Abstract
BackgroundAdaptative 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.DescriptionIMGT/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 .ConclusionIMGT/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.
Highlights
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
The TR genes are located in four loci, designated as TRA, TRB, TRG and T cell receptor delta (TRD) which contribute to the synthesis of the alpha, beta, gamma and delta chains, respectively[2,5,6]
We are extending to the Homo sapiens and Mus musculus TRG and TRD loci whose gene rearrangements allow the synthesis of the two γ and δ chains of the TR [2,6]
Summary
IMGT/GeneInfo is an information system dedicated to immunogenetic sequences It summarizes the publicly existing available information on human and mouse V(D)J recombinations. IMGT/GeneInfo extension to the Homo sapiens and Mus musculus TRD and TRG loci will be helpful for users to gather pertinent information about antigen receptor genes which is required to accurately describe the αβ or γδ T cells. This integrated bioinformatics information system will allow a rapid and secure selection of all TR DNA sequences to study the rearrangement frequency by molecular approaches such as Southern blot, real time PCR, multiplex PCR or microarray assays.
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