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; Eric J. Gowans

doi:10.1038/ncomms3333

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
, Eric J. Gowans

Pharmacological Sciences

University of Melbourne
Burnet Institute
Monash University
Université Montpellier 2
Queensland Institute of Medical Research
Cardiff University
University of Queensland
Canada's Michael Smith Genome Sciences Centre
Walter and Eliza Hall Institute of Medical Research
University of Adelaide

Research output: Contribution to journal › Article › peer-review

190 Scopus citations

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.

Original language	English
Article number	2333
Journal	Nature Communications
Volume	4
DOIs	https://doi.org/10.1038/ncomms3333
State	Published - 2013

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Li, S., Lefranc, M. P., Miles, J. J., Alamyar, E., Giudicelli, V., Duroux, P., Freeman, J. D., Corbin, V. D. A., Scheerlinck, J. P., Frohman, M. A., Cameron, P. U., Plebanski, M., Loveland, B., Burrows, S. R., Papenfuss, A. T., & Gowans, E. J. (2013). IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. Nature Communications, 4, Article 2333. https://doi.org/10.1038/ncomms3333

@article{fc3a908f918c427da73d1ff5a5d366d3,

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

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.",

author = "Shuo Li and Lefranc, \{Marie Paule\} and Miles, \{John J.\} and Eltaf Alamyar and V{\'e}ronique Giudicelli and Patrice Duroux and Freeman, \{J. Douglas\} and Corbin, \{Vincent D.A.\} and Scheerlinck, \{Jean Pierre\} and Frohman, \{Michael A.\} and Cameron, \{Paul U.\} and Magdalena Plebanski and Bruce Loveland and Burrows, \{Scott R.\} and Papenfuss, \{Anthony T.\} and Gowans, \{Eric J.\}",

year = "2013",

doi = "10.1038/ncomms3333",

language = "English",

volume = "4",

journal = "Nature Communications",

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Li, S, Lefranc, MP, Miles, JJ, Alamyar, E, Giudicelli, V, Duroux, P, Freeman, JD, Corbin, VDA, Scheerlinck, JP, Frohman, MA, Cameron, PU, Plebanski, M, Loveland, B, Burrows, SR, Papenfuss, AT & Gowans, EJ 2013, 'IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling', Nature Communications, vol. 4, 2333. https://doi.org/10.1038/ncomms3333

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T1 - IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling

AU - Li, Shuo

AU - Lefranc, Marie Paule

AU - Miles, John J.

AU - Alamyar, Eltaf

AU - Giudicelli, Véronique

AU - Duroux, Patrice

AU - Freeman, J. Douglas

AU - Corbin, Vincent D.A.

AU - Scheerlinck, Jean Pierre

AU - Frohman, Michael A.

AU - Cameron, Paul U.

AU - Plebanski, Magdalena

AU - Loveland, Bruce

AU - Burrows, Scott R.

AU - Papenfuss, Anthony T.

AU - Gowans, Eric J.

PY - 2013

Y1 - 2013

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AB - 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.

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DO - 10.1038/ncomms3333

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SN - 2041-1723

VL - 4

JO - Nature Communications

JF - Nature Communications

M1 - 2333

ER -

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

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