IMGT®, the international ImMunoGeneTics information system®

logo IMGT

Information on IMGT®

IMGT® institutions french version

IMGT®, the international ImMunoGeneTics information system®, http://www.imgt.org, created in 1989 by Marie-Paule Lefranc in Montpellier, France (Laboratoire d'ImmunoGénétique Moléculaire (LIGM)), University of Montpellier(UM) and French National Center for Scientific Research (CNRS) has for mission to be the global reference in immunogenetics and immunoinformatics.

IMGT® is in charge, since its creation, of the International Union of Immunological Societies (IUIS) Nomenclature SubCommittee, IMGT-NC, for the nomenclature of the genes and alleles of the immunoglobulins (IG) or antibodies and T cell receptors (TR) of all vertebrate species with jaws (gnasthostomata).

IMGT® is attached to CNRS, to the University of Montpellier and to the Ministry of Higher Education, Research and Innovation (MESRI).

LIGM

Acknowledgments and Funding support

Livre d'Or

Sponsorships

IMGT® attachment and affiliation french version

International

National

Interregional

Regional

Certifications

  • HON Certification (since July 1999).
  • Quality management systems: ISO 9001:2008 (since October 2010), NFX 50-900, IQuaRe.

IMGT® authority: LIGM (Montpellier) french version

The Laboratoire d'ImmunoGénétique Moléculaire (LIGM) (Prof. Marie-Paule Lefranc and Prof. Gérard Lefranc), Université Montpellier 2, 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.

IMGT® information system overview french version

IMGT®, founded in Montpellier in 1989 by Marie-Paule Lefranc (Université Montpellier 2 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:

  • basic research,
  • medical research (analysis of repertoires of antibody and T cell receptor recognition sites in normal (infections, cancers) and abnormal (autoimmune diseases, immunodeficiencies) immune responses and in proliferative syndromes (leukemias, lymphomas, myelomas)),
  • veterinary research (study of the IG and TR repertoires in domestic and wild species),
  • genomic research (study of the diversity and evolution of genes of the adaptive immune response),
  • research in structural biology (evolution of IgSF and MhSF protein domains),
  • biotechnology related projects of the Human Proteome Organisation (HUPO) and antibody engineering (single chain variable fragment scFv, Fab, combinatorial libraries, phage display, chimeric, humanized and human antibodies),
  • diagnosis, prognosis and therapeutic monitoring of leukemias, lymphomas and myelomas (identification of the malignant clone(s) and assessment of residual diseases),
  • therapeutic approaches (grafts, immunotherapy, vaccinology).

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

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 Montpellier 2
IMGT, LIGM, IGH, UPR CNRS 1142, Montpellier (France)

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:

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 immunoinformaticsâ€�. 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 “genesâ€� 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 “Geneâ€�) 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.

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® 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, 8:1:2,
PMID: 23995877
PMID: 25378316
pdf
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)

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

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 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
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)

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

  • The operating system is Linux.
  • The Web servers are HTTP and Tomcat from The Apache Software Foundation.
  • The databases are hosted on Sybase system (Sybase Inc.) and MySQL™.
  • The programs are written in Java, Perl and Bourne shell.

Network environment

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

IMGT history french version

The project of an integrated system in Immunogenetics has been started in 1989 by Marie-Paule Lefranc, Professor Université Montpellier 2, 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 Montpellier 2, 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 Montpellier 2, 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

  • Creation of IMGT® at the Human Gene Mapping 10 Workshop (HGM10), New Haven (USA) (11-17 June 1989)

1993-1996

  • European Union BIOMED1 funding (BIOCT930038)

1995

  • IMGT/LIGM-DB on the Web, for the first time, at the 9th International Congress of Immunology (9,000 participants), San Francisco (USA) (23-29 July 1995)

1996-1999

  • European Union BIOTECH2 funding (BIO4CT960037)

1997

  • First IMGT Collier de Perles on the Web (April 1997)
  • IMGT/V-QUEST on the Web (07 July 1997)

1998

  • IMGT/MHC-HLA on the Web (December 1998)

