Immunogenetics

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Marie-paule Lefranc - One of the best experts on this subject based on the ideXlab platform.

  • imgt biocuration and comparative study of the t cell receptor beta locus of veterinary species based on homo sapiens trb
    Frontiers in Immunology, 2020
    Co-Authors: Perrine Pegorier, Véronique Giudicelli, Géraldine Folch, Patrice Duroux, Morgane Bertignac, Imene Chentli, Viviane Nguefack Ngoune, Joumana Jabadomichaloud, Saida Hadisaljoqi, Marie-paule Lefranc
    Abstract:

    IMGT®, the international Immunogenetics information system® is the global reference in Immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Universite de Montpellier and CNRS), IMGT® marked the advent of immunoinformatics, which emerged at the interface between Immunogenetics and bioinformatics. IMGT® is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH), and proteins of the IgSF and MhSF superfamilies. T cell receptors are divided into two groups, αβ and γδ TR, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRβ locus (TRB) was recently described and annotated by IMGT® biocurators for several veterinary species, i.e., cat (Felis catus), dog (Canis lupus familiaris), ferret (Mustela putorius furo), pig (Sus scrofa), rabbit (Oryctolagus cuniculus), rhesus monkey (Macaca mulatta), and sheep (Ovis aries). The aim of the present study is to compare the genes of the TRB locus among these different veterinary species based on Homo sapiens. The results reveal that there are similarities but also differences including the number of genes by subgroup which may demonstrate duplications and/or deletions during evolution.

  • imgt the international Immunogenetics information system 25 years on
    Nucleic Acids Research, 2015
    Co-Authors: Marie-paule Lefranc, Véronique Giudicelli, Géraldine Folch, Patrice Duroux, Joumana Jabadomichaloud, Safa Aouinti, Emilie Carillon, Hugo Duvergey, Amelie Houles, Typhaine Paysanlafosse
    Abstract:

    IMGT(®), the international Immunogenetics information system(®)(http://www.imgt.org) is the global reference in Immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Universite de Montpellier and CNRS), IMGT(®) marked the advent of immunoinformatics, which emerged at the interface between Immunogenetics and bioinformatics. IMGT(®) is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT(®) is built on the IMGT-ONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGT(®) standardized keywords (identification), IMGT(®) standardized labels (description), IMGT(®) standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGT(®) comprises 7 databases, 17 online tools and 15,000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGT(®) is freely available at http://www.imgt.org.

  • Immunoinformatics of the V, C, and G domains: IMGT® definitive system for IG, TR and IgSF, MH, and MhSF.
    Methods in molecular biology (Clifton N.J.), 2014
    Co-Authors: Marie-paule Lefranc
    Abstract:

    By its creation in 1989, IMGT(®), the international Immunogenetics information system(®) ( http://www.imgt.org , CNRS and Universite Montpellier 2), marked the advent of immunoinformatics, which emerged at the interface between Immunogenetics and bioinformatics. IMGT(®) is the global reference in Immunogenetics and immunoinformatics. The accuracy and the consistency of the IMGT(®) data are based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts, which comprise IMGT standardized labels (DESCRIPTION), IMGT gene and allele nomenclature (CLASSIFICATION), IMGT unique numbering, and IMGT Collier de Perles (NUMEROTATION). The IMGT(®) standards have bridged the gap between genes, sequences, and three-dimensional (3D) structures for the receptors, chains, and domains. Started specifically for the immunoglobulins (IG) or antibodies and T cell receptors (TR), the IMGT-ONTOLOGY concepts have been extended to conventional genes of the immunoglobulin superfamily (IgSF) and major histocompatibility (MH) superfamily (MhSF), members of which are defined by the presence of at least one variable (V) or constant (C) domain, or two groove (G) domains, respectively. In this chapter, we review the IMGT(®) definitive system for the V, C, and G domains, based on the IMGT-ONTOLOGY concepts of IMGT unique numbering and IMGT Collier de Perles.

