Géraldine Folch

IMGT/LIGM-DB, the IMGT® comprehensive database of immunoglobulin and T cell receptor nucleotide sequences

IMGT/LIGM-DB is the IMGT® comprehensive database of immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and other vertebrate species. It was created in 1989 by LIGM, Montpellier, France and is the oldest and the largest database of IMGT®. IMGT/LIGM-DB includes all germline (non-rearranged) and rearranged IG and TR genomic DNA (gDNA) and complementary DNA (cDNA) sequences published in generalist databases. IMGT/LIGM-DB allows searches from the Web interface according to biological and immunogenetic criteria through five distinct modules depending on the user interest. For a given entry, nine types of display are available including the IMGT flat file, the translation of the coding regions and the analysis by the IMGT/V-QUEST tool. IMGT/LIGM-DB distributes expertly annotated sequences. The annotations hugely enhance the quality and the accuracy of the distributed detailed information. They include the sequence identification, the gene and allele classification, the constitutive and specific motif description, the codon and amino acid numbering, and the sequence obtaining information, according to the main concepts of IMGT-ONTOLOGY. They represent the main source of IG and TR gene and allele knowledge stored in IMGT/GENE-DB and in the IMGT reference directory. IMGT/LIGM-DB is freely available at .

IMGT®, the international ImMunoGeneTics information system® 25 years on

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 (Université 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.

The human T cell receptor beta variable (TRBV) genes.

‘Human T Cell Receptor Beta Variable (TRBV) Genes’, the seventh report of the ‘IMGT Locus on Focus‘ section, comprises four tables: (1) ‘Number of human germline TRBV genes at 7q35 and potential repertoire’; (2) ‘Human germline TRBV genes at 7q35’; (3) ‘Human TRBV orphons on chromosome 9 (9p21)’, and (4) ‘Human TRBV allele table’. These tables are available at the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr: 8104) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.

Protein Displays of the Human T Cell Receptor Alpha, Beta, Gamma and Delta Variable and Joining Regions

‘Protein Displays of the Human T Cell Receptor Alpha, Beta, Gamma and Delta Variable and Joining Regions’, the 13th report of the ‘IMGT Locus in Focus’ section, comprises 8 figures: (1) ‘Protein display of the human TRA V-REGIONs’; (2) ‘Protein display of the human TRB V-REGIONs’; (3) ‘Protein display of the human TRG V-REGIONs’; (4) ‘Protein display of the human TRD V-REGIONs’; (5) ‘Protein display of the human TRA J-REGIONs’; (6) ‘Protein display of the human TRB J- REGIONs’; (7) ‘Protein display of the human TRG J-REGIONs’; (8) ‘Protein display of the human TRD J-REGIONs’, and 4 tables entitled: (1) ‘FR-IMGT and CDR-IMGT length of the human TRAV genes’; (2) ‘FR-IMGT and CDR-IMGT length of the human TRBV genes’; (3) ‘FR-IMGT and CDR-IMGT length of the human TRGV genes’; (4) ‘FR-IMGT and CDR-IMGT length of the human TRDV genes’. These figures and tables are available at the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http:// imgt.cines.fr:8104) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, Montpellier, France.

Nomenclature and Overview of the Mouse (Mus musculus and Mus sp.) Immunoglobulin Kappa (IGK) Genes

‘Nomenclature and overview of the mouse (Mus musculus and Mus sp.) immunoglobulin kappa (IGK) Genes’, the 19th report of the ‘IMGT Locus in Focus’ section, provides the first complete list of all the mouse (M. musculus) IGK genes. The mouse (M. musculus) locus spans 3,200 kb. The total number of mouse (M. musculus) IGK genes per haploid genome is 164 (174 if the orphons are included). The functional genomic repertoire comprises 93 IGKV belonging to 18 subgroups, 5 IGKJ and 1 IGKC gene. IMGT gene names and definitions of the mouse (M. musculus) IGK genes on chromosome 6 and IGK orphons are provided with the gene functionality and the number of alleles, according to the concepts of IMGT-ONTOLOGY and to rules of the IMGT Scientific chart, with the accession numbers of the IMGT reference sequences. These tables and figures are available at the IMGT Marie-Paule page of IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr) created by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.

The Human T Cell Receptor Beta Diversity (TRBD) and Beta Joining (TRBJ) Genes

‘Human T cell Receptor Beta Diversity (TRBD) and Beta Joining (TRBJ) Genes’, the 10th report of the ‘IMGT Locus in Focus’ section, comprises 6 tables: (1) ‘Human germline TRBD genes’; (2) ‘Human TRBD allele table’; (3) ‘Nucleotide and protein displays of the human TRBD alleles (overview)’; (4) ‘Human germline TRBJ genes’; (5) ‘Human TRBJ allele table’, and (6) ‘Nucleotide and protein displays of the human TRBJ alleles (overview)’. These tables are available on the IMGT Marie-Paule page from IMGT, the international ImMunoGeneTics database (http://imgt.cines.fr:8104) created in 1989 by Marie-Paule Lefranc, Université Montpellier II, CNRS, France.