Developing and running software tools and methods able to organise, store, retrieve and analyse large volumes of biological data is what Bioinformatics is all about.
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) in plants. However, our expertise and the underlying infrastructure may also be applied to genetic information from animals, bacteria, fungi and humans, which allows extending Bioinformatics to other research fields like food fraud, medical diagnostics and environment.
Fast lane to GMO detection
Our Bioinformatics activity took off to enable the JRC-hosted European Union Reference Laboratory for Genetically Modified Food & Feed (EU-RL GMFF) to respond to latest needs in the validation of GMO detection methods, an essential step in the procedure for the authorisation of new GM food and feed in the European Union.
According to the Commission Regulation (EC) No 641/2004 a Biotech Company seeking authorisation for a new genetically modified food and feed must send to the EURL-GMFF a description of an analytical method which can be used to detect that GMO. That must include DNA sequence information to allow verifying the specificity of the method by using Bioinformatics tools.
To this aim, JRC researchers developed the Central Core Sequence Information System (CCSIS), a database where GMO sequence data submitted by applicants and retrieved from publicly available sources, like patents, is stored to run similarity searches.
Nowadays Bioinformatics is an essential part of any research activity related to GMOs. The JRC has pioneered the application of Next Generation Sequencing (NGS) in this field, using this technology to sequence GMOs.
Furthermore, a High Performance Computing facility helps coping with the huge amount of genetic data to analyse and explore with specific tools, like the GMO-Matrix and that uses the CCSIS as well as the GMOMETHODS database, providing GMO testing laboratories with practical input.
With this know-how, we support the EU GMO control via the European Network of GMO Laboratories (ENGL) to face GMO emergencies. For example, JRC generated and analysed sequence data of unauthorized GMOs (like Papaya, Bacillus subtilis) can be used to develop new GMO detection methods.
Bioinformatics help to fight food fraud
Nowadays DNA- or protein based detection methods can disclose the animal or plant species that are present in a food or feed product (e.g. minced meat, dairy products, ready-made fish dishes), but not their relative quantity/abundance. Within a project entitled "Species Identification by Ultra-Conserved Elements (SpI-UCEs)", JRC researchers will look for a new DNA based detection method based on the analysis of parts of the genomes that are always present (UCEs).
Bioinformatics require powerful databases and software to process the information. The JRC runs several highly specialised databases and tools:
- Central Core DNA Sequence Information System (CCSIS): this molecular database stores all GMO related sequence data submitted by applicant companies, as part of their legal obligations, to the European Union Reference Laboratory for GM Food and Feed (EU-RL GMFF). It is regularly amended by GMO sequence data from other sources (patents, scientific publications, sequencing), developing it towards a comprehensive while specialised and unique database.
- Next Generation Sequencing facility (NGS): it is used to "read" the genetic information, the sequence, from GMOs that allow verifying their genetic structure. Every experiment provides many gigabytes of data that have to be stored, processed and analysed.
- High Performance Computing facility (HPC): processing large data volumes in a short period of time requires very powerful computing equipment. The available multi-core HPC system reduces significantly the time needed for processing huge data volumes, such as sequence data generated in-house with the NGS facility, downloaded from public databanks, or received from the biotech industry.
- GMOMETHODS: the EURL GMFF maintains the European Union Database of Reference Methods for GMO Analysis. It contains complete descriptions of reference methods for GMO analysis. These methods are validated according to international standards and meet pre-defined performance criteria.
- GMO-Matrix: this is a decision support tool for the identification of GMOs on the basis of in-complete sequence information; it makes the analysis of GMOs in the food chain more efficient.
The Global Bioinformatics Network is a world-wide organisation that brings bioinformatics professionals together to serve, support and sustain the growing field of bioinformatics in the biological and biomedical research domains. The bioinformatics team at the JRC acts as one of its network-nodes.