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About IMGT

IMGT® attachment and affiliation french version

International

National

Interregional

Regional

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IMGT authority: LIGM (Montpellier) french version

The Laboratoire d'ImmunoGénétique Moléculaire (LIGM) (Prof. Marie-Paule Lefranc and Prof. Gérard Lefranc), Université de Montpellier, UPR CNRS 1142, IGH, has been involved for more than 30 years in the genetics, structure, polymorphism and function of the immunoglobulins (IG) and T cell receptors (TR).

The scientific contribution of LIGM is shown by publications in international journals, communications, invitations to congresses and seminars, the isolation of 40 genomic probes. These probes, released by ATCC (American Type Culture Collection), JCRB (Japanese Cancer Research Resources Bank) and ICRF (Imperial Cancer Research Fund, Human Genetic Resource Centre), are used by many laboratories abroad, for fundamental research and clinical applications. Some of these probes are powerful tools in the characterisation of the B and T cells, the analysis of clonality in leukemias and lymphomas, and the therapeutics follow up (residual diseases). 134 genomic sequences have been sent to the EMBL/GenBank databases.

In 1989, LIGM started IMGT/LIGM-DB, the first specialised and integrated database on immunoglobulins (IG) and T cell receptors (TR). Since May 2000 and owing to the considerable expansion and success of IMGT®, the international ImMunoGeneTics information system®, the LIGM scientific activity has been mainly devoted to the IMGT® research and development.

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IMGT information system overview french version

IMGT®, founded in Montpellier in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS) is the international reference in immunogenetics and immunoinformatics. IMGT® is specialized in the sequences, genes and structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins of vertebrates, IgSF and MhSF superfamily proteins of vertebrates and invertebrates, fusion proteins for immunological applications (FPIA) and composite proteins for clinical applications (CPCA).

IMGT® consists of databases, interactive tools and Web resources. IMGT® is used by researchers in academic and pharmaceutical laboratories in multiple areas of research:

IMGT® is labeled Bioinformatics Platform RIO (2001), IBiSA (since 2007), Grand Plateau Technique for Research and Innovation Languedoc-Roussillon (since 2005), Cancéropôle Grand Sud-Ouest, ReNaBi, GDR CNRS: BiM, ACCITH, Labex MabImprove, Academic Institutional Member of the International Medical Informatics Association (IMIA) (since 2006). IMGT® is certified ISO 9001:2008.

Databases

All databases are available at http://www.imgt.org

Sequence databases Gene database 3D and 2D structure database Monoclonal antibodies database

Interactive on-line tools

All interactive on-line tools are available at http://www.imgt.org

Sequence analysis Gene analysis 2D and 3D structure analysis

Web resources

All IMGT Web resources are available at http://www.imgt.org

IMGT® has been available on the Web since July 1995. IMGT® provides the biologists, researchers and clinicians with an easy to use and friendly interface. IMGT® has an exceptional response with more than 150,000 work sessions a month. Visitors are equally distributed between the European Union, the United States and the remaining world. IMGT/LIGM-DB data are also distributed by the HTTP or FTP and from many Sequence Retrieval System (SRS) sites. IMGT/LIGM-DB can be searched by BLAST or FASTA on different servers (EBI, Institut Pasteur, IGH...).

By its high quality and its easy data distribution, IMGT® has important implications in medical research (repertoires in autoimmune and infectious diseases, AIDS, leukemias, lymphomas, myelomas, allergy), veterinary research, functional genomics, genome diversity, genome evolution studies and comparative genomics of the adaptative immune system, biotechnology related to antibody engineering (combinatorial libraries, phage displays, single chain Fragment scFv, chimeric, humanized and human antibodies), diagnostic (detection and follow up of residual diseases), and therapeutical approaches (grafts, immunotherapy, vaccinology).

IMGT® has become the international reference in immunogenetics and immunoinformatics. At the cutting edge of immunology and bioinformatics, IMGT® is an invaluable integrated database for both fundamental, pharmaceutical, veterinary and clinical research.

IMGT initiator and coordinator: Marie-Paule Lefranc (Marie-Paule.Lefranc@igh.cnrs.fr), Senior Member of the Institut Universitaire de France, Professor Emeritus Université de Montpellier
IMGT, LIGM, IGH, UPR CNRS 1142, Montpellier (France)

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IMGT® databases and tools (ELIXIR)english version

Home page: http://www.imgt.org
Interface: Web UI
Affiliation: IMGT
Collection: IMGT databases and tools

Name Description Function Topic Contact Resource type Tag Publications

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IMGT/LIGM-DB The IMGT® database for nucleotide sequences with translation of immunoglobulins (IG) and T cell receptors (TR).
Annotation is based on the IMGT-ONTOLOGY concepts.
Query and retrieval -
Input: ID
Output: Flat file, annotation report (HTML)
Immunoinformatics, Immunogenetics, Nucleotide sequences Joumana Jabado-Michaloud
Joumana.Michaloud@igh.cnrs.fr Data
Patrice Duroux
Patrice.Duroux@igh.cnrs.fr Developer
Database - Immunoglobulin (IG)

