Resource description
IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org) is the global reference in immunogenetics and immunoinformatics, created in 1989 by Marie-Paule Lefranc (Université de Montpellier and CNRS).
IMGT® is a high-quality integrated knowledge resource specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) of human and other vertebrate species, and in the immunoglobulin superfamily (IgSF), MH superfamily (MhSF) and related proteins of the immune system (RPI) of vertebrates and invertebrates.
IMGT® provides a common access to sequence, genome and structure immunogenetics data, based on the concepts of IMGT-ONTOLOGY and on the IMGT Scientific chart rules. IMGT® works in close collaboration with EBI (Europe), DDBJ (Japan) and NCBI (USA).
More specifically, IMGT® uses the same accession numbers for nucleotide sequences as ENA, GenBank and DDBJ. IMGT genes are officially approved by HUGO Nomenclature Committee (HGNC) since 1999 and used by Ensembl and Vega (Hinxton, UK), NCBI Gene (all have direct links to IMGT/GENE-DB which is the international reference database for IG and TR genes).
IMGT® consists of 7 databases (IMGT/LIGM-DB, IMGT/GENE-DB, etc) and 17 online interactive tools for the analysis of sequences (IMGT/V-QUEST and its high throughput version IMGT/HighV-QUEST for next generation sequencing (NGS), IMGT/DomainGapAlign, etc.), and the analysis of genes and of three-dimensional (3D) structures. IMGT® also provides one standalone and more than 20,000 pages of Web resources.
A schematic representation of the data exchanges is provided in the figure given below. IMGT® resource is unique: there is no equivalent in the USA or elsewhere in the world.
Principal investigators:
Sofia KOSSIDA and
Marie-Paule LEFRANC
Sofia KOSSIDA is IMGT® Director since 01/01/2015, Professor Université de Montpellier.
Marie-Paule LEFRANC is IMGT® Founder, IMGT® Director for 25 years (since IMGT® creation in 1989 up to 2014), and currently IMGT® Executive Director Emeritus, Professor Emeritus Université de Montpellier.
Year of establishment
1989
Life cycle state :
Mature Stage: IMGT® is a mature ELIXIR Service. It is active and new data are currently integrated and reliable.
Overview :
The IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org) IMGT® consists of 7 databases (cylinders) and 17 tools (rectangles).
IMGT® also provides (not shown) IMGT/StatClonotype, a novel standalone tool which performs the statistical comparison of two sets of results from IMGT/HighV-QUEST for next generation sequencing (NGS) (500,000 sequences per batch) and more 20,000 pages de Web resources.
Access to the service/resource:
- Data provided by the French ELIXIR Node come from academic sources and are publicly available
Data provided by IMGT® come from academic sources and are publicly available. Six IMGT databases are publicly available to academic users: IMGT/LIGM-DB (the IMGT® nucleotide database (178,296 sequences from 351 species in October 2016), IMGT/PRIMER-DB (the IMGT®primer database), IMGT/GENE-DB (the IMGT® gene database (3,926 genes and 5,627 alleles from 24 species, of which 712 genes and 1,474 alleles for Homo sapiens and 868 genes and 1,317 alleles for Mus musculus in October 2016), IMGT/2Dstructure-DB (for antibodies and other proteins for which the 3D structure is not available) and IMGT/3Dstructure-DB (for 3D structures, contact analysis and paratope/epitope interactions of IG/antigen and TR/peptide-MH complexes), IMGT/mAb-DB (interface for therapeutic antibodies and fusion proteins for immune applications (FPIA). IMGT/CLL-DB, requires a password as it is a working place for a consortium of clinicians and contains sequences from patients prior to submission to generalist databases (ENA, GenBank, DDBJ) and publications.
- Tools are distributed with a business-friendly open source license
IMGT/StatClonotype, the IMGT® tool distributed as a standalone, is incorporated in the R package 'IMGTStatClonotype' under the LGPL licence. “The GNU Lesser General Public License (LGPL) is corporate-friendly and quite often used in R librairies. It allows for usage of certain library but modifications to it should be made public."