1999

  • IMGT® has the honour, for its 10th anniversary, of the cover of the Nucleic Acids Research database issue (January 1999)
  • Nucleic Acids Res., 27:209-212 (1999), PMID: 9847182
  • All the human IG and TR genes are known and all the IMGT gene names are approved by the HUGO Nomenclature Committee (HGNC)

2000-2003

2001

  • IMGT® identified as operational RIO platform (Bioinformatics) at the French national level (CNRS, INSERM, CEA, INRA)
  • IMGT/GeneSearch, IMGT/GeneView andIMGT/LocusView on the Web (17 April 2001)
  • IMGT/JunctionAnalysis on the Web (17 june 2001)
  • IMGT/3Dstructure-DB on the Web (01 October 2001)
  • Nucleic Acids Res., 29:207-209 (2001), PMID: 11125093

2002

  • IMGT/StructuralQuery on the Web (15 January 2002)
  • IMGT/Phylogene on the Web (10 February 2002)
  • IMGT/PRIMER-DB on the Web (22 February 2002)
  • IMGT/MHC-NHP, IMGT/MHC-DLA and -FLA on the Web (April 2002)
  • NetWatch of Science "Blueprints of Immunity"  , Science, vol. 296, p. 1207 (17 May 2002)
  • IMGT/AlleleAlign on the Web (3 June 2002)

2003

  • Editorial "The International ImMunoGeneTics database IMGT", by Warr, G.W., Clem, W. and Söderhäll, K. Dev. Comp. Immunol. 27,1 (2003)   (27 January 2003)
  • IMGT/GENE-DB on the Web (31 January 2003)
  • ADER Prize for IMGT/PRIMER-DB implementation
  • Nucleic Acids Res., 31:307-310 (2003), PMID: 12520009

2004

  • IMGT/GeneInfo on the Web (14 January 2003)
  • IMGT 15 years ! at the 12th International Congress of Immunology, Montreal (Canada) (18-23 July 2004)
  • IMGT-Choreography funded as BioSTIC project
  • IMGT-ONTOLOGY for immunogenetics and immunoinformatics: In Silico Biol. 4:17-29 (2004). PMID: 15089751 pdf
  • ACI IMPBio 2004 IMGT project accepted pdf

2005

2006

2007

  • IMGT® received the label IBiSA
  • ACI IMPBio 2007 Poster pdf

2008

  • Formal IMGT-ONTOLOGY, IMGT-Kaleidoscope

2009

  • IMGT/mAb-DB (4 December 2009)
  • Nucleic Acids Res., 37:D1006-1012 (2009), PMID: 18978023

2010

  • IMGT® is certified ISO 9001:2008 (15 October 2010)
  • IMGT/HighV-QUEST on the Web (22 November 2010)

2014

  • IMGT® is certified NF X 50-900 (8 October 2014)

2015

  • Nucleic Acids Res., 43:D413-422 (2015), PMID: 25378316

Demonstrations of IMGT

2011July 17-1919th Annual International Conference on Intelligent Systems for Molecular Biology and 10th European Conference on Computational BiologyVienna, Austria
2010July 11-1318th Annual International Conference on Intelligent Systems for Molecular BiologyBoston, USA
2010May 18-2114th Human Genome Meeting - Next Generation Genomics and MedicineMontpellier, France
2009June 27 - July 217th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and 8th European Conference on Computational BiologyECCBStockholm, Sweden
2008September 22-26European Conference on Computational BiologyECCBCagliari, Sardinia-Italy
2004July 18-2312th International Congress of Immunology and 4th Annual Conference of FOCISMontreal, Canada
2002November 29Internet et Pédagogie Médicale, IPMLille, France
2000October 16-22Fête de la ScienceMontpellier, France
1999October 21-23Science en FêteMontpellier, France
1998October 23Salon ETIC, Université Montpellier IIMontpellier, France
1998January 4-9Pacific Symposium on BiocomputingHawaï, USA
1997October 10-12Science en FêteMontpellier, France
1996October 11-13Science en FêteMontpellier, France
1995July 22-299th International Congress of ImmunologySan Francisco, USA
1994December 15-16Réunion d'Automne de la SFIMontpellier, France
1994June 14-1712th European Immunology Meeting, EFIS 94Barcelona, Spain
1993November 14-17Human Genome Mapping Workshop 93, HGM 93Kobe, Japan