- Antibody

- T cell receptor (TR)
PMID: 16381979
PMID: 25378316
IMGT/PRIMER-DB The IMGT® database for oligonucleotides (primers) of immunoglobulins (IG) and T cell receptors (TR).
Annotation is based on the IMGT-ONTOLOGY concepts.
Query and retrieval -
Input : ID
Output : Entry cards (HTML)
Immunoinformatics, Immunogenetics, Nucleotide sequences Geraldine Folch
Geraldine.Folch@igh.cnrs.fr Data
Patrice Duroux
Patrice.Duroux@igh.cnrs.fr Developer
Database - Immunoglobulin (IG)
- Antibody
- T cell receptor (TR)
PMID: 15089751
PMID: 15972004
PMID: 25378316
IMGT/GENE-DB The IMGT® database for immunoglobulin (IG) and T cell receptor (TR) genes and alleles (international nomenclature).
Annotation is based on the IMGT-ONTOLOGY concepts.
Query and retrieval -
Input : ID
Output : Entry cards (HTML)
Immunoinformatics, Immunogenetics, Genes and alleles Véronique Giudicelli Veronique.Giudicelli@igh.cnrs.fr Database - Immunoglobulin (IG)
- Antibody
- T cell receptor (TR)
PMID: 15608191
PMID: 25378316
IMGT/3Dstructure-DB The IMGT® database for 3D structures of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins, related proteins of the immune system (RPI) and fusion proteins for immune applications (FPIA).
Annotation is based on the IMGT-ONTOLOGY concepts.
Query and retrieval -
Input : ID
Output : Entry cards (HTML)
Immunoinformatics, Immunogenetics, Structures, Contact analysis Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Database - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Major histocompatibility (MH)
- Immunoglobulin superfamily (IgSF)
- Major histocompatibility (MhSF)
PMID: 14681396
PMID: 19900967
PMID: 21632774
PMID: 25378316
IMGT/2Dstructure-DB The IMGT® database for 2D structures (IMGT Colliers de Perles) of immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) proteins and related proteins of the immune system (RPI).
Annotation is based on the IMGT-ONTOLOGY concepts.
Query and retrieval -
Input : ID
Output : Entry cards (HTML)
Immunoinformatics, Immunogenetics Amino acid sequences Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Database - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Major histocompatibility (MH)
- Immunoglobulin superfamily (IgSF)
- Major histocompatibility (MhSF)
PMID: 25378316
IMGT/mAb-DB The IMGT® database for monoclonal antibodies (mAb) or immunoglobulins (IG), fusion proteins for immune applications (FPIA) and composite proteins for clinical applications (CPCA).
IMGT/mAb-DB provides links to IMGT/2Dstructure-DB and IMGT/3Dstructure-DB.
Query and retrieval -
Input : ID
Output : Entry cards (HTML)
IMGT-ONTOLOGYand Immunoinformatics, Immunogenetics, IG, antibodies, FPIA, CPCA, Specificity Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Database - Immunoglobulin (IG) or antibody
- Fusion proteins for immune applications (FPIA)
- Composite proteins for clinical applications (CPCA)
PMID: 25378316
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IMGT/V-QUEST IMGT® tool for nucleotide sequence alignment and analysis of immunoglobulin (IG) or antibody and T cell receptor (TR) variable domains, integrates IMGT/JunctionAnalysis, IMGT/Automat and IMGT/Collier-de-Perles.
Analysis is based on the IMGT-ONTOLOGY concepts.
Nucleotide sequence analysis
Input : FASTA
Output: Report (HTML, Excel)
Immunoinformatics, Immunogenetics, IG, TR, Nucleotide sequence analysis, V domain, V-(D)-J-region Véronique Giudicelli
Veronique.Giudicelli@igh.cnrs.fr
Tool (analysis) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
PMID:15215425 PMID: 18503082, PMID: 21632778, PMID: 25378316
IMGT/HighV-QUEST IMGT® portal for NGS high-throughput nucleotide sequence analysis of immunoglobulins (IG) and T cell receptors (TR) variable domains, integrates IMGT/JunctionAnalysis and IMGT/Automat.
Analysis is based on the IMGT-ONTOLOGY concepts.
Next Generation Sequencing (NGS) nucleotide sequence analysis
Input : FASTA
Output: Files (pdf, csv)
Immunoinformatics, Immunogenetics, NGS nucleotide sequence analysis Véronique Giudicelli
Veronique.Giudicelli@igh.cnrs.fr
Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (analysis) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
Immunome Research 2012, 8(1):26,
PMID: 23995877
PMID: 25378316
IMGT/JunctionAnalysis IMGT® tool for the analysis of the nucleotide sequences of the V-J and V-D-J junctions of the variable domains of the immunoglobulins (IG) or antibodies and T cell receptors (TR).
Analysis is based on the IMGT-ONTOLOGY concepts.
Nucleotide sequence analysis
Input: FASTA
Output: Report (HTML)
Immunoinformatics, Immunogenetics, Nucleotide sequence analysis Véronique Giudicelli
Veronique.Giudicelli@igh.cnrs.fr
Tool (analysis) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
PMID: 15262823
PMID: 21632777
PMID: 25378316
IMGT/Allele-Align IMGT® tool for the comparison of two alleles highlighting the nucleotide and amino acid differences. Nucleotide sequence alignment
Input: FASTA
Output: Display (HTML)
Sequence alignment, Alleles, Nucleotide sequence analysis Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (analysis) PMID: 15089751
PMID: 15972004
PMID: 25378316
IMGT/PhyloGene IMGT® tool to compute and draw phylogenetic trees for immunoglobulin (IG) and T cell receptor (TR) V-REGION nucleotide sequences.
Analysis is based on the IMGT-ONTOLOGY concepts.
Nucleotide sequence alignment and phylogeny trees
Input: FASTA
Output: Display (HTML)
Immunoinformatics, Immunogenetics, Gene families, Phylogeny Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (analysis) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
PMID: 12818634
PMID: 25378316
IMGT/DomainDisplay The IMGT® tool for the display of the amino acid sequences of the variable (V), constant (C) and groove (G) domains.
