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IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling

Author

Listed:
  • Shuo Li

    (The University of Melbourne
    Burnet Institute
    Monash University)

  • Marie-Paule Lefranc

    (IMGT, the international ImMunoGeneTics information system, Université Montpellier 2, Institut de Génétique Humaine, UPR CNRS, 1142)

  • John J. Miles

    (Queensland Institute of Medical Research
    Institute of Infection and Immunity, Cardiff University
    School of Medicine, University of Queensland)

  • Eltaf Alamyar

    (IMGT, the international ImMunoGeneTics information system, Université Montpellier 2, Institut de Génétique Humaine, UPR CNRS, 1142)

  • Véronique Giudicelli

    (IMGT, the international ImMunoGeneTics information system, Université Montpellier 2, Institut de Génétique Humaine, UPR CNRS, 1142)

  • Patrice Duroux

    (IMGT, the international ImMunoGeneTics information system, Université Montpellier 2, Institut de Génétique Humaine, UPR CNRS, 1142)

  • J. Douglas Freeman

    (Michael Smith Genome Sciences Centre)

  • Vincent D. A. Corbin

    (The Walter & Eliza Hall Institute of Medical Research
    University of Melbourne)

  • Jean-Pierre Scheerlinck

    (Centre for Animal Biotechnology, University of Melbourne)

  • Michael A. Frohman

    (Stony Brook University)

  • Paul U. Cameron

    (Burnet Institute)

  • Magdalena Plebanski

    (Monash University)

  • Bruce Loveland

    (Burnet Institute
    Monash University)

  • Scott R. Burrows

    (Queensland Institute of Medical Research)

  • Anthony T. Papenfuss

    (The Walter & Eliza Hall Institute of Medical Research
    University of Melbourne
    University of Melbourne)

  • Eric J. Gowans

    (Burnet Institute
    Discipline of Surgery, University of Adelaide)

Abstract

T cell repertoire diversity and clonotype follow-up in vaccination, cancer, infectious and immune diseases represent a major challenge owing to the enormous complexity of the data generated. Here we describe a next generation methodology, which combines 5′RACE PCR, 454 sequencing and, for analysis, IMGT, the international ImMunoGeneTics information system (IMGT), IMGT/HighV-QUEST web portal and IMGT-ONTOLOGY concepts. The approach is validated in a human case study of T cell receptor beta (TRB) repertoire, by chronologically tracking the effects of influenza vaccination on conventional and regulatory T cell subpopulations. The IMGT/HighV-QUEST paradigm defines standards for genotype/haplotype analysis and characterization of IMGT clonotypes for clonal diversity and expression and achieves a degree of resolution for next generation sequencing verifiable by the user at the sequence level, while providing a normalized reference immunoprofile for human TRB.

Suggested Citation

  • Shuo Li & Marie-Paule Lefranc & John J. Miles & Eltaf Alamyar & Véronique Giudicelli & Patrice Duroux & J. Douglas Freeman & Vincent D. A. Corbin & Jean-Pierre Scheerlinck & Michael A. Frohman & Paul , 2013. "IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling," Nature Communications, Nature, vol. 4(1), pages 1-13, December.
    • Handle: RePEc:nat:natcom:v:4:y:2013:i:1:d:10.1038_ncomms3333
    DOI: 10.1038/ncomms3333
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    Cited by:

    1. Safa Aouinti & Dhafer Malouche & Véronique Giudicelli & Sofia Kossida & Marie-Paule Lefranc, 2015. "IMGT/HighV-QUEST Statistical Significance of IMGT Clonotype (AA) Diversity per Gene for Standardized Comparisons of Next Generation Sequencing Immunoprofiles of Immunoglobulins and T Cell Receptors," PLOS ONE, Public Library of Science, vol. 10(11), pages 1-22, November.
    2. Ulrike Menzel & Victor Greiff & Tarik A Khan & Ulrike Haessler & Ina Hellmann & Simon Friedensohn & Skylar C Cook & Mark Pogson & Sai T Reddy, 2014. "Comprehensive Evaluation and Optimization of Amplicon Library Preparation Methods for High-Throughput Antibody Sequencing," PLOS ONE, Public Library of Science, vol. 9(5), pages 1-12, May.

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