  • Immunogenetic sequence annotation based on IMGT-ONTOLOGY
    Nature Precedings, 2009
    Co-Authors: Joumana Jabado-michaloud, Véronique Giudicelli, Géraldine Folch, Fatena Bellahcene, François Ehrenmann, Patrice Duroux, Marie-paule Lefranc
    Abstract:

    IMGT founder and director: Marie-Paule Lefranc (Marie-Paule.Lefranc@igh.cnrs.fr) Bioinformatics manager: Veronique Giudicelli (Veronique.Giudicelli@igh.cnrs.fr) Computer manager: Patrice Duroux (Patrice.Duroux@igh.cnrs.fr) Interface design: Chantal Ginestoux (Chantal.Ginestoux@igh.cnrs.fr) © Copyright 1995-2009 IMGT®, the international Immunogenetics information system® IMGT® is funded by CNRS, MESR and EU ImmunoGrid IST-2004-028069 The DESCRIPTION axiom Immunogenetic sequence annotation based on IMGT-ONTOLOGY

  • Immunogenetic sequence annotation based on IMGT-ONTOLOGY
    Nature Precedings, 2009
    Co-Authors: Joumana Jabado-michaloud, Véronique Giudicelli, Géraldine Folch, Fatena Bellahcene, François Ehrenmann, Patrice Duroux, Marie-paule Lefranc
    Abstract:

    IMGT/LIGM-DB^1^ is the first and the largest IMGT^®^ database^2^ in which are managed, analysed and annotated more than 136,000 immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and 235 other vertebrate species (April 2009). The expert annotation of these sequences and the added standardized knowledge are based on IMGT-ONTOLOGY, the first ontology developed in the field of Immunogenetics and immunoinformatics.^3^ The annotation of immunogenetic sequences requires important expertise, owing to the unusual structure (non-classical exon/intron structure) of the IG and TR genes and characteristic chain synthesis owing to DNA V-J and V-D-J rearrangements. The way to annotate these sequences depends on the molecular type (gDNA, mRNA, cDNA or protein) and the configuration type (germline or rearranged), and if sequences from the concerned species are present or not in the IMGT reference directory sets. IMGT/V-QUEST^5^ and internal tools (IMGT/Automat, IMGT/LIGMotif, IMGT/BLAST and IMGT/DomainGapAlign) were developed. The first step in annotation allows to identify the chain type (for instance IG-Heavy) and to assign standardized keywords (IDENTIFICATION axiom). The second step is the classification of IG and TR genes and alleles (CLASSIFICATION axiom). The third step is the description (DESCRIPTION axiom) of the V, D, J and C genes and alleles with specific standardized labels. There are more than 590 IMGT standardized labels from which 64 have been entered in Sequence Ontology (SO). The delimitation of the FR-IMGT and CDR-IMGT lengths and the positions of conserved amino acids based on the IMGT unique numbering (NUMEROTATION axiom) allow to bridge the gap between sequences and 3D structures.^6^ The complete annotation of immunogenetic germline (V, D, J) and C sequences is followed by the update of the IMGT Repertoire (IMGT Gene tables, Alignments of alleles, Protein displays, Colliers de Perles, etc.), IMGT® gene database (IMGT/GENE-DB) and IMGT reference directory sets of the IMGT® tools (IMGT/V-QUEST, IMGT/JunctionAnalysis and IMGT/DomainGapAlign).

Bradley A. Mullens - One of the best experts on this subject based on the ideXlab platform.

  • MHC haplotype involvement in avian resistance to an ectoparasite
    Immunogenetics, 2008
    Co-Authors: Jeb P. Owen, Mary E. Delany, Bradley A. Mullens
    Abstract:

    Research on immune function in evolutionary ecology has frequently focused on avian ectoparasites (e.g., mites and lice). However, host Immunogenetics involved with bird resistance to ectoparasites has not been determined. The critical role of the major histocompatibility complex (MHC) in adaptive immunity and high genetic variation found within the MHC make this gene complex useful for exploring the immunogenetic basis for bird resistance to ectoparasites. The objective of this study was to determine if the avian MHC influenced resistance to a blood-feeding ectoparasite. Four congenic lines of chickens, differing only at the MHC, were comparatively infested with a cosmopolitan ectoparasite of birds—northern fowl mite (NFM)—which is also a serious pest species of poultry. Mite infestations were monitored over time and mite densities (weekly and maximum) were compared among lines. Chickens with the MHC haplotype B21 were relatively resistant to NFM, compared with birds in the B15 congenic line ( P  