Analysis is based on the IMGT-ONTOLOGY concepts.
Amino acid sequence analysis
Input: FASTA
Output: Display (HTML)
Immunoinformatics, Immunogenetics, Amino acid sequences, Domain Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (analysis) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Major histocompatibility (MH)
- Immunoglobulin superfamily (IgSF)
- Major histocompatibility (MhSF)
PMID: 25378316
IMGT/LocusView IMGT® tool providing a view of immunoglobulin (IG), T cell receptor (TR) and major histocompatibility (MH) loci.
Display is based on the IMGT-ONTOLOGY concepts.
Query and retrieval -
Input : locus name
Output: Display (HTML)
Immunoinformatics, Immunogenetics, Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (visualiser) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Major histocompatibility (MH)
PMID: 15089751
PMID: 15972004
PMID: 25972004
IMGT/GeneView IMGT® tool providing the view of a gene in IMGT/LocusView. Display is based on the IMGT-ONTOLOGY concepts. Query and retrieval -
Input : gene name
Output: Display (HTML)
Immunoinformatics, Immunogenetics, Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (query and retrieval) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Major histocompatibility (MH)
PMID: 15089751
PMID: 15972004
PMID: 25378316
IMGT/GeneSearch IMGT® tool allowing the search of a gene in IMGT/LocusView. Search is based on the IMGT-ONTOLOGY concepts. Query and retrieval -
Input : gene name
Output: Report (HTML)
Immunoinformatics, Immunogenetics, IG, TR, MH, Gene names Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (query and retrieval) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Major histocompatibility (MH)
PMID: 15089751
PMID: 15972004
PMID: 25378316
IMGT/CloneSearch IMGT® tool allowing the search of a clone in IMGT/LocusView. Search is based on the IMGT-ONTOLOGY concepts. Query and retrieval -
Input: clone name Output: Report (HTML)
Immunoinformatics, Immunogenetics Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (query and retrieval) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Major histocompatibility (MH)
PMID: 15089751
PMID: 15972004
PMID: 25378316
IMGT/GeneInfo IMGT® tool providing combination (V-J and V-V) information for the human and mouse T cell receptor (TR) loci. Analysis is based on the IMGT-ONTOLOGY concepts. Query and retrieval - Immunoinformatics, Immunogenetics, Nucleotide sequences Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (visualiser) - T cell receptor (TR) PMID: 14681357
PMID: 16640788
PMID: 25378316
IMGT/GeneFrequency IMGT® tool providing the frequency usage of immunoglobulin (IG) and T cell receptor (TR) variable (V), diversity (D) and joining (J) genes in Homo sapiens and Mus musculus rearranged sequences from IMGT/LIGM-DB.
Analysis is based on the IMGT-ONTOLOGY concepts.
Query and retrieval -
Input: sequences from IMGT/LIGM-DB
Output: Bar graphs of gene usage (V, D or J).
Immunoinformatics, Immunogenetics Gene names Patrice Duroux Patrice.Duroux@igh.cnrs.fr Tool (visualiser) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
PMID: 15972004
PMID: 16640788
PMID: 25378316
IMGT/DomainGapAlign IMGT® tool for the analysis of amino acid sequences of variable (V), constant (C) or groove (G) domains. Analysis is based on the IMGT-ONTOLOGY concepts. Amino acid sequence analysis Input: FASTA
Output: Display of aligned V, C or G domain sequences, gapped according to the IMGT unique numbering
Immunoinformatics, Immunogenetics, Amino acid sequences Gene families Domain Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (analysis) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Major histocompatibility (MH)
- Immunoglobulin superfamily (IgSF)
- Major histocompatibility (MhSF)
PMID: 19900967
PMID: 21632775
PMID: 25378316
IMGT/Collier-de-Perles IMGT® tool to draw standardized IMGT 2D graphical representations, or IMGT Colliers de Perles, of variable (V), constant (C), groove (G) domains, starting from the user own domain amino acid sequences. IMGT Colliers de Perles are based on amino acid sequences gapped according to the IMGT-ONTOLOGY concept of IMGT unique numbering. Graphical representation or IMGT Colliers de Perles of V, C or G domain
Input: Amino acid sequences, gapped based on the IMGT unique numbering
Output: IMGT Collier de Perles
Immunoinformatics, Immunogenetics, Amino acid sequence Gene families Domain Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (visualiser) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Major histocompatibility (MH)
- Immunoglobulin superfamily (IgSF)
- Major histocompatibility superfamily (MhSF)
PMID: 11862387
PMID: 18208865
PMID: 21632776
PMID: 25378316
IMGT/DomainSuperimpose IMGT® tool to superimpose 3D structures of two domains from IMGT/3Dstructure-DB. Domain 3D structures are numbered according to the IMGT-ONTOLOGY concept of IMGT unique numbering. Domain 3D structure comparison Input: 3D structure domain ID
Output: Display of the superimposed 3D structures
Immunoinformatics, Immunogenetics Domain Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (visualiser) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Major histocompatibility (MH)
- Immunoglobulin superfamily (IgSF)
- Major histocompatibility superfamily (MhSF)
PMID: 25378316
IMGT/StructuralQuery IMGT® tool to retrieve IMGT/3Dstructure-DB entries using amino acid structural criteria for variable (V), constant (C) or groove (G) domains.
Annotation is based on the IMGT-ONTOLOGY concepts.
Query and retrieval - Immunoinformatics, Immunogenetics, Domain Patrice Duroux
Patrice.Duroux@igh.cnrs.fr
Tool (query and retrieval) - Immunoglobulin (IG) or antibody
- T cell receptor (TR)
- Immunoglobulin superfamily (IgSF)
PMID: 15089751
PMID: 14681396
PMID: 25378316
Created 31/03/2016 (G. Folch)