- Online services are freely accessible to users
IMGT® online services are freely accessible to academic users. IMGT interactive tools accessible from the IMGT® Home page comprise: IMGT/V-QUEST (analysis of rearranged nucleotide sequence) and its high-throughput version IMGT/HighV-QUEST (500,000 nucleotide sequences per batch), IMGT/JunctionAnalysis, IMGT/Allele-Align, IMGT/PhyloGene, IMGT/DomainDisplay (amino acid sequences), IMGT/LocusView, IMGT/GeneView, IMGT/GeneSearch, IMGT/CloneSearch, IMGT/GeneInfo, IMGT/GeneFrequency, IMGT/DomainGapAlign (for amino acid sequence analysis of IG and TR variable and constant domains, and of MH groove domains), IMGT/Collier-de-Perles (for domain graphical 2D representation), IMGT/DomainSuperimpose, IMGT/StructuralQuery (for 3D structures). A password is required from the IMGT/HighV-QUEST users as this portal requires important computational resources for which IMGT® needs to apply twice a year (GENCI). All the IMGT® reference directories are publicly available online.
Indicators used to measure the quality and impact of service/resource
IMGT® uses the indicators of its Quality Management System. IMGT® has been approved by Lloyd's Register Quality Assurance France SAS to the Quality Management System Standards:
ISO 9001:2008 since October, 18, 2010 and
NFX 50-900 since October 13, 2014.
“Research, development and provision of an integrated system (databases, tools and Web resources in immunogenetics and immunoinformatics”. These indicators are analyzed regularly, by the Pilots of the SMQ processes and every year in January at the Steering Committee.
Since the NFX certification, IMGT® has established Key Performance Indicators (KPI). These KPI will be reevaluated at the next Steering Committee in January 2017 to take into account the perspective of the NFX 50-900: 2016 and ISO 9001: 2015.
Scientific focus and quality of science are measured by the number of publications, participations to meetings, invitations, new external collaborations and new contracts.
Community served by the resource is measured by the annual survey (fundamental research, clinicians, biotechnology, big pharma, etc), e-mail exchanges, number of academic collaborations, educational workshops (IG-CLL), networks (EuroClonality), participation to education abroad on antibody informatics (USTH Hanoi, Vietnam), permanent education (Biocampus).
Quality of service is measured by the SMQ indicators (e.g., response time to user messages, survey).
Translational stories
IMGT® is in charge, since its creation in 1989 (HGM10, New Haven), of providing the international immunoglobulin (IG) and T cell receptor (TR) gene nomenclature for vertebrate species from fishes to humans.
By its creation in 1989, IMGT® marked the advent of immunoinformatics, which emerged at the interface between immunogenetics and bioinformatics. For the first time, immunoglobulin (IG) or antibody and T cell receptor (TR) variable (V), diversity (D), joining (J), and constant (C) genes were officially recognized as “genes” as well as the conventional genes. This major breakthrough allowed genes and data of the complex and highly diversified adaptive immune responses to be managed in genomic databases and tools.
The IMGT® Homo sapiens IG and TR gene names were approved by the Human Genome Organisation (HUGO) Nomenclature Committee (HGNC) in 1999 and were endorsed by the WHO–IUIS Nomenclature Subcommittee for IG and TR. The IMGT® IG and TR gene names are the official international reference and, as such, have been entered in IMGT/GENE-DB, in the Genome Database (GDB), in LocusLink at the National Center for Biotechnology Information (NCBI) USA, in Entrez Gene (NCBI) when this database (now designated as “Gene”) superseded LocusLink, in NCBI MapViewer, in Ensembl at the European Bioinformatics Institute (EBI), and in the Vertebrate Genome Annotation (Vega) Browser at the Wellcome Trust Sanger Institute (UK). HGNC, Gene NCBI, Ensembl, and Vega have direct links to IMGT/GENE-DB.
IMGT® human IG and TR genes were also integrated in IMGT-ONTOLOGY on the NCBO BioPortal and, on the same site, in the HUGO ontology and in the National Cancer Institute (NCI) Metathesaurus. Since 2007, IMGT® gene and allele names have been used for the description of the therapeutic mAb and FPIA of the WHO INN Programme. Amino acid sequences of human IG and TR constant genes (e.g., Homo sapiens IGHM, IGHG1, IGHG2) were provided to UniProt in 2008. The current collaboration has for aim the entry of the Homo sapiens germline IG variable genes in UniProt.
As an ELIXIR resource, IMGT® will actively pursue the current collaborations with the different genome databases of species newly sequenced and the laboratories engaged in the characterization of the IG and TR genes (UK, Italy, USA, etc.). Indeed the same IMGT concepts IDENTIFICATION (standardized keywords), DESCRIPTION (labels), CLASSIFICATION (gene and allele nomenclature), NUMEROTATION (IMGT unique numbering) and IMGT Scientific chart rules are used whatever the species from fishes to humans.
