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

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 U. Cameron, Magdalena Plebanski, Bruce Loveland, Scott R. Burrows, Anthony T. Papenfuss and Eric J. Gowans ()
Additional contact information
Shuo Li: The University of Melbourne
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
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
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
Scott R. Burrows: Queensland Institute of Medical Research
Anthony T. Papenfuss: The Walter & Eliza Hall Institute of Medical Research
Eric J. Gowans: Burnet Institute

Nature Communications, 2013, vol. 4, issue 1, 1-13

Abstract: 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.

Date: 2013
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DOI: 10.1038/ncomms3333

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