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IMGT®, the international ImMunoGeneTics information system® (IFB-ReNaBi)french version

IMGT®, the international ImMunoGeneTics information system®

Information | Infrastructure | Données | Outils | Expertise | Formations | Ouverture | Publications

Information

Contact

ADRESSE POSTALE

IMGT®, the international ImMunoGeneTics information system®,
Laboratoire d'ImmunoGénétique Moléculaire (LIGM),
Institut de Génétique Humaine (IGH), UPR CNRS 1142,
141 rue de la Cardonille, cedex 5
34396 Montpellier cedex 5, France

WEB SITE http://www.imgt.org

logoIMGT

Responsables

DIRECTEUR EXECUTIF EMERITE
Marie-Paule Lefranc

DIRECTEUR
Sofia Kossida

RESPONSABLE INFORMATIQUE
Patrice Duroux

RESPONSABLE BIOINFORMATIQUE
Véronique Giudicelli

Divers

POLE REGIONAL
IFB Grand Sud

CERTIFICATIONS
ISO 9001
NFX 50-900
IQuaRe
HON Certification

LABELLISATION

Internationale:

Nationale:
Interrégionale:
Régionale:
MARQUE DEPOSEE
IMGT® est une marque enregistrée CNRS (registered trademark) (Union Européenne, Canada, Etats-Unis).

logoIMGT

STRUCTURE
CNRS Université de Montpellier

Université de Montpellier

Equipe

Lefranc Marie-Paule, PU Emérite Université de Montpellier, 100%
Kossida Sofia, PU, Université de Montpellier, 50%
Lefranc Gérard, PU Emérite, Université de Montpellier, 10%
Patrice Duroux, IR CNRS, 100%
Véronique Giudicelli, IR Université de Montpellier, 100%
Joumana Jabado-Michaloud, IE CNRS, 100%
Géraldine Folch, IE CDI CNRS, 100%
Aouinti Safa, IE CDD CNRS, 100%
Arrivet Mélanie, IE CDD CNRS, 100%
Bento Pascal, IE CDD CNRS, 100%
Cambon Mélissa, IE CDD CNRS, 100%
Chentli Imène, IE CDD CNRS, 100%
Lavoie Arthur, IE CDD CNRS, 100%
Paysan-Lafosse Typhaine, IE CDD CNRS, 100%
Peralta Marine, IE CDD CNRS, 100%
Sasorith Souphatta, IE CDD CNRS, 100%

Infrastructure

Information infrastructure

DESCRIPTION DES SERVEURS

HEURES DE CALCUL

En réponse aux appels à projets du GENCI (Grand Equipement National de Calcul Intensif), les heures de calcul suivantes ont été attribuées à IMGT® sur le Centre de Calcul du CINES [allocation 036029]:
2009 : 60.000h (IBM)
2010 : 50.000h (IBM)
2011 : 80.000h (IBM) et 80.000h (SGI)
2012 : 50.000h (IBM) et 100.000h (SGI)
2013 : 45.000h (IBM) et 320.000h (SGI)
2014 : 70.000h (IBM) et 224.000h (SGI)
En 2015, en réponse aux appels à projets du GENCI:
10.000h (IBM) et 500.000h (BULL) ont été attribuées à IMGT® (projet x2015036029) sur le Centre de Calcul du CINES, ainsi que 300.000h (BULL) sur le Très Grand Centre de calcul (TGCC) du Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA).
En première session DARI 2016, 250.000h (BULL, CINES) et 200.000 h (BULL, TGCC CEA) ont été attribuées à IMGT®.
IMGT a également accès au HPC@LR.

Données

BASES DE DONNEES

IMGT® comprend sept bases de données:
1. IMGT/LIGM-DB est la base de données internationale pour les séquences nucléotidiques d'IG et TR de l'homme et des autres espèces de vertébrés avec traduction des séquences entièrement annotées.
2. IMGT/PRIMER-DB.
3. IMGT/GENE-DB. Des liens réciproques existent entre IMGT/GENE-DB et la base de données 'Gene' au NCBI (ceci est le seul exemple de liens directs effectués par Gene au NCBI sur une base de données externe).
4. IMGT/3Dstructure-DB.
5. IMGT/2Dstructure-DB.
6. IMGT/CLL-DB, la base de données IMGT® des séquences IG de patients atteints de leucémie lymphoïde chronique, créée en 2007.
7. IMGT/mAb-DB, la base de données IMGT® des anticorps monoclonaux et des protéines de fusion à visée thérapeutique, créée en 2009.

RESSOURCES WEB

Les ressources Web IMGT® comprennent plus de 15.000 pages, organisées en plusieurs sections:
1. IMGT Scientific chart fournit le vocabulaire contrôlé et les règles d'annotation basés sur IMGT-ONTOLOGY.
2. IMGT Repertoire fournit une interface conviviale aux données soigneusement expertisées qui concernent le génome, le protéome, le polymorphisme et la structure des IG et TR de l'homme et des autres vertébrés.
3. IMGT Index, IMGT Education, IMGT Aide-mémoire, IMGT Bloc-notes.
4. IMGT Immunoinformatics page.
5. IMGT Medical page fournit aux cliniciens les informations d'IMGT® sur les bases, outils et données d'intérêt médical.
6. IMGT Veterinary page fournit aux vétérinaires les informations d'IMGT® sur les génomes, séquences et structures 3D des IG et TR des espèces animales.
7. IMGT Biotechnology page fournit un ensemble d'informations sur l'ingénierie des anticorps (phage display), les anticorps de camélidés, l'humanisation des anticorps monoclonaux thérapeutiques.

Outils

IMGT® OUTILS EN LIGNE

IMGT® comprend dix-sept outils interactifs en ligne pour l'analyse des séquences (5), des gènes (7), des domaines protéiques (3) et des données structurales (2).

ANALYSE DES SEQUENCES

1. IMGT/V-QUEST, l'outil le plus utilisé d'IMGT®, intègre
2. IMGT/JunctionAnalysis.
3. IMGT/HighV-QUEST, pour les séquences IG et TR issues du Next Generation Sequencing (NGS).
4. IMGT/Allele-Align permet la comparaison de deux allèles.
5. IMGT/PhyloGene calcule et représente les arbres phylogénétiques des séquences nucléotidiques d'IG et de TR.

