IMGT®, biocuration of IG and TR in IMGT/LIGM-DB and IMGT/GENE-DB
Creators: name: Folch, Géraldine
name: Jabado-Michaloud, Joumana
name: Peralta, Marine
name: Arrivet, Mélanie
name: Imène Chentli
name: Cambon, Mélissa
name: Bento, Pascal
name: Souphatta Sasorith
name: Paysan-Lafosse, Typhaine
name: Duroux, Patrice
name: Giudicelli, Véronique
name: Kossida, Sofia
name: Marie-Paule Lefranc
Publisher: name: F1000Research
Year: 2016

description: IMGT®, the international ImMunoGeneTics information system, http://www.imgt.org, is the global reference in immunogenetics and immunoinformatics. By managing the extreme diversity and complexity of the antigen receptors of the adaptive immune response, the immunoglobulins (IG) or antibodies and the T cell receptors (TR) (2.1012 different specificities per individual), IMGT® is at the origin of immunoinformatics, a science at the interface between immunogenetics and bioinformatics. IMGT® is based on the concepts of IMGT-ONTOLOGY and these concepts are used for expert annotation and standardized knowledge in IMGT/LIGM-DB, the IMGT® database of IG and TR nucleotide sequences from human and other vertebrate species and in IMGT/GENE-DB, the IMGT® gene and allele database. The IMGT/LIGM-DB biocuration pipeline of IG and TR sequences includes IMGT/LIGMotif, for the analysis of large genomic DNA sequences, and IMGT/Automat, for the automatic annotation of rearranged cDNA sequences. Analysis results are checked for consistency, both manually and by using IMGT® tools (IMGT/NtiToVald, IMGT/V-QUEST, IMGT/BLAST, etc.). The annotated sequences are integrated in IMGT/LIGM-DB and include the sequence identification (IMGT® keywords), the gene and allele classification (IMGT® nomenclature), the constitutive and specific motif description (IMGT® labels in capital letters, no plural), the translation of the coding regions (IMGT® unique numbering). For genomic IMGT/LIGM-DB sequences containing either an IG or TR variable (V), diversity (D) or joining (J) gene in germline configuration or a constant (C) gene, the gene and allele information is entered in IMGT/GENE-DB. In parallel, the IMGT® Repertoire is updated (Locus representations, Gene tables and Protein displays (for new genes), Alignments of alleles (for new and/or confirmatory alleles)) and the IMGT® reference directory is completed (sequences used for gene and allele comparison and assignment in IMGT® tools (IMGT/V-QUEST, IMGT/HighV-QUEST for next generation sequencing (NGS), IMGT/DomainGapAlign) and databases (IMGT/2Dstructure-DB, IMGT/3Dstructure-DB). An IMGT/GENE-DB entry also provides information on the rearranged cDNA and gDNA entries (with links to IMGT/LIGM-DB) and on the three-dimensional structures (with links to IMGT/3Dstructure-DB). IMGT/GENE-DB is the official repository of IG and TR genes and alleles. IMGT® gene names were approved by HGNC and endorsed by WHO-IUIS, the World Health Organization (WHO)-International Union of Immunological Societies (IUIS) Nomenclature Subcommittee for IG and TR. Reciprocal links exist between IMGT/GENE-DB and HGNC, NCBI and Vega. The definition of antibodies published by the WHO International Nonproprietary Name (INN) Programme is based on the IMGT® concepts, and allows easy retrieval via IMGT/mAb-DB query. The IMGT® standardized annotation has allowed to bridge the gaps for IG or antibodies and TR between fundamental and medical research, veterinary research, repertoire analysis, biotechnology related to antibody engineering, diagnostics and therapeutical approaches.<br>