The purpose of the LIGAN-PM (Lille Integrated Genomics Advanced Network for personalised medicine) genomics platform is to offer public and private research teams a comprehensive set of tools and skills to simplify the study of genetics, genomics and transcriptomics.
Our integrated solutions aim to resolve the challenges of genetic analysis and speed up the rate at which breakthroughs are made. This IBISA-certified platform brings together high-quality technological resources capable of conducting genotyping projects (medium/high throughput), sequencing projects and bioinformatic and biostatistic analyses.
For about 10 years now, the genomic analysis laboratory (LAG) has been developing the following activities: the collection, treatment, storage, management and distribution of samples of human origin.
The LAG is currently administrator for blood samples from over 22,500 subjects coming mainly from epidemiological studies based on topics such as cardiovascular, metabolic and neurodegenerative diseases.
Transcriptomics and Applied Genomics Group [TAG]
Inserm U 1019, CNRS UMR 8204, Institut Pasteur de Lille, University of Lille
Manager : David HOT
The TAG (Transcriptomics & Applied Genomics) team of the "Centre d’Infection et d’Immunité de Lille" (CIIL – Lille infection and immunity centre) is developing high-throughput genomic solutions and applications and using high-throughput micro-array and sequencing technologies. These applications are offered to the scientific community in response to collaboration proposals or in the form of services. An expertise is particularly developed for genomics and the transcriptomics of micro-organisms. In this way, the following solutions were developed: (re-)sequencing solutions for entire microbial genomes to characterise study strains or variants, RNA-sequencing and "differential RNA-seq" protocols on bacterial transcriptomes in order to determine the level of expression and the mapping of the transcriptome respectively and finally, metagenomic approaches by sequencing the RNAr 16s gene for bacterial microbiota studies. In addition to these experimental aspects particular effort has gone into developing bioinformatic and biostatistic analyses in order to offer relevant analysis solutions. This effort involves evaluating and setting up protocols and existing analysis methods and/or by developing new bioinformatic tools Recently, a complete protocol was proposed to evaluate the quality of mapping algorithms according to the quality of the sequences obtained at the outlet of the sequencer. On the same diagram, a study on the analysis pipelines of the diversity of microbiota by targeted sequencing is currently being published. Finally, an automatic analysis pipeline of the (re-)sequencing data of microbial genomes used to automatically extract the relevant information of a neo-sequenced genome was implemented. The TAG platform is equipped with a high-throughput sequencer (PGM Ion Torrent, Life Technologies), a library preparation and insulation system starting with single cells (C1 Single Cell Fluidigm) and integrated solutions for working on Agilent Technologies (SureScan) micro-arrays and Illumina (iScan). A series of small pieces of equipment for quantifying and qualifying nucleic acids that supplement the available facilities (BioAnalyzer, Nanodrop, Thermal cyclers, etc.)
The peptide chemistry platform is of particular interest in academic development and industrial collaborations for the development of therapeutic peptides and proteins.
Peptide chemistry offers two complementary areas of expertise. The first is the synthesis and characterisation of peptides and proteins. The use of new innovative peptides coming from chemistry provides access to their different complexes and scaffolds (cycles, ramifications, polycycles, etc.), but it also helps to gain a greater understanding thanks to a drop counter inspection of atoms forming the structure of small proteins.
The chemistry of biological systems facilitates the use of automated systems for synthesising the peptides and proteins used in libraries and projections.
The second complementary expertise concerns the study of peptides and proteins based on a combination of biochemistry, biophysics, cells and in vivo models.
Modified Peptide and Proteomics Platform Plateau (P3M)
INSERM U1019 - CNRS UMR 8204 - Université de Lille, Institut Pasteur de Lille
Contact : Jean Michel SALIOU
The Modified Peptide and Proteomics Platform Plateau (P3M) provides the research teams of the LabEx ParaFrap, the Lille immunity and infection centre (CIIL) and, more generally, the national and international public and private laboratories with the most recent cutting-edge technologies for analysing proteomics and characterising proteins.
The platform was created at the instigation of the LabEx ParaFrap ("Alliance Française contre les Maladies Parasitaires" – French Alliance against parasitic diseases) thanks to the financial support of the PIA and the FEDER. It is attached to the CIIL (INSERM U1019 - CNRS UMR 8204), is managed by Institut Pasteur de Lille, with the support of the CNRS and is incorporated within the coordination of the Lille biology and health platforms (Lille University, INSERM, CNRS, IPL).
Platform that combines a chemical library and all the high-throughput screening tools (except for the techniques based on high-throughput confocal imaging which are available on the microscopic imaging platform).
Platform for the qualitative and quantitative characterisation of the future of experimental active principles in in vivo models.
Nuclear Magnetic Resonance
CNRS UMR 8576, Institut Pasteur de Lille, University of Lille
Manager :Guy LIPPENS
The nuclear magnetic resonance (NMR) platform is used to study samples based on their magnetic properties. The 300 and 600 MHz spectrometers are available on the Pasteur-Lille campus. The platform conducts projects in the areas of biology and chemistry. NMR is used to characterise biological macromolecules and medicines.
Regarding the latter, the cryogenic probe of the 600 MHz spectrometer, which is capable of detecting fluorine, is of particular interest. The screening of small molecules, which can be used for therapeutic purposes, is carried out using a sample changer fitted with the 600 MHz device. The NMR study of the Tau neuronal protein within the context of Alzheimer's disease is used to highlight pathological forms of the protein
Since 2010, the BioImaging Center Lille-Nord of France (BICeL) has provided improved support for research in the Region thanks to an organisation that brings together the cellular and tissue imaging platforms of the university hospital campus (CHRU-Lille2), the University of Science and Technology of Lille 1 (campus Lille 1) and the Pasteur and Biology Institutes of Lille (Pasteur campus).
This organisation, thanks to the dedication of the staff on the three sites, has received national recognition by obtaining the GIS-IBISA certification in 2010 and a PIA-EquipEx ImagInEx BioMed (Rank 1) in 2011 backed by the European fund for regional development ("Fond Européen de Développement Régional") (FEDER) implemented by the Regional Council of the Nord Pas-de-Calais.