ANALYSE DES GENES

1. IMGT/GeneView,
2. IMGT/GeneSearch,
3. IMGT/LocusView
4. IMGT/CloneSearch
5. IMGT/GeneInfo
6. IMGT/GeneFrequency
7. IMGT/LIGMotif.

ANALYSE DES DOMAINES PROTEIQUES

1. IMGT/DomainDisplay affiche les domaines protéiques selon la numérotation unique IMGT.
2. IMGT/DomainGapAlign permet de créer les « gaps » selon la numérotation unique IMGT.
3. IMGT/Collier-de-Perles fournit la représentation standardisée « IMGT Colliers de Perles » des domaines.

ANALYSE DES DONNEES STRUCTURALES

1. IMGT/StructuralQuery permet de faire des requêtes basées sur une description structurale.
2. IMGT/DomainSuperimpose superpose deux structures 3D de domaines.

Expertise

Domaines d'activité

IMMUNOGENETIQUE
IMMUNOINFORMATIQUE
IMMUNOLOGIE
ANTICORPS THERAPEUTIQUES
BIOMEDICAL
BIOTECHNOLOGIE
DIAGNOSTIC

Description des expertises

IMGT®, the international ImMunoGeneTics information system® http://www.imgt.org, est la référence internationale en immunogénétique et immunoinformatique. IMGT® est une marque déposée du CNRS (Union Européenne, Canada et Etats-Unis). IMGT® est membre institutionnel académique de l'International Medical Informatics Association (IMIA) depuis 2006. IMGT® est spécialisé dans les séquences, structures et données génétiques des immunoglobulines (IG), des récepteurs T (TR), des protéines majeures d'histocompatibilité (MH) des vertébrés, des protéines apparentées du système immunitaire (RPI, pour Related Proteins of the Immune system) des superfamilles IgSF et MhSF des vertébrés et invertébrés, des protéines de fusion pour applications immunologiques (FPIA, pour fusion proteins for immune applications)et des protéines composites pour applications cliniques (CPCA, pour composite proteins for clinical applications). IMGT® est composé de sept bases de données (séquences, gènes et structures tridimensionnelles (3D)), de dix-sept outils interactifs et de plus de 15.000 pages de ressources Web .

IMGT® est reconnu internationalement pour la richesse et la qualité de ses données scientifiques et son interface conviviale. Le nombre d'équipes utilisatrices d'IMGT® est supérieur à 80.000. Ces équipes académiques et industrielles appartiennent à des domaines d'activité de recherche professionnelle variés et sont réparties dans le monde entier, à parts égales entre les Etats-Unis et Canada, l'Europe et le reste du monde. Ceci représente plus de 200.000 requêtes par mois et un nombre de sessions de travail sans cesse croissant (300.000 en 2015).

IMGT® est utilisé par des chercheurs d'équipes académiques et industrielles dans de multiples domaines de recherche:
(1) recherche fondamentale,
(2) recherche médicale (analyse des répertoires des anticorps et des sites de reconnaissance des récepteurs T dans les réponses immunitaires normales (infections, cancers), les réponses anormales (maladies autoimmunes, immunodéficiences) et dans les syndromes prolifératifs (leucémies, lymphomes, myélomes)),
(3) recherche vétérinaire (étude des répertoires des IG et TR dans les espèces domestiques et sauvages),
(4) recherche génomique (étude de la diversité et de l'évolution des gènes de la réponse immunitaire adaptative),
(5) recherche en biologie structurale (évolution des domaines des protéines des superfamilles IgSF et MhcSF des vertébrés et invertébrés),
(6) biotechnologies relatives aux projets de l'Human Proteome Organisation (HUPO) et à l'ingénierie des anticorps (single chain Fragment variable scFv, Fab, banques combinatoires, phage display, anticorps chimériques, humanisés et humains),
(7) recherche pour le diagnostic, le pronostic et le suivi thérapeutique des leucémies, lymphomes et myélomes (identification du ou des clone(s) malin(s) et évaluation de la maladie résiduelle), (8) approches thérapeutiques (greffes, immunothérapie, vaccinologie).

Formations

FORMATION PROFESSIONNELLE

1. Atelier technologique. Biologie moléculaire appliquée aux anticorps: Analyse des séquences et structures d'anticorps à l'aide des outils IMGT®
Montpellier 4-5 juin 2012
Responsable Scientifique: Marie-Paule Lefranc
Intervenants: Marie-Paule Lefranc, Véronique Giudicelli
Pré-requis: Biologistes (biologie moléculaire et immunologie) ayant un projet d'analyse de séquences d'anticorps
Public: Etudiants, techniciens, ingénieurs et chercheurs
Nombre de participants: 12
Programme Formation théorique :
- Analyse du gène à la protéine
- Synthèse des immunoglobulines
- Concepts d'identification, de description, de classification et de numérotation d'IMGT-ONTOLOGY
Programme Formation pratique : Utilisation en ligne des outils IMGT® :
- IMGT/V-QUEST
- IMGT/JunctionAnalysis
- IMGT/Collier-de-Perles
- IMGT/DomainGapAlign
- IMGT/3Dstructure-DB

2. Atelier technologique de BioCampus Montpellier. Utilisation des bases de données et outils IMGT® pour l'ingénierie et l'humanisation des anticorps
Montpellier, 6-7 juin 2013
Responsable Scientifique: Marie-Paule Lefranc
Intervenants: Marie-Paule Lefranc, Souphatta Sasorith

3. Atelier technologique de BioCampus Montpellier. Utilisation des bases de données et outils IMGT pour l'ingénierie et l'humanisation des anticorps
Montpellier, 5-6 juin 2014
Responsable Scientifique: Marie-Paule Lefranc
Intervenants: Marie-Paule Lefranc, Souphatta Sasorith