IMGT® is the international reference resource for standardized analysis of the adaptive immune responses in humans and other vertebrate species
IMGT® high-quality and integrated system provides the resource for the standardized analysis of the expressed IG and TR repertoire of the adaptive immune responses in humans and other vertebrate species (e.g., animal models). They are used in basic, veterinary, and medical research, and are at the forefront of major methodological advances and medical implications. Examples of clinical applications (mutation analysis in leukemia and lymphoma, NGS repertoire analysis of the adaptive immune responses) and of pharmaceutical research and biotechnology (therapeutic antibody engineering and humanization) are given below.
- Mutation analysis in leukemia and lymphoma
IMGT/V-QUEST is frequently used by clinicians for the analysis of IG somatic hypermutations in leukemia, lymphoma, and myeloma, and more particularly in chronic lymphocytic leukemia (CLL) in which a low percentage of mutations of the rearranged IGHV gene in the VH of the leukemic clone has a poor prognostic value for the patients. For this evaluation, IMGT/V-QUEST is the standard recommended by the European Research Initiative on CLL (ERIC) for comparative analysis between laboratories. The sequences of the V-(D)-J junctions determined by IMGT/JunctionAnalysis are also used in the characterization of stereotypic patterns in CLL and for the synthesis of probes specific of the junction for the detection and follow-up of minimal residual diseases (MRD) in leukemias and lymphomas. A new era is opening up in hemato-oncology with the use of NGS for analysis of the clonality and MRD identification, making IMGT® standards usage more needed as ever.
- NGS repertoire analysis of the adaptive immune responses
IMGT/HighV-QUEST is the first web portal for next generation sequencing (NGS) immunoprofiling (online since October 2010). It is a paradigm for identification of IMGT clonotype diversity and standardized comparison of the NGS IG and TR repertoire analysis (diversity and expression) of the adaptive immune responses in normal (vaccination) and pathological situations (infectious diseases, cancers).
- More than 10.7 billions of sequences analyzed to date (October 2016)
- 1862 users from 46 countries (46% from USA, 34% from EU, 20% from the remaining world)
- About 5.7 million hours of computational resources
- 255 terabytes of results generated.
IMGT® is the international reference resource for standardized analysis of therapeutic antibody and T cell receptor engineering and antibody humanization
The therapeutic monoclonal antibody engineering field represents the most promising potential in medicine. IMGT® standards usage is needed more than ever before in antibody humanization and engineering, IG and TR engineering for immunotherapy, search of new specificities and targets, paratope/epitope characterization as demonstrated by the IMGT/DomainGapAlign tool and the IMGT/2Dstructure-DB, IMGT/3Dstructure-DB and IMGT/mAb-DB databases. Indeed, a standardized analysis of IG genomic and expressed sequences, structures, and interactions is crucial for a better molecular understanding and comparison of the mAb specificity, affinity, half-life, Fc effector properties, and potential immunogenicity. IMGT-ONTOLOGY concepts have become a necessity for IG loci description of newly sequenced genomes, antibody structure/function characterization, antibody engineering [single chain Fragment variable (scFv), phage displays, combinatorial libraries] and antibody humanization (chimeric, humanized, and human antibodies). IMGT® standardization allows repertoire analysis and antibody humanization studies to move to novel high-throughput methodologies with the same high-quality criteria. The CDR-IMGT lengths are now required for mAb INN applications and are included in the WHO INN definitions, bringing a new level of standardized information in the comparative analysis of therapeutic antibodies.
Funding of the service/resource
(1) IMGT® is a team of the Institut de Génétique Humaine (UPR CNRS 1142). The permanent positions depend on the French Ministère de la Recherche et de l’Enseignement Supérieur. The present and former IMGT® directors are Professors of the Université de Montpellier. There are 7 permanent positions: 4 from the University (1 PU, 2 Emeritus PU, 1 research engineer IR) and 3 from CNRS (1 research engineer IR, 2 engineers IE).
(2) The salaries of the 8-10 CDD IE CNRS (biocurators, bioinformaticians) (turn-over of 3 years) are financed on pharmaceutical industry agreements with CNRS.
(3) Biocampus contributes to the renewal of PC and/or servers.
(4) IMGT/HighV-QUEST is granted access to the HPC@LR and to the High Performance Computing (HPC) resources of the Centre Informatique National de l’Enseignement Supérieur (CINES) and to Très Grand Centre de Calcul (TGCC) of the Commissariat l’Energie Atomique et aux Energies Alternatives (CEA) under the allocation [036029] (2010–2016) made by GENCI (Grand Equipement National de Calcul Intensif).
