A center resulting from the ambition of the INCA, with the support of the actors in cancer research in Lyon

Professor Gilles Thomas, a high level expert in genetics, came from the United States in the framework of a Senior chair of excellence financed by the Synergie Lyon Cancer Foundation. His duel expertise and the desire of INCa to join in the European project BASIS (Breast Cancer Genetics Somatic Study) gave the impetus required to set up a bioinformatics center specialized in cancerology.

Thus, in 2009 the INCa and the Synergie Lyon Cancer Foundation organized the Bioinformatics Center with the support of other partners in Lyon: the Lyon Auvergne Rhône-Alpes Cancer Cluster (CLARA), the Léon Bérard Center for the Fight Against Cancer (CLB) and the Rhône-Alpes Bioinformatics Cluster (PRABI). The center also collaborates  closely with the International Agency for Research on Cancer (CIRC).

A precious technological tool undergoing constant development  

Professor Gilles Thomas took over responsibility for setting up the center and from the outset instilled it with all his energy and originality. He quickly forged a rare technological tool whose pertinence has won national recognition and praise and which is subject to increasing demand from local research teams, especially in the field of cancer. The projects in which the platform participates have therefore multiplied, consolidating the center’s resources and expertise.

Now directed by Alain Viari, the Bioinformatics Center has become an indispensable tool for analyzing the data generated by existing technologies. Its originality is based on its team’s knowledge of cancer genetics and data processing.

Competences whose scope is focused on the genomic analysis of tumors

The mission of the Bioinformatics Center of the Synergie Lyon Cancer Foundation is to provide resources to research teams working in the field of oncology so they can benefit from recent high throughput genomic technology. All the bioinformatics engineers, biostatisticians and technological resources of the center are totally dedicated to taking the genomic projects to their conclusion. Particular emphasis has been placed on new generation sequencing.

At the heart of an organization dedicated to fighting against cancer, the Bioinformatics Center of the Synergie Lyon Cancer Foundation is very close to the realities faced by doctors and the questions raised by researchers. It also interacts intensively with the main regional actors involved in the development of bioinformatics and automation. This close interface between informatics and cancerology illustrates the whole interest of this laboratory.

Professor Gilles Thomas.

The Bioinformatics Center of the Synergie Lyon Cancer Foundation places its expertise and human and technological resources at the service of researchers.  The structure and interpretation of cancer genomic data make up its core occupation.

A team in the service of biomedical programs

Directed by Alain Viari, the Bioinformatics Center of the Synergie Lyon Cancer Foundation now has a team of 11 members.

The team develops computer pipelines for analyzing genomic data mainly obtained by new generation sequencing. These infrastructures ensure the selection of the biological material to be analyzed, the quality control of the data obtained by genomic techniques and the extraction from these data of information useful to the biomedical teams. The process modeling system developed by the center’s bioinformatics engineers has led to the automation of most of the analyses and the traceability of the operations is ensured.

Real-time interactions with the teams

The bioinformatics platform is committed to keeping its partners informed  at all times of the information generated from their samples. A Web application has been developed so it can provide its partners in real time of the quality control status of the sample and the characterizations performed. The team will also implement a server and a genome browser that will help investigators to explore huge collections of genomic data.

Leading edge equipment under development

The center currently has available 64 computers each with 8 processors (i.e. 512 cores) and 48 Gb of RAM. Storage of 170 Tb can be accessed quickly from these calculation nodes. A 24 processor computer with 256Gb of RAM is reserved for operations requiring a large amount of live memory, while two other computers (including one virtual computer) are dedicated to databases and user interfaces.

A highly qualified place of exchange and pooling

The team of the Bioinformatics center is also in contact with other French and foreign research groups so it can pool competences and experiences. This pooling leads to genuine emulation between teams that permits optimizing the computer analysis and development process and gives the center national and international standing. The result is a significant improvement of the quality of the center’s databases and the analyses performed there.

The Bioinformatics center can therefore assert itself as a genuine crucible of high level competences and innovation.

The Bioinformatics Center of the Synergie Lyon Cancer Foundation is currently responsible for the bioinformatics aspects of several national and international research projects in the field of cancer genomics.

The creation of the Bioinformatics Center was driven by the INCa, in collaboration with the Léon Bérard Center (CLB) to work on breast cancer, the cancer most frequent in women. With the Wellcome Trust Sanger Institute in the United Kingdom as partner, the Bioinformatics Center is involved in the European project BASIS (Breast Cancer Genetics Somatic Study). The aim of this program is to perform whole genome DNA sequencing (compared to matching healthy DNA) of aggressive breast cancers, in particular of ER+ and HER- types. BASIS is also part of the project International Cancer Genome Consortium (ICGC).

The center is involved in particular in the following fields:

• The collection of biological materials to be analyzed using high throughput techniques,
• Procedures to identify the most informative samples for study,
• Procedures for evaluating the quality of the genomic data generated from the biological samples of patients and controls, 
• Construction of analytical pipelines characterizing the genomic mutations of patients in order to isolate specificities of interest for diagnostics and treating cancer.

In 2013, the bioinformatics center was involved in 4 biomedical projects:

• ICGC / Breast cancer, a project developed with the Breast Cancer Working Group* in partnership with the INCa, dedicated to characterizing the genome of very aggressive tumours from a limited group of patients with a specific breast cancer.
• ICGC / Prostate cancer, initiated by the Inserm/ITMO and in collaboration with Olivier Cussenot devoted to the characterization of aggressive prostate cancers of European and/or African patients.
• ProfiLER : in the framework of the ProfiLER protocol of the LYric project, two engineers (a bioinformatics engineer and a biostatistician) were recruited by the center.
  ProfiLER is aimed at analyzing tumor and blood samples to establish the genetic profile of tumors, all tumors confounded.
• ABS4NGS (algorithmic, bioinformatics and software solutions for analyzing high throughput sequencing data), an ANR project “Investments for the Future”, in collaboration with Dr Olivier Delattre of the Institut Curie. The aim is to implement computer methods for processing sequencing data, ranging from computer data originating from different tumors to biology and, more particularly, the genome.
  This project uses NGS (Next Generation Sequencing), a tool that opens up a whole new approach to high throughput DNA sequencing, making it possible to obtain a large number of results at unprecedented speed.
• IMODI (Innovative MODels Initative) : The Bioinformatics Center processes data stemming from the molecular analyses of this national project, winner of the Investments for the Future Program. The aim is to develop predictive models in oncology and, finally, propose preclinical models dedicated to personalized medicine.

For more information: the ICGC web site

ICGC breast : https://lumiere.lyon.unicancer.fr/SampleTracker/

ICGC prostate : https://lumiere.lyon.unicancer.fr/GenericTracker/