  • MHC haplotype involvement in avian resistance to an ectoparasite.
    Immunogenetics, 2008
    Co-Authors: Jeb P. Owen, Mary E. Delany, Bradley A. Mullens
    Abstract:

    Research on immune function in evolutionary ecology has frequently focused on avian ectoparasites (e.g., mites and lice). However, host Immunogenetics involved with bird resistance to ectoparasites has not been determined. The critical role of the major histocompatibility complex (MHC) in adaptive immunity and high genetic variation found within the MHC make this gene complex useful for exploring the immunogenetic basis for bird resistance to ectoparasites. The objective of this study was to determine if the avian MHC influenced resistance to a blood-feeding ectoparasite. Four congenic lines of chickens, differing only at the MHC, were comparatively infested with a cosmopolitan ectoparasite of birds—northern fowl mite (NFM)—which is also a serious pest species of poultry. Mite infestations were monitored over time and mite densities (weekly and maximum) were compared among lines. Chickens with the MHC haplotype B21 were relatively resistant to NFM, compared with birds in the B15 congenic line (P < 0.02). To test for similar effects in an outbred genetic background, a separate experiment was performed with 107 commercial chickens (white leghorn, W-36 strain) infested with NFM. Hens were genotyped using a MHC microsatellite marker (LEI0258) and associations between MHC haplotype and NFM density were tested. The highest peak NFM populations occurred more often on hens with the B15 haplotype versus the B21 haplotype (P = 0.012), which supported the results of the congenic study. These data indicate the avian MHC influences ectoparasite resistance, which is relevant to disease ecology and avian–ectoparasite interaction.

Véronique Giudicelli - One of the best experts on this subject based on the ideXlab platform.

  • imgt biocuration and comparative study of the t cell receptor beta locus of veterinary species based on homo sapiens trb
    Frontiers in Immunology, 2020
    Co-Authors: Perrine Pegorier, Véronique Giudicelli, Géraldine Folch, Patrice Duroux, Morgane Bertignac, Imene Chentli, Viviane Nguefack Ngoune, Joumana Jabadomichaloud, Saida Hadisaljoqi, Marie-paule Lefranc
    Abstract:

    IMGT®, the international Immunogenetics information system® is the global reference in Immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Universite de Montpellier and CNRS), IMGT® marked the advent of immunoinformatics, which emerged at the interface between Immunogenetics and bioinformatics. IMGT® is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH), and proteins of the IgSF and MhSF superfamilies. T cell receptors are divided into two groups, αβ and γδ TR, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRβ locus (TRB) was recently described and annotated by IMGT® biocurators for several veterinary species, i.e., cat (Felis catus), dog (Canis lupus familiaris), ferret (Mustela putorius furo), pig (Sus scrofa), rabbit (Oryctolagus cuniculus), rhesus monkey (Macaca mulatta), and sheep (Ovis aries). The aim of the present study is to compare the genes of the TRB locus among these different veterinary species based on Homo sapiens. The results reveal that there are similarities but also differences including the number of genes by subgroup which may demonstrate duplications and/or deletions during evolution.

  • imgt the international Immunogenetics information system 25 years on
    Nucleic Acids Research, 2015
    Co-Authors: Marie-paule Lefranc, Véronique Giudicelli, Géraldine Folch, Patrice Duroux, Joumana Jabadomichaloud, Safa Aouinti, Emilie Carillon, Hugo Duvergey, Amelie Houles, Typhaine Paysanlafosse
    Abstract:

    IMGT(®), the international Immunogenetics information system(®)(http://www.imgt.org) is the global reference in Immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Universite de Montpellier and CNRS), IMGT(®) marked the advent of immunoinformatics, which emerged at the interface between Immunogenetics and bioinformatics. IMGT(®) is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT(®) is built on the IMGT-ONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGT(®) standardized keywords (identification), IMGT(®) standardized labels (description), IMGT(®) standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGT(®) comprises 7 databases, 17 online tools and 15,000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGT(®) is freely available at http://www.imgt.org.