Reviews on IMGT

2007

IMGT®: un langage commun pour l'immunogénétique
In: INNOVATION, l'Economie de la croissance, Septembre-Octobre 2007, n° 10, p. 80.
IMGT®: un langage commun pour l'immunogénétique
In: INNOVATION, l'Economie de la croissance, n° 6, Janvier-Février 2007, p. 37.
Laboratoire d'ImmunoGénétique Moléculaire. IMGT®: un langage commun pour l'immunogénétique
In: Guide Européen de l'Innovation, site Internet du magazine Référence Innovation.

2006

IMGT®: a common language for immunogenetics
IMGT®: un langage commun pour l'immunogénétique
In: Reference INNOVATION, n° 5, November-December 2006, pp. 60-61.
IMGT®: un langage commun pour l'immunogénétique
In: Reference Business, Industries Sante/Agro, septembre/octobre 2006, n°11, p. 63.
IMGT®: un langage commun pour l'immunogénétique
In: Reference Business, Les industries de la santé, janvier/février 2006, n°8, p. 94.

2005

Cover of Tissue Antigens
Tissue Antigens, Vol 65, 6 issues (January 2005 to July 2005).

2004

WebWatch BioTechniques "French collection" pdficon
A WebWatch report on IMGT, by Kevin Ahern, BioTechniques Euro Edition, The Journal of Laboratory Technology for Bioresearch n° 66, p. 17 (July/August 2004).
Portail Institut Pasteur. Médiathèque. La sélection de la semaine: The international ImMunoGeneTics information system : IMGT
Novembre 2004.

2003

ADER Prize 2003 for IMGT/PRIMER-DB (LIGM and EUROGENTEC S.A.)
Life Sciences Prize for "Innovation-Research-Enterprise" by the Association for Education and Research Development (ADER).
The International ImMunoGeneTics database IMGT pdficon
Editorial by Warr G.W., Clem W. and Söderhall K. in Developmental Comparative Immunology (DCI) for the launch of the IMGT Locus in Focus section in DCI, in January 2003. Dev Comp. Immunol. 27,1 (2003) PMID: 12477495.
We thank Elsevier Science for allowing IMGT to make available, on the IMGT site, the PDF file of the Editorial.
IMGT
In: Nucleic Acids Research - The Molecular Biology Database Collection: 2003 update.

2002

NetWatch of Science "Blueprints of Immunity" pdficon
A NetWatch report on IMGT, by Mitch Leslie, Science, vol. 296, n°5571, p.1207 (17 May 2002).
Des nouvelles de l'IMGT, la base de données internationale en ImMunoGénéTique
La Gazette du Laboratoire n°64, p. 21 (2002).

2001

Compiling immune system data, Infrastructures, Contract BI04-CT96-0037
In: Biotechnology programme (1994-98) Project reports (Vol. 2), p. 84.
Quality of Life and management of living resources, European Commission EUR19405 (2001) ISBN: 92-894-0240-7.

2000

Genome Biology web report on IMGT "A high-quality database of molecules of the immune system"
A Genome Biology report by Christopher I. Thorpe.
Report date: 1st September 1999 - Published: 17 March 2000.
Genome Biology 2000 1:reports202.

1999

Cover page of Nucleic Acids Research For the 10th Anniversary of IMGT
Nucl. Acids Res., vol. 27 n°1 (January 1999) Database issue.
The cover features an example of IMGT/Colliers de Perles and 3D representation for T cell receptor V-REGIONs, available at IMGT, The international ImMunoGeneTics information system®, http://www.imgt.org, created in 1989 by Marie-Paule Lefranc, Montpellier, and described in the article on pp. 209-212 of this issue. Lefranc, M.-P. et al., Nucleic Acids Research, 27, 209-212 (1999) PMID: 9847182 LIGM:209.