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; Veronique Giudicelli; Patrice Duroux; John Douglas Freeman; Vincent D A Corbin; Jean-Paul Scheerlinck; Michael A Frohman; Paul Urquhart Cameron; Magdalena Plebanski; Bruce E Loveland; Scott R Burrows; Anthony Troy 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
, Veronique Giudicelli
, Patrice Duroux
, John Douglas Freeman
, Vincent D A Corbin
, Jean-Paul Scheerlinck
, Michael A Frohman
, Paul Urquhart Cameron
, Magdalena Plebanski
, Bruce E Loveland
, Scott R Burrows
, Anthony Troy Papenfuss
, Eric J Gowans

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

189 Citations (Scopus)

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. ? 2013 Macmillan Publishers Limited.

Original language	English
Pages (from-to)	1 - 13
Number of pages	13
Journal	Nature Communications
Volume	4
Issue number	Art #: 2333
DOIs	https://doi.org/10.1038/ncomms3333
Publication status	Published - 2013

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This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1038/ncomms3333

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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. E., 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(Art #: 2333), 1 - 13. https://doi.org/10.1038/ncomms3333

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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. ? 2013 Macmillan Publishers Limited.",

author = "Shuo Li and Marie-Paule Lefranc and Miles, \{John J\} and Eltaf Alamyar and Veronique Giudicelli and Patrice Duroux and Freeman, \{John Douglas\} and Corbin, \{Vincent D A\} and Jean-Paul Scheerlinck and Frohman, \{Michael A\} and Cameron, \{Paul Urquhart\} and Magdalena Plebanski and Loveland, \{Bruce E\} and Burrows, \{Scott R\} and Papenfuss, \{Anthony Troy\} and Gowans, \{Eric J\}",

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doi = "10.1038/ncomms3333",

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Li, S, Lefranc, M-P, Miles, JJ, Alamyar, E, Giudicelli, V, Duroux, P, Freeman, JD, Corbin, VDA, Scheerlinck, J-P, Frohman, MA, Cameron, PU, Plebanski, M, Loveland, BE, 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, no. Art #: 2333, pp. 1 - 13. https://doi.org/10.1038/ncomms3333

TY - JOUR

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, Veronique

AU - Duroux, Patrice

AU - Freeman, John Douglas

AU - Corbin, Vincent D A

AU - Scheerlinck, Jean-Paul

AU - Frohman, Michael A

AU - Cameron, Paul Urquhart

AU - Plebanski, Magdalena

AU - Loveland, Bruce E

AU - Burrows, Scott R

AU - Papenfuss, Anthony Troy

AU - Gowans, Eric J

PY - 2013

Y1 - 2013

N2 - 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. ? 2013 Macmillan Publishers Limited.

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. ? 2013 Macmillan Publishers Limited.

UR - http://www.nature.com/ncomms/2013/130902/ncomms3333/pdf/ncomms3333.pdf

U2 - 10.1038/ncomms3333

DO - 10.1038/ncomms3333

M3 - Article

SN - 2041-1723

VL - 4

SP - 1

EP - 13

JO - Nature Communications

JF - Nature Communications

IS - Art #: 2333

ER -

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

Abstract

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