  • Immunogenetic sequence annotation based on IMGT-ONTOLOGY
    Nature Precedings, 2009
    Co-Authors: Joumana Jabado-michaloud, Véronique Giudicelli, Géraldine Folch, Fatena Bellahcene, François Ehrenmann, Patrice Duroux, Marie-paule Lefranc
    Abstract:

    IMGT founder and director: Marie-Paule Lefranc (Marie-Paule.Lefranc@igh.cnrs.fr) Bioinformatics manager: Veronique Giudicelli (Veronique.Giudicelli@igh.cnrs.fr) Computer manager: Patrice Duroux (Patrice.Duroux@igh.cnrs.fr) Interface design: Chantal Ginestoux (Chantal.Ginestoux@igh.cnrs.fr) © Copyright 1995-2009 IMGT®, the international Immunogenetics information system® IMGT® is funded by CNRS, MESR and EU ImmunoGrid IST-2004-028069 The DESCRIPTION axiom Immunogenetic sequence annotation based on IMGT-ONTOLOGY

  • Immunogenetic sequence annotation based on IMGT-ONTOLOGY
    Nature Precedings, 2009
    Co-Authors: Joumana Jabado-michaloud, Véronique Giudicelli, Géraldine Folch, Fatena Bellahcene, François Ehrenmann, Patrice Duroux, Marie-paule Lefranc
    Abstract:

    IMGT/LIGM-DB^1^ is the first and the largest IMGT^®^ database^2^ in which are managed, analysed and annotated more than 136,000 immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and 235 other vertebrate species (April 2009). The expert annotation of these sequences and the added standardized knowledge are based on IMGT-ONTOLOGY, the first ontology developed in the field of Immunogenetics and immunoinformatics.^3^ The annotation of immunogenetic sequences requires important expertise, owing to the unusual structure (non-classical exon/intron structure) of the IG and TR genes and characteristic chain synthesis owing to DNA V-J and V-D-J rearrangements. The way to annotate these sequences depends on the molecular type (gDNA, mRNA, cDNA or protein) and the configuration type (germline or rearranged), and if sequences from the concerned species are present or not in the IMGT reference directory sets. IMGT/V-QUEST^5^ and internal tools (IMGT/Automat, IMGT/LIGMotif, IMGT/BLAST and IMGT/DomainGapAlign) were developed. The first step in annotation allows to identify the chain type (for instance IG-Heavy) and to assign standardized keywords (IDENTIFICATION axiom). The second step is the classification of IG and TR genes and alleles (CLASSIFICATION axiom). The third step is the description (DESCRIPTION axiom) of the V, D, J and C genes and alleles with specific standardized labels. There are more than 590 IMGT standardized labels from which 64 have been entered in Sequence Ontology (SO). The delimitation of the FR-IMGT and CDR-IMGT lengths and the positions of conserved amino acids based on the IMGT unique numbering (NUMEROTATION axiom) allow to bridge the gap between sequences and 3D structures.^6^ The complete annotation of immunogenetic germline (V, D, J) and C sequences is followed by the update of the IMGT Repertoire (IMGT Gene tables, Alignments of alleles, Protein displays, Colliers de Perles, etc.), IMGT® gene database (IMGT/GENE-DB) and IMGT reference directory sets of the IMGT® tools (IMGT/V-QUEST, IMGT/JunctionAnalysis and IMGT/DomainGapAlign).

  • IMGT, the international Immunogenetics information system.
    Nucleic acids research, 2008
    Co-Authors: Marie-paule Lefranc, Véronique Giudicelli, Joumana Jabado-michaloud, Géraldine Folch, Fatena Bellahcene, Chantal Ginestoux, Elodie Gemrot, Xavier Brochet, Jérôme Lane
    Abstract:

    IMGT, the international Immunogenetics information system (http://www.imgt.org), was created in 1989 by Marie-Paule Lefranc, Laboratoire d'ImmunoGénétique Moléculaire LIGM (Université Montpellier 2 and CNRS) at Montpellier, France, in order to standardize and manage the complexity of Immunogenetics data. The building of a unique ontology, IMGT-ONTOLOGY, has made IMGT the global reference in Immunogenetics and immunoinformatics. IMGT is a high-quality integrated knowledge resource specialized in the immunoglobulins or antibodies, T cell receptors, major histocompatibility complex, of human and other vertebrate species, proteins of the IgSF and MhcSF, and related proteins of the immune systems of any species. IMGT provides a common access to standardized data from genome, proteome, genetics and 3D structures. IMGT consists of five databases (IMGT/LIGM-DB, IMGT/GENE-DB, IMGT/3Dstructure-DB, etc.), fifteen interactive online tools for sequence, genome and 3D structure analysis, and more than 10,000 HTML pages of synthesis and knowledge. IMGT is used in medical research (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas and myelomas), veterinary research, biotechnology related to antibody engineering (phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (clonalities, detection and follow-up of residual diseases) and therapeutical approaches (graft, immunotherapy, vaccinology). IMGT is freely available at http://www.imgt.org.

