropriate methods, provides the experimental protocol and information on methods performance, ring-trial design, plasmid standards, reference materials and links to published articles or validation reports.
• The JRC GMO-Matrix web application provides in silico e-PCR predictions of the GM events possibly detected by the EU reference methods in the GMOMETHODS database. The assembled two-dimensional matrices (chosen GMO events vs chosen EU reference methods) visualise the analytical coverage of the methods and identify potential gaps in the screening approach.
• The application GMO-Event finder allows identifying potential GMO(s) present in a sample based on a set of EU reference methods defined by the user and the obtained positive and negative experimental results.
• The application GMO-Screen provides a general screening proposal and a set of screening methods specific for EU authorised GMOs. A web interface supports the interpretation of the results obtained. The tool may be applied in combination with the ready to-use, multi-target screening device developed by the JRC known as the Pre-Spotted Plates (PSP), allowing the qualitative analysis of multiple GMO-targets in a single PCR experiment.
• Finally, JRC GMO-Amplicons compiles putative GMO-related amplicons from public sequence databanks by in silico PCR simulations with primers from selected EU reference methods. The tool allows predicting primers’ specificity and GM targets’ coverage. It can also help developing detection methods for selected species or non-authorised GMOs by retrieving and characterising related sequences from public databases and patents documentation.

With these tools, the EURL GMFF also supports the European Network of GMO Laboratories (ENGL) in addressing GMO emergencies and developing new detection methods for unauthorised GMOs.

All these applications may contribute to the design of more efficient approaches and promote better harmonisation for EU legislative enforcement and inspection control. Finally, the EU reference methods from the GMOMETHODS database, all validated following internationally accepted standard protocols, may foster the global harmonisation of GMO analysis, facilitating trade and promoting consumer trust.