Abstract
IMGT®, the international ImMunoGeneTics information system®, created in 1989, by Marie-Paule Lefranc (Université de Montpellier and CNRS), marked the advent of immunoinformatics, a new science which emerged at the interface between immunogenetics and bioinformatics for the study of the adaptive immune responses. IMGT® is based on a standardized nomenclature of the immunoglobulin (IG) and T cell receptor (TR) genes and alleles from fish to humans and on the IMGT unique numbering for the variable (V) and constant (C) domains of the immunoglobulin superfamily (IgSF) of vertebrates and invertebrates, and for the groove (G) domain of the major histocompatibility (MH) and MH superfamily (MhSF) proteins. IMGT® comprises 7 databases, 17 tools and more than 25,000 pages of web resources for sequences, genes and structures, based on the IMGT Scientific chart rules generated from the IMGT-ONTOLOGY axioms and concepts. IMGT® reference directories are used for the analysis of the NGS high-throughput expressed IG and TR repertoires (natural, synthetic and/or bioengineered) and for bridging sequences, two-dimensional (2D) and three-dimensional (3D) structures. This manuscript focuses on the IMGT® Homo sapiens IG and TR loci, gene order, copy number variation (CNV) and haplotypes new concepts, as a paradigm for jawed vertebrates genome assemblies.
Highlights
The adaptive immune response of the jawed vertebrates, which appeared in evolution about 450 million years ago is characterized by a remarkable immune specificity and memory, which are the properties of the B and T cells owing to an extreme diversity of their antigen receptors, the immunoglobulins (IG) or antibodies and the T cell receptors (TR), respectively [1]
IMGT®, http://www.imgt.org, the global reference in immunogenetics and immunoinformatics created by Marie-Paule Lefranc (LIGM, Université de Montpellier and CNRS), provides a unique scientific and computing frame for bridging loci, genes, alleles, sequences and structures of the IG or antibodies, TR and major histocompatibility (MH) of the adaptive immune responses in humans and in other jawed vertebrates [167–182]
The IMGT standards are used for the description of the polymorphisms [183–190], molecular mechanisms, genome evolution [191,192], susceptibility to diseases, autoimmunity, structure-functions, repertoire in infectious diseases [193–198], clonality and sequence analysis in leukemia and lymphoma [199–206], analysis of the content of the Fab and scFv combinatorial phage display libraries screened for identification of novel therapeutic antibody specificities [207–213], antibody engineering [5,23,26,42,45,47,50,196]
Summary
The adaptive immune response of the jawed vertebrates (or gnathostomata), which appeared in evolution about 450 million years ago is characterized by a remarkable immune specificity and memory, which are the properties of the B and T cells owing to an extreme diversity of their antigen receptors, the immunoglobulins (IG) or antibodies and the T cell receptors (TR), respectively [1]. The accuracy and the consistency of the IMGT data through the IMGT information system [1–5] are based on IMGT-ONTOLOGY [92–113], the first ontology for immunogenetics and immunoinformatics, and on the IMGT Scientific chart rules generated from its axioms and concepts [1] They include the controlled vocabulary and annotation rules that comprise the IMGT® standardized keywords (IDENTIFICATION axiom) [96], the IMGT® standardized labels (DESCRIPTION axiom) [97], the IMGT® gene and allele nomenclature (CLASSIFICATION axiom) [98], the IMGT® unique numbering [99–106] for variable V [101], constant C [102] and groove G [103] domains, and IMGT® Colliers de Perles [107–112] (NUMEROTATION axiom), with standardized IMGT physicochemical classes of the 20 common amino acids [113]. New IMGT genes and alleles, described with the IMGT nomenclature, IMGT unique numbering and IMGT standardized keywords and labels [1], enrich the IMGT® databases, tool reference directories and web resources for a better knowledge of natural IG and TR repertoires These data are used for the analysis of the generation sequencing (NGS) high-throughput expressed IG and TR repertoires (natural, synthetic and/or bioengineered) and for bridging sequences and two-dimensional (2D) and threedimensional (3D) structures. The human (Homo sapiens) IG and TR IMGT gene names [6,7] were approved by the Human Genome Organization (HUGO) Nomenclature Committee (HGNC) in 1999 [122] and entered in the NCBI gene database (first LocusLink, EntrezGene, superseded by Gene)
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