Database

IMGT/GeneInfo: T cell receptor gamma TRG and delta TRD genes in database give access to all TR potential V(D)J recombinations

Thierry-Pascal Baum¹ , Vivien Hierle¹ , Nicolas Pasqual^2,5 , Fatena Bellahcene^2,5 , Denys Chaume³ , Marie-Paule Lefranc^3,4 , Evelyne Jouvin-Marche² , Patrice Noël Marche² and Jacques Demongeot¹

¹  Laboratoire TIMC-IMAG-CNRS UMR 5525, Techniques de l'Imagerie, de la Modélisation et de la Cognition; Université Joseph Fourier, Grenoble 1, Faculté de Médecine, Domaine de la Merci, 38706 La Tronche, France

²  Laboratoire d'Immunochimie, CEA-Grenoble/DRDC/ICH; INSERM U548; Université Joseph Fourier Grenoble 1, 17 rue des Martyrs, 38054 Grenoble Cedex 09, France

³  Laboratoire d'ImmunoGénétique Moléculaire, LIGM; Université Montpellier II, UPR CNRS 1142, IGH, 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France

⁴  Institut Universitaire de France, 103 Boulevard Saint-Michel, 75005 Paris, France

⁵  ImmunID Technologies, 17 rue des Martyrs, 38054 Grenoble Cedex 09, France

author email corresponding author email

BMC Bioinformatics 2006, 7:224doi:10.1186/1471-2105-7-224

Published:	26 April 2006

Abstract

Background

Adaptative immune repertoire diversity in vertebrate species is generated by recombination of variable (V), diversity (D) and joining (J) genes in the immunoglobulin (IG) loci of B lymphocytes and in the T cell receptor (TR) loci of T lymphocytes. These V-J and V-D-J gene rearrangements at the DNA level involve recombination signal sequences (RSS). Whereas many data exist, they are scattered in non specialized resources with different nomenclatures (eg. flat files) and are difficult to extract.

Description

IMGT/GeneInfo is an online information system that provides, through a user-friendly interface, exhaustive information resulting from the complex mechanisms of T cell receptor V-J and V-D-J recombinations. T cells comprise two populations which express the αβ and γδ TR, respectively. The first version of the system dealt with the Homo sapiens and Mus musculus TRA and TRB loci whose gene rearrangements allow the synthesis of the αβ TR chains. In this paper, we present the second version of IMGT/GeneInfo where we complete the database for the Homo sapiens and Mus musculus TRG and TRD loci along with the introduction of a quality control procedure for existing and new data. We also include new functionalities to the four loci analysis, giving, to date, a very informative tool which allows to work on V(D)J genes of all TR loci in both human and mouse species. IMGT/GeneInfo provides more than 59,000 rearrangement combinations with a full gene description which is freely available at http://imgt.cines.fr/GeneInfo webcite.

Conclusion

IMGT/GeneInfo allows all TR information sequences to be in the same spot, and are now available within two computer-mouse clicks. This is useful for biologists and bioinformaticians for the study of T lymphocyte V(D)J gene rearrangements and their applications in immune response analysis.