High-Throughput sequencing and rare diseases
Since 2011, we are involved in a national research program aimed at identifying causative genes responsible for rare diseases using next generation sequencing technologies such as Whole Exome (WES),Â Whole Genome Sequencing (WGS), RNA-sequencing...
The program â€śHigh-throughput sequencing and rare diseasesâ€ť is promoted by the French Foundation for rare diseases (Fondation maladies rares), who financially support investigators through the launch of specific calls for projects. The service provided includes the library preparation, sequencing, reads alignment on human genome, and the detection and annotation of variants. Together with our facitlity, 4 other national platforms are involved in this program: Centre National de GĂ©notypage, GĂ©nomique Imagine, Integragen and Biogenouest GĂ©nomique.
France GĂ©nomique Network
The platform is a partner of theÂ France GĂ©nomiqueÂ national network that has been selected among the â€śInvestissements d'avenirâ€ť projects.
France GĂ©nomique brings together and shares resources of the main French genomics and bioinformatics platforms (7 genomics and 11 bioinformatics platforms from several French cities locatedÂ on this map). It offers to the scientific community access to the main platforms, support during their projects, high-level expertise and competences on next generation sequencing and bioinformatics. Each platform proposes services in its areas of expertise describedÂ on France Genomique website. Platforms work together within serveral work packages in order to share expertise and competences on several sequencing areas and applications (quality control and technology evaluation, evaluation of mapping software, analysis of gene expression, regulation of gene expression, variant detection in genomic data, metagenomics, ...).
Sequencing projects that require less than one run can be submitted onÂ France Genomique portalÂ at any time. For large-scale sequencing projects researchers are encouraged to apply forÂ the following call for proposal.
Our facility is involved in the management and maintenance of theÂ GalaxEastÂ platform.
GalaxEast is based upon Galaxy, one of the most popular bioinformatics workflow management systems, which is becoming a standard for sharing bioinformatics tools worldwide. It is aimed at providing a large range of bioinformatics tools for the analysis of various types of Omics data. It supports reproducible computational research by providing an environment for performing and recording bioinformatics analyses.
GalaxEast is open to the entire academic scientific community with a guaranteed availability. Unlike other public Galaxy platforms, GalaxEast is designed for intensive computing as it relies on a high performance computing cluster.
GalaxEast allows complete analyses from different sources of data from various research projects. It provides access to tools and algorithms devoted to Next Generation Sequencing (NGS) of epigenome (MACS, Homer), transcriptome (Cufflinks, HTSeq, TopHat), statistical analyses (DeepTools, S-mart, DESeq) and genomic sequence e.g tools for variant detection (GATK, Samtools) and variant annotation (SnpEff, SnpSift). In the future, GalaxEast will implement tools for other research fields (proteomics and imaging) to go toward a complete integrative analysis platform.
GalaxEast implements up-to-date standard Galaxy tools, plus bioinformatics developments from local research institutes. Local developments are packaged and released through the openÂ GalaxEast Toolshed. GalaxEast also grants access to workflows developed for Omics data analyses either by the GalaxEast team or by the scientific community.
Tumor Identity Card
The â€śTumor Identity CardÂ (CIT)â€ť project is dedicated to cancer genomics. Initiated in early 2000â€™s, this program is financed by the French cancer charity â€śLigue Nationale Contre le Cancer (LNCC)â€ť. Its aim is to establish molecular signatures for a large panel of tumor types using multi-omic analyses coupled to clinical data.
The program relies on a network of numerous fundamental and clinical research teams as well as several technological platforms.Â Our facility has been an essential node within this large project since the beginning. Indeed, we have generated several thousand transcriptome profiles of human tumors on Affymetrix microarrays,Â few hundred profiles of murine tumors on custom cDNA microarrays and few transcriptome profilesÂ on our high throughput Illumina sequencer.