Patrice Duroux - One of the best experts on this subject based on the ideXlab platform.

  • imgt biocuration and comparative study of the t cell receptor beta locus of veterinary species based on homo sapiens trb
    Frontiers in Immunology, 2020
    Co-Authors: Perrine Pegorier, Véronique Giudicelli, Géraldine Folch, Patrice Duroux, Morgane Bertignac, Imene Chentli, Viviane Nguefack Ngoune, Joumana Jabadomichaloud, Saida Hadisaljoqi, Marie-paule Lefranc
    Abstract:

    IMGT®, the international Immunogenetics information system® is the global reference in Immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Universite de Montpellier and CNRS), IMGT® marked the advent of immunoinformatics, which emerged at the interface between Immunogenetics and bioinformatics. IMGT® is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH), and proteins of the IgSF and MhSF superfamilies. T cell receptors are divided into two groups, αβ and γδ TR, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRβ locus (TRB) was recently described and annotated by IMGT® biocurators for several veterinary species, i.e., cat (Felis catus), dog (Canis lupus familiaris), ferret (Mustela putorius furo), pig (Sus scrofa), rabbit (Oryctolagus cuniculus), rhesus monkey (Macaca mulatta), and sheep (Ovis aries). The aim of the present study is to compare the genes of the TRB locus among these different veterinary species based on Homo sapiens. The results reveal that there are similarities but also differences including the number of genes by subgroup which may demonstrate duplications and/or deletions during evolution.

  • imgt the international Immunogenetics information system 25 years on
    Nucleic Acids Research, 2015
    Co-Authors: Marie-paule Lefranc, Véronique Giudicelli, Géraldine Folch, Patrice Duroux, Joumana Jabadomichaloud, Safa Aouinti, Emilie Carillon, Hugo Duvergey, Amelie Houles, Typhaine Paysanlafosse
    Abstract:

    IMGT(®), the international Immunogenetics information system(®)(http://www.imgt.org) is the global reference in Immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Universite de Montpellier and CNRS), IMGT(®) marked the advent of immunoinformatics, which emerged at the interface between Immunogenetics and bioinformatics. IMGT(®) is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT(®) is built on the IMGT-ONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGT(®) standardized keywords (identification), IMGT(®) standardized labels (description), IMGT(®) standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGT(®) comprises 7 databases, 17 online tools and 15,000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGT(®) is freely available at http://www.imgt.org.

  • Immunogenetic sequence annotation based on IMGT-ONTOLOGY
    Nature Precedings, 2009
    Co-Authors: Joumana Jabado-michaloud, Véronique Giudicelli, Géraldine Folch, Fatena Bellahcene, François Ehrenmann, Patrice Duroux, Marie-paule Lefranc
    Abstract:

    IMGT founder and director: Marie-Paule Lefranc (Marie-Paule.Lefranc@igh.cnrs.fr) Bioinformatics manager: Veronique Giudicelli (Veronique.Giudicelli@igh.cnrs.fr) Computer manager: Patrice Duroux (Patrice.Duroux@igh.cnrs.fr) Interface design: Chantal Ginestoux (Chantal.Ginestoux@igh.cnrs.fr) © Copyright 1995-2009 IMGT®, the international Immunogenetics information system® IMGT® is funded by CNRS, MESR and EU ImmunoGrid IST-2004-028069 The DESCRIPTION axiom Immunogenetic sequence annotation based on IMGT-ONTOLOGY

  • Immunogenetic sequence annotation based on IMGT-ONTOLOGY
    Nature Precedings, 2009
    Co-Authors: Joumana Jabado-michaloud, Véronique Giudicelli, Géraldine Folch, Fatena Bellahcene, François Ehrenmann, Patrice Duroux, Marie-paule Lefranc
    Abstract:

    IMGT/LIGM-DB^1^ is the first and the largest IMGT^®^ database^2^ in which are managed, analysed and annotated more than 136,000 immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and 235 other vertebrate species (April 2009). The expert annotation of these sequences and the added standardized knowledge are based on IMGT-ONTOLOGY, the first ontology developed in the field of Immunogenetics and immunoinformatics.^3^ The annotation of immunogenetic sequences requires important expertise, owing to the unusual structure (non-classical exon/intron structure) of the IG and TR genes and characteristic chain synthesis owing to DNA V-J and V-D-J rearrangements. The way to annotate these sequences depends on the molecular type (gDNA, mRNA, cDNA or protein) and the configuration type (germline or rearranged), and if sequences from the concerned species are present or not in the IMGT reference directory sets. IMGT/V-QUEST^5^ and internal tools (IMGT/Automat, IMGT/LIGMotif, IMGT/BLAST and IMGT/DomainGapAlign) were developed. The first step in annotation allows to identify the chain type (for instance IG-Heavy) and to assign standardized keywords (IDENTIFICATION axiom). The second step is the classification of IG and TR genes and alleles (CLASSIFICATION axiom). The third step is the description (DESCRIPTION axiom) of the V, D, J and C genes and alleles with specific standardized labels. There are more than 590 IMGT standardized labels from which 64 have been entered in Sequence Ontology (SO). The delimitation of the FR-IMGT and CDR-IMGT lengths and the positions of conserved amino acids based on the IMGT unique numbering (NUMEROTATION axiom) allow to bridge the gap between sequences and 3D structures.^6^ The complete annotation of immunogenetic germline (V, D, J) and C sequences is followed by the update of the IMGT Repertoire (IMGT Gene tables, Alignments of alleles, Protein displays, Colliers de Perles, etc.), IMGT® gene database (IMGT/GENE-DB) and IMGT reference directory sets of the IMGT® tools (IMGT/V-QUEST, IMGT/JunctionAnalysis and IMGT/DomainGapAlign).

  • imgt a system and an ontology that bridge biological and computational spheres in bioinformatics
    Briefings in Bioinformatics, 2008
    Co-Authors: Marie-paule Lefranc, Véronique Giudicelli, Laetitia Regnier, Patrice Duroux
    Abstract:

    IMGT, the international Immunogenetics information system (http://imgt.cines.fr), is the reference in Immunogenetics and immunoinformatics. IMGT standardizes and manages the complex immunogenetic data that include the immunoglobulins (IG) or antibodies, theT cell receptors (TR), the major histocompatibility complex (MHC) and the related proteins of the immune system (RPI), which belong to the immunoglobulin superfamily (IgSF) and the MHC superfamily (MhcSF). The accuracy and consistency of IMGT data and the coherence between the different IMGT components (databases, tools and Web resources) are based on IMGT-ONTOLOGY, the first ontology for Immunogenetics and immunoinformatics. IMGT-ONTOLOGY manages the Immunogenetics knowledge through diverse facets relying on seven axioms, ‘IDENTIFICATION’, ‘DESCRIPTION’, ‘CLASSIFICATION’, ‘NUMEROTATION’, ‘LOCALIZATION’, ‘ORIENTATION’ and ‘OBTENTION’, that postulate that objects, processes and relations have to be identified, described, classified, numerotated, localized, orientated, and that the way they are obtained has to be determined. These axioms constitute the Formal IMGT-ONTOLOGY, also designated as IMGT-Kaleidoscope. These axioms have been essential for the conceptualization of the molecular Immunogenetics knowledge and for the creation of IMGT. Indeed all the components of the IMGT integrated system have been developed, based on standardized concepts and relations, thus allowing IMGT to bridge biological and computational spheres in bioinformatics. The same axioms can be used to generate concepts for multi-scale level approaches at the molecule, cell, tissue, organ, organism or population level, emphasizing the generalization of the application domain. In that way the Formal IMGT-ONTOLOGYrepresents a paradigm for the elaboration of ontologies in system biology.

Géraldine Folch - One of the best experts on this subject based on the ideXlab platform.

