1- Scientific context and project objectives

Medical research is crucial for moving forward in the fight against cancer and encompasses everything from the most fundamental research to clinical research at the patient’s bedside, and from laboratory technology transfer to clinical applications. Two main facilities have been set up at the Jean Perrin Centre:

• A clinical research unit for testing new innovative medicines
• A biological research unit involved in studying the molecular mechanisms of the genesis and development of cancer

The molecular oncology laboratory headed up by Prof. Yves Jean Bignon applies both these techniques in the study of breast cancer. Although the limits differ between clinical and biological research, both entail small-scale experimental stages to develop routine protocols for diagnosis and therapy. The development of such protocols requires the construction of information systems for the extensive testing, validation and distribution of procedures.

2- Project description

The information system involves the high-speed processing of transcriptome data with a view to detecting genetic factors and understanding their roles in the development of cancer. This work needs to result in the creation of diagnosis and prognosis tools for these diseases. This platform will comprise three protocols:

• Study of the level of gene expression, by analysing the data obtained from a biochip analysis.
• Study of gene mutations, by processing and sequencing DNA samples from the patient(s) and identifying the mutations to make a diagnosis.
• Medical annotation. This tool involves setting up a patient follow-up protocol in the clinical research stages specific to the problems of cancer. Questionnaires are provided to record the doctors’ notes. They are then stored in a database for carrying out queries with the two previous bases.

3- Public or controlled use

The information system is for public use, but the acquisition protocols and data are strictly confidential medical data that can only be used by rigorously accredited specialists.

4- Expected results

The programme developed will increase the Jean Perrin Centre’s research possibilities in the framework of the Cancéropôle Rhône-Alpes-Auvergne. In this way, it will also increase the possibilities of programmes that can be developed at national and European level. Knowledge of transcriptomes is relevant in the setting up of the medical research platform, for it seems increasingly likely that one of the future pathways of medical diagnosis lies in the development of transcriptome technologies that will enable the identification of cancers through gene expression studies (Jean Perrin Centre, Prof. Bignon). This technology will result in new diagnostic kits being developed for characterising tumours and deciding on the best treatments to follow (diagnostic, prognostic and theranostic nosology).

This project will considerably promote the work of the Jean Perrin Centre and the academic teams involved in the project indirectly. Moreover, 3 companies: Diagnogene (Imaxio), Greentech S.A, GENOME express / Cogenics will play a key role in promoting this project. The first company is extremely interested in the Study of the level of gene expression because it is currently developing a module that may be integrated into this information system.

The second may, through its competences in biology, bioinformatics modelling and its technical production capacities, develop, produce and market new molecules of interest from biotechnologies. The new products from this research will be made available to the partners of the Cancéropôle Lyon Auvergne Rhône Alpes (CLARA) for use during preventive and/or therapeutic studies against different types of cancer.

Given (i) the new directions in terms of R&D concerning Clinical Data, (ii) the involvement of GENOME express / Cogenics in the validation/expression analysis aspect, together with Applied, and lastly (iii) the bioinformatics experience of SynQuence, (Genostar, etc.), the third is offering to contribute to the development of analysis and biostatistics tools applied not only to Mutacancer (eg databank) but also micro-array studies, and even qPCR validation.

More generally, in the context of point 7.2 of the document describing the ex programme E-nnovegne and more precisely the creation of a biomedical resource centre, this programme is part of the more extensive medical research platform of the university hospital centre, the Jean Perrin Centre, the Blaise Pascal and Auvergne Universities and the French National Institute for Agricultural Research (INRA), comprising Inserm Units 384 and 484, the Inserm Clinical Investigation Centre (CIC), the Clinical Pharmacology Centre (CPC), the Pain Treatment and Assessment Centre (CETD), the Cancéropole, the National Reference Centre for Leucodystrophy Prevention, the protist biology laboratory, the small animal imagery platform and INRA’s metabolome platform. The purpose is to standardise and professionalise data exchange between the various research bodies, whether they be public or private.

LifeGrid, the regional information system