Previous funding sources include several EU grants (BIOMED, BIOTECH, 5th PCRDT, 7th PCRDT), IBiSA, ANR and Region Languedoc-Roussillon funding (listed on the web site).
SAB evaluating the resource
IMGT® has an international Scientific Committee since 1994. IMGT® is regularly evaluated scientifically by the SAB of the IGH.
Updates
IMGT® databases, tools and Web resources are constantly updated. New version numbers
and dates are indicated on the web site and the users have the possibility to subscribe to the IMGT news RSS to be informed.
Recent citations (over the last three years)
Aouinti S, Giudicelli V, Duroux P, Malouche D, Kossida S, Lefranc M-P. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST. Front Immunol. 2016 Sep 9;7:339. doi: 10.3389/fimmu.2016.00339. eCollection 2016. Free PMC Article. PMID: 27667992
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
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.
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
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. and 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.
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
Created 09/12/2016 (L. Picandet)
IMGT®, the international ImMunoGeneTics information system® (IFB-ReNaBi) 
Information | Infrastructure | Données | Outils | Expertise | Formations | Ouverture | Publications
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
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:
- Membre Académique Institutionnel de l'International Medical Informatics Association (IMIA).
- Membre de la Global Alliance for the Genomics and Health (GA4GH) depuis 2015.
Nationale:
- RIO depuis sa création en 2001, GIS IBiSA depuis sa création en 2007, ReNaBi depuis sa création.
- Labex MabImprove [ANR-10-LABX-53-01], GDR CNRS n° 3003 Molecular Bioinformatics (BiM), GDR CNRS n° 3260 Antibodies and Therapeutic targeting (ACCITH).
Interrégionale:
- Plateforme Bioinformatique du Cancéropôle Grand Sud-Ouest (GSO).
Régionale:
- SFR BioCampus Montpellier.
- Grand Plateau Technique pour la Recherche et l'Innovation Languedoc-Roussillon (GPTR), depuis la création des GPTR en 2005.
MARQUE DEPOSEE
IMGT® est une marque enregistrée CNRS (registered trademark) (Union Européenne, Canada, Etats-Unis).
STRUCTURE
CNRS
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 CNRS, 100%
Aouinti Safa, IE CDD CNRS, 100%
Cambon Mélissa, IE CDD CNRS, 100%
Chentli Imène, IE CDD CNRS, 100%
Kalyan Karthik, IE CDD CNRS, 100%
Lavoie Arthur, IE CDD CNRS, 100%
Lorenzi Claudio, IE CDD CNRS, 100%
Pegorier Perrine, IE CDD CNRS, 100%
Picandet Laurène, IE CDD CNRS, 100%
Saljoqi Saïda, IE CDD CNRS, 100%
Infrastructure
DESCRIPTION DES SERVEURS
- 1 serveur DELL/PE7250 (kappa) 2 processeurs 2 cœurs 4Go RAM, portail HTTP (IMGT, localisation IGH) 2004
- 1 serveur DELL/PE6850 (lambda) 2 processeurs 4 cœurs 8Go RAM, bases de données (IMGT, localisation IGH) 2006
- 1 serveur DELL/PE6850 (gamma) 4 processeurs 16 cœurs 32Go RAM, calcul (IMGT, localisation IGH) 2007
- 5 serveurs DELL/R200 (lef-beta1 à lef-beta5) 1 processeur 2 cœurs 4Go RAM, portail WebApp (IMGT, localisation IGH) 2009
- 1 serveur DELL/R710 (kappa2) 2 processeurs 12 cœurs 32Go RAM, utilisateurs (IMGT, localisation IGH) 2010
- 1 serveur DELL/R510 (delta) 1 processeurs 6 cœurs 1Go RAM, partage de fichiers (IMGT, localisation IGH) 2011
- 1 serveur DELL (pythie), bases de données (CINES) 2006
- 1 cluster IBM (yoda) 6.6 Tflop/s, 256 cœurs, calcul (CINES) 2012
- 1 cluster SGI ALTIX ICE (jade) 267 Tflop/s 23040 cœurs, calcul (CINES) 2011.
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).
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:
- Parcours «Bioinformatique, Connaissances, Données», http://www2.lirmm.fr/bcd/
Master Biologie-Agrosciences, Université de Montpellier:
- Parcours Sciences et procédés des agroressources pour l'alimentation et l'environnement (SPA2E)
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)