  • imgt biocuration and comparative study of the t cell receptor beta locus of veterinary species based on homo sapiens trb
    Frontiers in Immunology, 2020
    Co-Authors: Perrine Pegorier, Véronique Giudicelli, Géraldine Folch, Patrice Duroux, Morgane Bertignac, Imene Chentli, Viviane Nguefack Ngoune, Joumana Jabadomichaloud, Saida Hadisaljoqi, Marie-paule Lefranc
    Abstract:

    IMGT®, the international Immunogenetics information system® is the global reference in Immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Universite de Montpellier and CNRS), IMGT® marked the advent of immunoinformatics, which emerged at the interface between Immunogenetics and bioinformatics. IMGT® is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH), and proteins of the IgSF and MhSF superfamilies. T cell receptors are divided into two groups, αβ and γδ TR, which express distinct TR containing either α and β, or γ and δ chains, respectively. The TRβ locus (TRB) was recently described and annotated by IMGT® biocurators for several veterinary species, i.e., cat (Felis catus), dog (Canis lupus familiaris), ferret (Mustela putorius furo), pig (Sus scrofa), rabbit (Oryctolagus cuniculus), rhesus monkey (Macaca mulatta), and sheep (Ovis aries). The aim of the present study is to compare the genes of the TRB locus among these different veterinary species based on Homo sapiens. The results reveal that there are similarities but also differences including the number of genes by subgroup which may demonstrate duplications and/or deletions during evolution.

  • imgt the international Immunogenetics information system 25 years on
    Nucleic Acids Research, 2015
    Co-Authors: Marie-paule Lefranc, Véronique Giudicelli, Géraldine Folch, Patrice Duroux, Joumana Jabadomichaloud, Safa Aouinti, Emilie Carillon, Hugo Duvergey, Amelie Houles, Typhaine Paysanlafosse
    Abstract:

    IMGT(®), the international Immunogenetics information system(®)(http://www.imgt.org) is the global reference in Immunogenetics and immunoinformatics. By its creation in 1989 by Marie-Paule Lefranc (Universite de Montpellier and CNRS), IMGT(®) marked the advent of immunoinformatics, which emerged at the interface between Immunogenetics and bioinformatics. IMGT(®) is specialized in the immunoglobulins (IG) or antibodies, T cell receptors (TR), major histocompatibility (MH) and proteins of the IgSF and MhSF superfamilies. IMGT(®) is built on the IMGT-ONTOLOGY axioms and concepts, which bridged the gap between genes, sequences and 3D structures. The concepts include the IMGT(®) standardized keywords (identification), IMGT(®) standardized labels (description), IMGT(®) standardized nomenclature (classification), IMGT unique numbering and IMGT Colliers de Perles (numerotation). IMGT(®) comprises 7 databases, 17 online tools and 15,000 pages of web resources, and provides a high-quality and integrated system for analysis of the genomic and expressed IG and TR repertoire of the adaptive immune responses, including NGS high-throughput data. Tools and databases are used in basic, veterinary and medical research, in clinical applications (mutation analysis in leukemia and lymphoma) and in antibody engineering and humanization. The IMGT/mAb-DB interface was developed for therapeutic antibodies and fusion proteins for immunological applications (FPIA). IMGT(®) is freely available at http://www.imgt.org.

  • Immunogenetic sequence annotation based on IMGT-ONTOLOGY
    Nature Precedings, 2009
    Co-Authors: Joumana Jabado-michaloud, Véronique Giudicelli, Géraldine Folch, Fatena Bellahcene, François Ehrenmann, Patrice Duroux, Marie-paule Lefranc
    Abstract:

    IMGT founder and director: Marie-Paule Lefranc (Marie-Paule.Lefranc@igh.cnrs.fr) Bioinformatics manager: Veronique Giudicelli (Veronique.Giudicelli@igh.cnrs.fr) Computer manager: Patrice Duroux (Patrice.Duroux@igh.cnrs.fr) Interface design: Chantal Ginestoux (Chantal.Ginestoux@igh.cnrs.fr) © Copyright 1995-2009 IMGT®, the international Immunogenetics information system® IMGT® is funded by CNRS, MESR and EU ImmunoGrid IST-2004-028069 The DESCRIPTION axiom Immunogenetic sequence annotation based on IMGT-ONTOLOGY

