Immunogenetics pp 569-604 | Cite as

IMGT® Tools for the Nucleotide Analysis of Immunoglobulin (IG) and T Cell Receptor (TR) V-(D)-J Repertoires, Polymorphisms, and IG Mutations: IMGT/V-QUEST and IMGT/HighV-QUEST for NGS

  • Eltaf Alamyar
  • Patrice Duroux
  • Marie-Paule Lefranc
  • Véronique Giudicelli
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 882)

Abstract

IMGT/V-QUEST is the highly customized and 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 adaptive 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 the IG and TR molecular synthesis. These mechanisms include the combinatorial rearrangements of the variable (V), diversity (D) and joining (J) genes, the N-diversity (deletion and addition at random of nucleotides during the V-(D)-J rearrangement) and, for IG, somatic hypermutations. IMGT/V-QUEST 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 annotation of the sequences and also provides IMGT Collier de Perles. IMGT/HighV-QUEST, the high-throughput version of IMGT/V-QUEST, implemented to answer the needs of deep sequencing data analysis from Next Generation Sequencing (NGS), allows the analysis of thousands of IG and TR sequences in a single run. IMGT/V-QUEST and IMGT/HighV-QUEST are available at the IMGT® Home page, http://www.imgt.org.

Key words

IMGT Immunogenetics Immunoinformatics Immunoglobulin Antibody T cell receptor Somatic hypermutation Allelic polymorphism High-throughput sequencing IMGT-ONTOLOGY 

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Copyright information

© Springer Science+Business Media, LLC 2012

Authors and Affiliations

  • Eltaf Alamyar
    • 1
  • Patrice Duroux
    • 2
  • Marie-Paule Lefranc
    • 3
  • Véronique Giudicelli
    • 2
  1. 1.IMGT®, the International ImMunoGeneTics Information System®Université Montpellier 2, Laboratoire d’ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UPR CNRS 1142MontpellierFrance
  2. 2.IMGT®, The International ImMunoGeneTics Information System®Université Montpellier 2, Laboratoire d’ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UPR CNRS 1142MontpellierFrance
  3. 3.IMGT®, The International ImMunoGeneTics Information System®Université Montpellier 2, Laboratoire d’ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UPR CNRS1142MontpellierFrance

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