FORMATION UNIVERSITAIRE

Master de Biologie-Santé, Université de Montpellier:

Master Sciences & Numérique pour la Santé, Université de Montpellier:
Master Biologie-Agrosciences, Université de Montpellier:
Licence, Science de la Vie, tous les parcours, Université de Montpellier

Module "Bioinformatique et Ontologies" (annuel de 2007 à 2014)
Responsable: Marie-Paule Lefranc
Maison des Ecoles Doctorales de Montpellier

Immunoinformatics - Bioinformatics of antibodies
University of Science and Technology of Hanoi.
Faculty of Biotechnology - Pharmacology, Hanoi, Vietnam
Consortium USTH (participation of the University of Montpellier)
(in English, BP41, Master 2, 40h, 4 ECTS, students from Biomedicine and from Drug development)
Prof. Marie-Paule Lefranc
Teaching Unit Content
1. Knowledge of databases for sequences and structures of antibodies.
2. Using tools for sequence analysis: applications to the study of repertoires of antibody recognition sites and to the study of specificities (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas, myelomas...).
3. Bioinformatic structural analysis for the humanization of monoclonal antibodies for therapeutic purposes (IMGT Collier de Perles methodology).
4. Structural analysis of antibody fragments and their recognition sites for the discovery of new drugs.
This teaching unit is based in particular on the tools and databases developed by IMGT®, the international ImMunoGeneTics information system ®, http://www.imgt.org, the international reference system used by many pharmaceutical companies (JANSSEN Centocor Research and Development Inc. Johnson & Johnson USA, AMGEN Inc. USA, Sanofi-Aventis GmbH Germany, Merck & Co. Inc. USA, Chugai Pharmaceutical Co. Ltd. Japan, Astellas Pharma Inc. Japan, Agensys Inc. USA, Merck Serono SA Switzerland, F. HOFFMAN-LA ROCHE Switzerland, etc..).
The teaching requires a PC connected to Internet per student.

Ouverture

Description de la répartition

ACCES A IMGT®

Accès en ligne des 7 bases de données, 17 outils et aux 15.000 pages de ressources Web.

Caractère international de l'accès.

L'accès à IMGT® est libre, gratuit pour les académiques, sous licences et contrats avec le CNRS pour les industriels.

1. Site Web (http://www.imgt.org).
2. Distribution des données d'IMGT/LIGM-DB sur les serveurs IMGT (http://www.imgt.org/download/LIGM-DB) et par FTP sur les serveurs de l'EBI (ftp://ftp.ebi.ac.uk/pub/databases/imgt/LIGM-DB).
3. Distribution des données d'IMGT/GENE-DB sur les serveurs IMGT (http://www.imgt.org/download/GENE-DB/).
4. Distribution des données d'IMGT/3Dstructure-DB sur les serveurs IMGT(http://www.imgt.org/download/3Dstructure-DB/).
5. Accès aux données d'IMGT/LIGM-DB
- par SRS sur le serveur du Deutsche Krebsforschungszentrum (DKFZ) Heidelberg, Allemagne,
- par ARSA au DNA Data Bank of Japan (DDBJ).
6. Accès aux données par DAS et Dbfetch à l'EBI et LinkOut au NCBI.
7. Comparaison de séquences par rapport aux séquences de références d'IMGT/GENE-DB, d'IMGT/DomainDisplay, d'IMGT/3Dstructure-DB et des séquences de domaines par BLAST sur le serveur IMGT (IMGT/BlastSearch Query page).
8. Comparaison de séquences par BLAST et FASTA, par rapport à celles de IMGT/LIGM-DB, sur les serveurs de l'EBI et de l'Institut Pasteur.
9. Références croisées avec HGNC, NCBI Gene, Vega, UniProt, Sequence Ontology.
10. Aides spécifiques et conseils aux utilisateurs et API.

Répartition des utilisateurs

INTERNATIONAUX 99 %
NATIONAUX 1 %

Publications

PUBLICATIONS EXTERNES

2015

Aouinti S, Malouche D, Giudicelli V, Kossida S, Lefranc M-P.
IMGT/HighV-QUEST statistical significance of IMGT clonotype (AA) diversity per gene for standardized comparisons of next generation sequencing immunoprofiles of immunoglobulins and T cell receptors.
PLoS ONE. 2015 Nov 5;10(11):e0142353. doi: 10.1371/journal.pone.0142353. eCollection 2015. Free Article PMID: 26540440 Correction: PLoS ONE 2016 Jan 5;11(1): e0146702. doi: 10.1371/journal.pone.0146702 View correction. PMID: 26731095.

Piccinni B, Massari S, Caputi Jambrenghi A, Giannico F, Lefranc M-P, Ciccarese S, Antonacci R.
Sheep (Ovis aries) T cell receptor alpha (TRA) and delta (TRD) genes and genomic organization of the TRA/TRD locus.
BMC Genomics. 2015 Sep 18;16(1):709. doi: 10.1186/s12864-015-1790-z. PMID: 26383271

Giudicelli V, Duroux P, Lavoie A, Aouinti S, Lefranc M-P, Kossida S.
From IMGT-ONTOLOGY to IMGT/HighV-QUEST for NGS immunoglobulin (IG) and T cell receptor (TR) repertoires in autoimmune and infectious diseases
Autoimmun Infec Dis. 2015 Aug 10. 1(1): doi: 10.16966/aidoa.103. Free Article.

Lefranc M-P.
Antibody Informatics: IMGT, the International ImMunoGeneTics Information System, In: Crowe J, Boraschi D, Rappuoli R (Eds)
Antibodies for Infectious Diseases. ASM Press, Washington, DC. doi: 10.1128/microbiolspec. AID-0001-2012, 2015, pp. 363-379.

