• Health and Nutrition

Lille Integrated Genomic Advanced Network (LIGAN-PM)

Platform

Description

Our LIGAN-PM platform is dedicated to human genome sequencing and combines a range of technologies in the field of NGS (Next Generation Sequencing), allowing us to respond to various projects (medium/high throughput/very high throughput) in genotyping, sequencing, transcriptomics and bioinformatics and statistical analysis. Our platform is dedicated to precision medicine. In particular, we use NGS and genotyping tools to identify genetic predisposing factors to diabetes and obesity, in order to better understand the mechanisms of onset and complications of these pathologies, and to find an adequate treatment according to the genetic heritage of each patient. We are open to all academic and industrial collaborations and propose services in line with our expertise. Our laboratory is ISO15189 certified for the diagnosis of diabetes and associated diseases (obesity, kidney disease, cardiovascular disease, etc.).

Contacts

  • Amélie BONNEFOND
    Team director
  • Emmanuelle Durand
    Technical manager

Informations

1 place de Verdun
EGID, Faculté de Médecine, Campus Santé, Université de Lille
59045 LILLE

http://ligan.good.cnrs.fr/

Lille Integrated Genomic Advanced Network

Chiffres clés

• 1-2 runs of Illumina sequencing per week
• 50-100 projects per year
• 1.5 peta bytes of storage
• 10-20 publications per year

Effectif

Effectif total : 24

Expertises

Skills

• ISO15189 Medical Biology Laboratory
• NGS (Next Generation Sequencing)
• Bioinformatics
• DNA and RNA extracts
• DNA / protein interactions
• Genotyping
• Bioinformatics
• Biostatistics

Example(s) of projects

• CoDE-Seq technology (for Copy number variation Detection and Exome sequencing) single-step sequencing of DNA point mutations of all human genes, and very precise detection of large and small chromosomal abnormalities
• Declaration of invention VisuVAR (platform for analysis and visualization of genetic abnormalities identified by CoDE-Seq technology in patients with a rare disease)

Collaborations/Partners/Scientific clients

National:
AP-HP, CHU (Reims, Nantes, Poitiers, Amiens, Guadeloupe), INRA (Rennes), IFREMER, CNRS (U5554, U8727, U7144, UMR 7232, UMR 8198, UMR5244,…), INSERM (U894, U1018, U933, U1019, ...), Universités (Sorbonne, Montpellier, Aix Marseille, Amiens)

International:
Well Cornell (Qatar), Imperial College London (UK), UC Louvain (Belgium)

Collaborations/Partners/Private Clients

Genoscreen, Genes Diffusion, CIRCAGEN (UK), IMMATICS (D)

Services offers

Applications sectors

  • Health / wellness

Services provided

Extractions
• DNA extractions from whole blood, saliva samples, tissue sections
• RNA Extractions Genotyping/ Expression
• SNP genotyping
• Expression by Taqman probes
• High-throughput genotyping
• Expression via NCounter Nanostring
• Digital PCR

DNA sequencing on capillary sequencer and NGS sequencing
• Preparation of libraries
• Ready to Load Libraries
• Exome Sequencing (WES) / Genome Sequencing (WGS)
• 3D chromatin analysis (HiC)
• RNA sequencing (total RNA-seq, miRNA-seq, mRNA-seq)
• Re-sequencing & targeted sequencing
• De novo sequencing
• Mitochondrial sequencing
• Epigenetics (MethylSeq / methylation chip)
• Analysis of DNA/protein interactions (ChIPseq)

Bioinformatics and Biostatistics analysis
• Transverse and longitudinal genome-wide association study
• Detection of chromosomal events (mosaicism / CNV)
• Prioritization of genes / signaling pathways
• Pipelines & Package

Consulting services

We provide consulting services related to all our areas of expertise.

Equipments

Our platform possess innovative technologies dedicated to sequencing, NGS, genotyping, ddPCR, QPCR, proteomics and expression studies:
• next generation sequencing platforms (NovaSeq 6000, NextSeq 500, MiSeq, CBot – Illumina)
• targeted ultrasound device (E220 – Covaris)
• liquid handling workstations (STARlet (Hamilton), Bravo Automated Liquid Handling Platform (Agilent) and Sciclone® G3 NGSx iQ™ (Perkin Elmer))
• automated platform for DNA and RNA purification (Chemagic Prime - Perkin Elmer)
• platform for quantification and size analysis of DNA and RNA
• bioanalyzer for sample quality control (Agilent 2100)
• scanner for genetic analysis (iScan – Illumina)
• Real Time PCR System (Viia7 Real Time PCR System – Life Technologies)

See the detailed list of equipment: http://ligan.good.cnrs.fr/equipements/

Equipments

Nom Modèle Marque
Sequencing system NovaSeq 6000/ Illumina
Sequencer NextSeq 500/ Illumina
Sequencer MiSeq/ Illumina
Iscan and autoloader Illumina
Automaton Bravo/ Agilent
Automaton Sciclone G3 NGSx iQ/ Perkin Elmer
Automaton STARLet/ Hamilton Robotics
Nucleic acid counting nCounter/ Nanostring Technologies
Automated targeted ultrasound system E220/ Covaris

Ecosystem

Affiliated institutions / organisations

CHU de Lille
Inserm
CNRS

Unit(s) of attachment

Groups/Networks/Federations

France Génomique

Labellisations

Regional strategic areas of activity

  • Health and Nutrition
    • Food ingredients
    • New therapeutic approaches

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Thematics

Current thematics

  • Health and Nutrition
    • Food ingredients
    • New therapeutic approaches
Title