  • Immunogenetic sequence annotation based on IMGT-ONTOLOGY
    Nature Precedings, 2009
    Co-Authors: Joumana Jabado-michaloud, Véronique Giudicelli, Géraldine Folch, Fatena Bellahcene, François Ehrenmann, Patrice Duroux, Marie-paule Lefranc
    Abstract:

    IMGT/LIGM-DB^1^ is the first and the largest IMGT^®^ database^2^ in which are managed, analysed and annotated more than 136,000 immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and 235 other vertebrate species (April 2009). The expert annotation of these sequences and the added standardized knowledge are based on IMGT-ONTOLOGY, the first ontology developed in the field of Immunogenetics and immunoinformatics.^3^ The annotation of immunogenetic sequences requires important expertise, owing to the unusual structure (non-classical exon/intron structure) of the IG and TR genes and characteristic chain synthesis owing to DNA V-J and V-D-J rearrangements. The way to annotate these sequences depends on the molecular type (gDNA, mRNA, cDNA or protein) and the configuration type (germline or rearranged), and if sequences from the concerned species are present or not in the IMGT reference directory sets. IMGT/V-QUEST^5^ and internal tools (IMGT/Automat, IMGT/LIGMotif, IMGT/BLAST and IMGT/DomainGapAlign) were developed. The first step in annotation allows to identify the chain type (for instance IG-Heavy) and to assign standardized keywords (IDENTIFICATION axiom). The second step is the classification of IG and TR genes and alleles (CLASSIFICATION axiom). The third step is the description (DESCRIPTION axiom) of the V, D, J and C genes and alleles with specific standardized labels. There are more than 590 IMGT standardized labels from which 64 have been entered in Sequence Ontology (SO). The delimitation of the FR-IMGT and CDR-IMGT lengths and the positions of conserved amino acids based on the IMGT unique numbering (NUMEROTATION axiom) allow to bridge the gap between sequences and 3D structures.^6^ The complete annotation of immunogenetic germline (V, D, J) and C sequences is followed by the update of the IMGT Repertoire (IMGT Gene tables, Alignments of alleles, Protein displays, Colliers de Perles, etc.), IMGT® gene database (IMGT/GENE-DB) and IMGT reference directory sets of the IMGT® tools (IMGT/V-QUEST, IMGT/JunctionAnalysis and IMGT/DomainGapAlign).

  • IMGT, the international Immunogenetics information system.
    Nucleic acids research, 2008
    Co-Authors: Marie-paule Lefranc, Véronique Giudicelli, Joumana Jabado-michaloud, Géraldine Folch, Fatena Bellahcene, Chantal Ginestoux, Elodie Gemrot, Xavier Brochet, Jérôme Lane
    Abstract:

    IMGT, the international Immunogenetics information system (http://www.imgt.org), was created in 1989 by Marie-Paule Lefranc, Laboratoire d'ImmunoGénétique Moléculaire LIGM (Université Montpellier 2 and CNRS) at Montpellier, France, in order to standardize and manage the complexity of Immunogenetics data. The building of a unique ontology, IMGT-ONTOLOGY, has made IMGT the global reference in Immunogenetics and immunoinformatics. IMGT is a high-quality integrated knowledge resource specialized in the immunoglobulins or antibodies, T cell receptors, major histocompatibility complex, of human and other vertebrate species, proteins of the IgSF and MhcSF, and related proteins of the immune systems of any species. IMGT provides a common access to standardized data from genome, proteome, genetics and 3D structures. IMGT consists of five databases (IMGT/LIGM-DB, IMGT/GENE-DB, IMGT/3Dstructure-DB, etc.), fifteen interactive online tools for sequence, genome and 3D structure analysis, and more than 10,000 HTML pages of synthesis and knowledge. IMGT is used in medical research (autoimmune diseases, infectious diseases, AIDS, leukemias, lymphomas and myelomas), veterinary research, biotechnology related to antibody engineering (phage displays, combinatorial libraries, chimeric, humanized and human antibodies), diagnostics (clonalities, detection and follow-up of residual diseases) and therapeutical approaches (graft, immunotherapy, vaccinology). IMGT is freely available at http://www.imgt.org.