Li L, Wang XH, Williams C, Volsky B, Steczko O, Seaman MS, Luthra K, Nyambi P, Nadas A, Giudicelli V, Lefranc M-P, Zolla-Pazner S, Gorny MK.
A broad range of mutations in HIV-1 neutralizing human monoclonal antibodies specific for V2, V3, and the CD4 binding site.
Mol Immunol. 2015 May 18;66(2):364-374. doi: 10.1016/j.molimm.2015.04.011. PMID: 25965315

Baliakas P, Agathangelidis A, Hadzidimitriou A, Sutton LA, Minga E, Tsanousa A, Scarfò L, Davis Z, Yan XJ, Shanafelt T, Plevova K, Sandberg Y, Vojdeman FJ, Boudjogra M, Tzenou T, Chatzouli M, Chu CC, Veronese S, Gardiner A, Mansouri L, Smedby KE, Pedersen LB, Moreno D, Van Lom K, Giudicelli V, Francova HS, Nguyen-Khac F, Panagiotidis P, Juliusson G, Angelis L, Anagnostopoulos A, Lefranc M-P, Facco M, Trentin L, Catherwood M, Montillo M, Geisler CH, Langerak AW, Pospisilova S, Chiorazzi N, Oscier D, Jelinek DF, Darzentas N, Belessi C, Davi F, Ghia P, Rosenquist R, Stamatopoulos K.
Not all IGHV3-21 chronic lymphocytic leukemias are equal: prognostic considerations.
Blood. 2015 Jan 29;125(5):856-9. doi: 10.1182/blood-2014-09-600874. PMID: 25634617

Xochelli A, Agathangelidis A, Kavakiotis I, Minga E, Sutton LA, Baliakas P, Chouvarda I, Giudicelli V, Vlahavas I, Maglaveras N, Bonello L, Trentin L, Tedeschi A, Panagiotidis P, Geisler C, Langerak AW, Pospisilova S, Jelinek DF, Oscier D, Chiorazzi N, Darzentas N, Davi F, Ghia P, Rosenquist R, Hadzidimitriou A, Belessi C, Lefranc M-P, Stamatopoulos K.
Immunoglobulin heavy variable (IGHV) genes and alleles: new entities, new names and implications for research and prognostication in chronic lymphocytic leukemia.
Immunogenetics. 2015 67(1):61-6.doi: 10.1007/s00251-014-0812-3. PMID: 25388851

Lefranc M-P, Giudicelli V, Duroux P, Jabado-Michaloud J, Folch G, Aouinti S, Carillon E, Duvergey H, Houles A, Paysan-Lafosse T, Hadi-Saljoqi S, Sasorith S, Lefranc G, Kossida S.
IMGT®, the international ImMunoGeneTics information system® 25 years on.
Nucleic Acids Res. 2015 Jan;43(Database issue):D413-22. doi: 10.1093/nar/gku1056. Free Article. PMID: 25378316

2014

Lefranc M-P.
Immunoglobulins: 25 years of Immunoinformatics and IMGT-ONTOLOGY.
Biomolecules. 2014, 4(4), 1102-1139; doi:10.3390/biom4041102 Open access. PMID: 25521638

Lefranc M-P.
IMGT® immunoglobulin repertoire analysis and antibody humanization.
In: Alt, F.W, Honjo, T, Radbruch A. and Reth, M. (Eds.), Molecular Biology of B cells, Second edition, Academic Press, Elsevier Ltd, London, UK, Chapter 26, 2014, pp. 481-514. dx.doi.org, ISBN : 978-0-12-397933-9.

Lefranc M-P.
How to use IMGT® for therapeutic antibody engineering
In: Dübel S, Reichert J (Eds), Handbook of Therapeutic Antibodies (4 vol.), Second edition, Wiley, Volume 1: Defining the right antibody composition, Chapter 10, 2014, pp. 229-264.

Shirai H, Prades C, Vita R, Marcatili P, Popovic B, Xu J, Overington JP, Hirayama K, Soga S, Tsunoyama K, Clark D, Lefranc M-P, Ikeda K.
Antibody informatics for drug discovery.
Biochim Biophys Acta. 2014 Nov;1844(11):2002-2015. pii: S1570-9639(14)00174-5. doi: 10.1016/j.bbapap.2014.07.006. PMID: 25110827

Lefranc M-P.
Immunoinformatics of the V, C, and G Domains: IMGT® Definitive System for IG, TR and IgSF, MH, and MhSF
Methods Mol Biol. 2014;1184:59-107. doi: 10.1007/978-1-4939-1115-8_4. PMID: 25048119

Gogoladze G, Grigolava M, Vishnepolsky B, Chubinidze M, Duroux P, Lefranc M-P, Pirtskhalava M.
DBAASP: Database of Antimicrobial Activity and Structure of Peptides
FEMS Microbiol Lett. 2014 Aug; 357(1):63-68. doi: 10.1111/1574-6968.12489. PMID: 24888447

Ciccarese S, Vaccarelli G, Lefranc M-P, Tasco G, Consiglio A, Casadio R, Linguiti G, Antonacci R.
Characteristics of the somatic hypermutation in the Camelus dromedarius T cell receptor gamma (TRG) and delta (TRD) variable domains.
Dev Comp Immunol. 2014 May Oct;46(2):300-313. doi: 10.1016/j.dci.2014.05.001. PMID: 24836674

Alamyar A, Giudicelli V, Duroux P, Lefranc M-P.
Antibody V and C domain sequence, structure and interaction analysis with special reference to IMGT®
In: Ossipow V and Fischer N. (Eds.), Monoclonal antibodies: Methods and Protocols, Second edition. Humana Press, Springer Science+Business Media, LLC, New York, USA. Methods Mol Biol. 2014.1131:337-81. doi: 10.1007/978-1-62703-992-5_21. PMID: 24515476

Lefranc M-P.
Antibody informatics: IMGT®, the international ImMunoGeneTics information system®, the international ImMunoGeneTics information system®
Microbiol Spectrum 2014, 2(2):AID-0001-2012. doi:10.1128/microbiolspec.AID-0001-2012.

