IMGT/V-QUEST: IMGT Standardized Analysis of the Immunoglobulin (IG) and T Cell Receptor (TR) Nucleotide Sequences

Abstract

INTRODUCTIONIMGT/V-QUEST is the integrated online IMGT tool for the standardized analysis of the immunoglobulin (IG) or antibody and T cell receptor (TR) rearranged nucleotide sequences. The analysis of these antigen receptors represents a crucial challenge for the study of the adaptative immune response in normal and disease-related situations. The expressed IG and TR repertoires represent a potential of 1012 IG and 1012 TR per individual. This huge diversity results from mechanisms that occur at the DNA level during IG molecular synthesis, including the combinatorial rearrangement of the variable (V), diversity (D), and joining (J) genes, the N diversity (V, D, and J exonuclease trimming and addition at random of nucleotides by the terminal deoxynucleotidyl transferase during the V-(D)-J rearrangement) and, for IG, somatic hypermutations. IMGT/V-QUEST, as described here, identifies the V, D, J genes and alleles by alignment with the germline IG and TR gene and allele sequences of the IMGT reference directory. The tool describes the V-REGION mutations and identifies the hot spot positions in the closest germline V gene. IMGT/V-QUEST integrates IMGT/JunctionAnalysis for a detailed analysis of the V-J and V-D-J junctions and IMGT/Automat for a complete sequence annotation of the sequences, and provides IMGT Collier de Perles.