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 journalArticleResearchpeer-review

111 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 languageEnglish
Pages (from-to)1 - 13
Number of pages13
JournalNature Communications
Volume4
Issue numberArt #: 2333
DOIs
Publication statusPublished - 2013

Cite this

Li, S., Lefranc, M-P., Miles, J. J., Alamyar, E., Giudicelli, V., Duroux, P., ... 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
Li, Shuo ; Lefranc, Marie-Paule ; Miles, John J ; Alamyar, Eltaf ; Giudicelli, Veronique ; Duroux, Patrice ; Freeman, John Douglas ; Corbin, Vincent D A ; Scheerlinck, Jean-Paul ; Frohman, Michael A ; Cameron, Paul Urquhart ; Plebanski, Magdalena ; Loveland, Bruce E ; Burrows, Scott R ; Papenfuss, Anthony Troy ; Gowans, Eric J. / IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. In: Nature Communications. 2013 ; Vol. 4, No. Art #: 2333. pp. 1 - 13.
@article{8f3d504b298745f0b48e641a2e77b827,
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}",
year = "2013",
doi = "10.1038/ncomms3333",
language = "English",
volume = "4",
pages = "1 -- 13",
journal = "Nature Communications",
issn = "2041-1723",
publisher = "Nature Publishing Group",
number = "Art #: 2333",

}

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

IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling. / Li, Shuo; Lefranc, Marie-Paule; Miles, John J; Alamyar, Eltaf; Giudicelli, Veronique; Duroux, Patrice; Freeman, John Douglas; Corbin, Vincent D A; Scheerlinck, Jean-Paul; Frohman, Michael A; Cameron, Paul Urquhart; Plebanski, Magdalena; Loveland, Bruce E; Burrows, Scott R; Papenfuss, Anthony Troy; Gowans, Eric J.

In: Nature Communications, Vol. 4, No. Art #: 2333, 2013, p. 1 - 13.

Research output: Contribution to journalArticleResearchpeer-review

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

VL - 4

SP - 1

EP - 13

JO - Nature Communications

JF - Nature Communications

SN - 2041-1723

IS - Art #: 2333

ER -