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

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,...

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Autores principales: Li, Shuo, Lefranc, Marie-Paule, Miles, John J., Alamyar, Eltaf, Giudicelli, Véronique, Duroux, Patrice, Freeman, J. Douglas, Corbin, Vincent D. A., Scheerlinck, Jean-Pierre, Frohman, Michael A., Cameron, Paul U., Plebanski, Magdalena, Loveland, Bruce, Burrows, Scott R., Papenfuss, Anthony T., Gowans, Eric J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Pub. Group 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3778833/
https://www.ncbi.nlm.nih.gov/pubmed/23995877
http://dx.doi.org/10.1038/ncomms3333
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author Li, Shuo
Lefranc, Marie-Paule
Miles, John J.
Alamyar, Eltaf
Giudicelli, Véronique
Duroux, Patrice
Freeman, J. Douglas
Corbin, Vincent D. A.
Scheerlinck, Jean-Pierre
Frohman, Michael A.
Cameron, Paul U.
Plebanski, Magdalena
Loveland, Bruce
Burrows, Scott R.
Papenfuss, Anthony T.
Gowans, Eric J.
author_facet Li, Shuo
Lefranc, Marie-Paule
Miles, John J.
Alamyar, Eltaf
Giudicelli, Véronique
Duroux, Patrice
Freeman, J. Douglas
Corbin, Vincent D. A.
Scheerlinck, Jean-Pierre
Frohman, Michael A.
Cameron, Paul U.
Plebanski, Magdalena
Loveland, Bruce
Burrows, Scott R.
Papenfuss, Anthony T.
Gowans, Eric J.
author_sort Li, Shuo
collection PubMed
description 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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spelling pubmed-37788332013-09-23 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, Véronique Duroux, Patrice Freeman, J. Douglas Corbin, Vincent D. A. Scheerlinck, Jean-Pierre Frohman, Michael A. Cameron, Paul U. Plebanski, Magdalena Loveland, Bruce Burrows, Scott R. Papenfuss, Anthony T. Gowans, Eric J. Nat Commun Article 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. Nature Pub. Group 2013-09-02 /pmc/articles/PMC3778833/ /pubmed/23995877 http://dx.doi.org/10.1038/ncomms3333 Text en Copyright © 2013, Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved. http://creativecommons.org/licenses/by-nc-nd/3.0/ This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivs 3.0 Unported License. To view a copy of this license, visit http://creativecommons.org/licenses/by-nc-nd/3.0/
spellingShingle Article
Li, Shuo
Lefranc, Marie-Paule
Miles, John J.
Alamyar, Eltaf
Giudicelli, Véronique
Duroux, Patrice
Freeman, J. Douglas
Corbin, Vincent D. A.
Scheerlinck, Jean-Pierre
Frohman, Michael A.
Cameron, Paul U.
Plebanski, Magdalena
Loveland, Bruce
Burrows, Scott R.
Papenfuss, Anthony T.
Gowans, Eric J.
IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling
title IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling
title_full IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling
title_fullStr IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling
title_full_unstemmed IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling
title_short IMGT/HighV QUEST paradigm for T cell receptor IMGT clonotype diversity and next generation repertoire immunoprofiling
title_sort imgt/highv quest paradigm for t cell receptor imgt clonotype diversity and next generation repertoire immunoprofiling
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3778833/
https://www.ncbi.nlm.nih.gov/pubmed/23995877
http://dx.doi.org/10.1038/ncomms3333
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