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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

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Immunogenetics

Part of the book series: Methods in Molecular Biology ((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.

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Acknowledgements

We are grateful to Gérard Lefranc for helpful discussion and to the IMGT® team for its expertise and constant motivation. IMGT® received funding from Centre National de la Recherche Scientifique CNRS, Ministère de l’Enseignement Supérieur et de la Recherche MESR (University Montpellier 2), Région Languedoc-Roussillon (GPTR, GEPETOS), Agence Nationale de la Recherche ANR (ANR-06-BYOS-0005-01), and European Community (ImmunoGrid, FP6-2004-IST-4). This work was granted access to the HPC resources of CINES under the allocations 2010-036029 and 2011-036029 made by GENCI (Grand Equipement National de Calcul Intensif).

Author information

Authors and Affiliations

  1. IMGT®, the International ImMunoGeneTics Information System®, Université Montpellier 2, Laboratoire d’ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UPR CNRS 1142, Montpellier, France

    Eltaf Alamyar

  2. IMGT®, The International ImMunoGeneTics Information System®, Université Montpellier 2, Laboratoire d’ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UPR CNRS 1142, Montpellier, France

    Patrice Duroux & Véronique Giudicelli

  3. IMGT®, The International ImMunoGeneTics Information System®, Université Montpellier 2, Laboratoire d’ImmunoGénétique Moléculaire (LIGM), Institut de Génétique Humaine (IGH), UPR CNRS1142, Montpellier, France

    Marie-Paule Lefranc

Authors
  1. Eltaf Alamyar
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  2. Patrice Duroux
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  3. Marie-Paule Lefranc
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  4. Véronique Giudicelli
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Corresponding author

Correspondence to Marie-Paule Lefranc .

Editor information

Editors and Affiliations

  1. PathWest Laboratory Medicine, Department of Clinical Immunology, Royal Perth Hospital, Wellington Street, Perth, 6000, Australia

    Frank T. Christiansen

  2. Australian Red Cross Blood Service, National Transplant Services, The Royal Melbourne Hospital, 150-154 Batman Street, Melbourne VIC, 3000, Australia

    Brian D. Tait

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Alamyar, E., Duroux, P., Lefranc, MP., Giudicelli, V. (2012). 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. In: Christiansen, F., Tait, B. (eds) Immunogenetics. Methods in Molecular Biology, vol 882. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-61779-842-9_32

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  • DOI: https://doi.org/10.1007/978-1-61779-842-9_32

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  • Publisher Name: Humana Press, Totowa, NJ

  • Print ISBN: 978-1-61779-841-2

  • Online ISBN: 978-1-61779-842-9

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