Current content

Lille Integrated Genomic Advanced Network
Type

Current content

Plateforme de services
Description

Current content

Our LIGAN-PM platform is dedicated to human genome sequencing and combines a range of technologies in the field of NGS (Next Generation Sequencing), allowing us to respond to various projects (medium/high throughput/very high throughput) in genotyping, sequencing, transcriptomics and bioinformatics and statistical analysis. Our platform is dedicated to precision medicine. In particular, we use NGS and genotyping tools to identify genetic predisposing factors to diabetes and obesity, in order to better understand the mechanisms of onset and complications of these pathologies, and to find an adequate treatment according to the genetic heritage of each patient. We are open to all academic and industrial collaborations and propose services in line with our expertise. Our laboratory is ISO15189 certified for the diagnosis of diabetes and associated diseases (obesity, kidney disease, cardiovascular disease, etc.).
Contact informations
Contact

Current content

Contact name Email phone number
BONNEFOND Amélie amelie.bonnefond@inserm.fr +33 3 74 00 81 18
DURAND Emmanuelle emmanuelle.durand@cnrs.fr (+33) 3 74 00 81 22
URL

Current content

http://ligan.good.cnrs.fr/

Address

Current content

1 place de Verdun
EGID, Faculté de Médecine, Campus Santé, Université de Lille
59045 LILLE
Keywords

Current content

ISO15189, NGS, next generation sequencing, personalized medicine, whole exome sequencing, whole genome sequencing, high throughput sequencing, targeted sequencing, transcriptome analysis, biostatistics
Our search domains
Skills

Current content

• ISO15189 Medical Biology Laboratory • NGS (Next Generation Sequencing) • Bioinformatics • DNA and RNA extracts • DNA / protein interactions • Genotyping • Bioinformatics • Biostatistics
Key data

Current content

• 1-2 runs of Illumina sequencing per week • 50-100 projects per year • 1.5 peta bytes of storage • 10-20 publications per year
Workforce

Current content

Effectif total : 24
Example(s) of projects

Current content

• CoDE-Seq technology (for Copy number variation Detection and Exome sequencing) single-step sequencing of DNA point mutations of all human genes, and very precise detection of large and small chromosomal abnormalities • Declaration of invention VisuVAR (platform for analysis and visualization of genetic abnormalities identified by CoDE-Seq technology in patients with a rare disease)
Example(s) of publications

Current content

Collaborations/Partners/Scientific clients

Current content

National: AP-HP, CHU (Reims, Nantes, Poitiers, Amiens, Guadeloupe), INRA (Rennes), IFREMER, CNRS (U5554, U8727, U7144, UMR 7232, UMR 8198, UMR5244,…), INSERM (U894, U1018, U933, U1019, ...), Universités (Sorbonne, Montpellier, Aix Marseille, Amiens) International: Well Cornell (Qatar), Imperial College London (UK), UC Louvain (Belgium)
Collaborations/Partners/Private Clients

Current content

Genoscreen, Genes Diffusion, CIRCAGEN (UK), IMMATICS (D)
Services offers
Training offers

Current content

Services offers

Current content

Extractions • DNA extractions from whole blood, saliva samples, tissue sections • RNA Extractions Genotyping/ Expression • SNP genotyping • Expression by Taqman probes • High-throughput genotyping • Expression via NCounter Nanostring • Digital PCR DNA sequencing on capillary sequencer and NGS sequencing • Preparation of libraries • Ready to Load Libraries • Exome Sequencing (WES) / Genome Sequencing (WGS) • 3D chromatin analysis (HiC) • RNA sequencing (total RNA-seq, miRNA-seq, mRNA-seq) • Re-sequencing & targeted sequencing • De novo sequencing • Mitochondrial sequencing • Epigenetics (MethylSeq / methylation chip) • Analysis of DNA/protein interactions (ChIPseq) Bioinformatics and Biostatistics analysis • Transverse and longitudinal genome-wide association study • Detection of chromosomal events (mosaicism / CNV) • Prioritization of genes / signaling pathways • Pipelines & Package
Consulting services

Current content

We provide consulting services related to all our areas of expertise.
Equipments
Equipements spécifiques

Current content

  • Sequencing system
    NovaSeq 6000/ Illumina
  • Sequencer
    NextSeq 500/ Illumina
  • Sequencer
    MiSeq/ Illumina
  • Iscan and autoloader
    Illumina
  • Automaton
    Bravo/ Agilent
  • Automaton
    Sciclone G3 NGSx iQ/ Perkin Elmer
  • Automaton
    STARLet/ Hamilton Robotics
  • Nucleic acid counting
    nCounter/ Nanostring Technologies
  • Automated targeted ultrasound system
    E220/ Covaris
Ecosystem
Affiliated institutions / organisations

Current content

  • University of Lille
  • CHU de Lille
  • Inserm
  • CNRS
Établissement(s) partenaire(s)

Current content

Unit(s) of attachment

Current content

  • Metabolic functional (epi)genomics and molecular mechanisms involved in type 2 diabetes and related diseases
Groups/Networks/Federations

Current content

France Génomique
Competitive cluster

Current content

Regional strategic areas of activity

Current content

  • Health and Nutrition
  • Food ingredients
  • New therapeutic approaches
Labelling

Current content

Personal informations
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