Lefranc M-P.
Immunoglobulin (IG) and T cell receptor genes (TR): IMGT® and the birth and rise of immunoinformatics.
Front Immunol. 2014 Feb 05;5:22. doi: 10.3389/fimmu.2014.00022. Open access. PMID: 24600447

Ouled-Haddou H, Ghamlouch H, Regnier A, Trudel S, Herent D, Lefranc M-P, Marolleau J, Gubler B.
Characterization of a new V gene replacement in the absence of activation-induced cytidine deaminase and its contribution to human BcR diversity.
Immunology. 2014 Feb;141(2):268-75. doi: 10.1111/imm.12192. PMID: 24134819

2013

Six A, Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham H-P, Lefranc M-P, Mora T, Thomas-Vaslin V, Walczak AM, Boudinot P.
The past, present and future of immune repertoire biology - the rise of next-generation repertoire analysis.
Front Immunol. 2013 Nov 27;4:413. doi: 10.3389/fimmu.2013.00413 Open access. PMID: 24348479

Lefranc M-P.
IMGT Collier de Perles
In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds), Encyclopedia of Systems Biology, New York: Springer Science+Business Media, LLC, 2013, pp. 944-952.

Lefranc M-P.
IMGT unique numbering
In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds), Encyclopedia of Systems Biology, New York: Springer Science+Business Media, LLC, 2013, pp. 952-959.

Giudicelli V, Lefranc M-P.
IMGT-ONTOLOGY
In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds), Encyclopedia of Systems Biology, New York: Springer Science+Business Media, LLC, 2013, pp. 964-972.

Lefranc M-P.
IMGT® information system
In: Dubitzky W, Wolkenhauer O, Cho K-H, Yokota H (Eds), Encyclopedia of Systems Biology, Springer Science+Business Media, LLC, New York, 2013, pp. 959-964.

Li S, Lefranc M-P, Miles JJ, Alamyar E, Giudicelli V, Duroux, P, Freeman JD, Corbin VDA, Scheerlinck J-P, Frohman MA, Cameron PU, Plebanski M, Loveland B, Burrows SR, Papenfuss AT, Gowans EJ.
IMGT/HighV-QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling
Nat. Commun. 4:2333 doi: 10.1038/ncomms3333 (2013) Open access. PMID: 23995877

Lefranc M-P, Lefranc G.
Consanguinity In: Stanley Maloy and Kelly Hughes, editors. Brenner's Encyclopedia of Genetics 2nd edition, Vol 2. San Diego: Academic Press; 2013. pp. 158-162.

Castro R, Jouneau L, Pham HP, Bouchez O, Giudicelli V, Lefranc M-P, Quillet E, Benmansour A, Cazals F, Six A, Fillatreau S, Sunyer O, Boudinot P.
Teleost fish mount complex clonal IgM and IgT responses in spleen upon systemic viral infection
PLoS Pathog. 2013 Jan;9(1):e1003098. doi: 10.1371/journal.ppat.1003098. PMID: 23326228


Created 31/03/2016 (G. Folch)

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IMGT server environment french version

Computing environment

The IMGT® information system is localized at the Laboratoire d'ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH) of the Centre National de la Recherche Scientifique (CNRS), Montpellier, France.
IMGT/HighV-QUEST HPC resources are hosted at the Centre Informatique National de l'Enseignement Supérieur (CINES).

Software environment

Network environment

The Internet access is provided by the french academic network RENATER.

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IMGT® major historical steps french version

The project of an integrated system in Immunogenetics has been started in 1989 by Marie-Paule Lefranc, Professor Université de Montpellier, CNRS, Montpellier, France.

A prototype of the ImMunoGeneTics information system was developed in France for Immunoglobulin and T cell receptor sequences (LIGM-DB) by the Laboratoire d'ImmunoGénétique Moléculaire (LIGM, CNRS, Université de Montpellier, Montpellier), in collaboration with the Centre National Universitaire Sud de Calcul (CNUSC, Montpellier, Sophie Creuzet and Denys Chaume) and the Laboratoire d'Informatique, de Robotique et de Micro-électronique de Montpellier (LIRMM, CNRS, Université de Montpellier, Montpellier, Isabelle Mougenot and Patrice Déhais).

In 1992 the database became truly european with the collaboration of EMBL (Rainer Fuchs), IFG (Werner Müller), ICRF (Julia Bodmer) and the obtention of a EU European Union BIOMED1 funding (BIOCT930038).
IMGT/LIGM-DB is available on the Web server of CINES at Montpellier since July 1995. The first demonstration on-line was performed at the 9th International Congress of Immunology at San Francisco, USA (23-29 July 1995). IMGT/MHC-HLA, for human MH1 and MH2 (or HLA) sequences maintained by ANRI, London, is on the EBI server since December 1998.

IMGT®, the international ImMunoGeneTics information system®, enhanced its development through the European Community 5th PCRDT funding QLG2-2000-01287 (collaboration between LIGM, EMBL-EBI, Cancer Research UK, EUROGENTEC and BPRC), and then ImmunoGrid of the EU 6th PCRDT (IST-2004-028069). Since 2008, IMGT® is part of ELIXIR.

IMGT significant dates

1989

1993-1996

1995

1996-1999

1997

1998

1999

2000-2003

2001

2002

2003

2004

2005

2006

2007

2008

2009

2010

2014

2015

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IMGT executive and scientific committees french version

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Created : 15/07/1995
Last updated : Friday, 01-Apr-2016 14:08:33 CEST
Editor : Chantal Ginestoux, Amélie Houles.