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Aouinti S, Giudicelli V, Duroux P, et al. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST. Front Immunol. 2016;7:339doi: 10.3389/fimmu.2016.00339.
Aouinti, S., Giudicelli, V., Duroux, P., Malouche, D., Kossida, S., & Lefranc, M. P. (2016). IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST. Frontiers in immunology, 7339. https://doi.org/10.3389/fimmu.2016.00339
Aouinti, Safa, et al. "IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST." Frontiers in immunology vol. 7 (2016): 339. doi: https://doi.org/10.3389/fimmu.2016.00339
Aouinti S, Giudicelli V, Duroux P, Malouche D, Kossida S, Lefranc MP. IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST. Front Immunol. 2016 Sep 09;7:339. doi: 10.3389/fimmu.2016.00339. eCollection 2016. PMID: 27667992; PMCID: PMC5016520.
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Front Immunol. 2016 Sep 09;7:339. doi: 10.3389/fimmu.2016.00339. eCollection 2016.

IMGT/StatClonotype for Pairwise Evaluation and Visualization of NGS IG and TR IMGT Clonotype (AA) Diversity or Expression from IMGT/HighV-QUEST.

Frontiers in immunology

Safa Aouinti, Véronique Giudicelli, Patrice Duroux, Dhafer Malouche, Sofia Kossida, Marie-Paule Lefranc

Affiliations

  1. IMGT®, The international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University, Montpellier, France; Higher School of Statistics and Information Analysis, Unité Modélisation et Analyse Statistique et Economique, University of Carthage, Tunis, Tunisia.
  2. IMGT®, The international ImMunoGeneTics information system®, Laboratoire d'ImmunoGénétique Moléculaire LIGM, Institut de Génétique Humaine IGH, UPR CNRS 1142, Montpellier University , Montpellier , France.
  3. Higher School of Statistics and Information Analysis, Unité Modélisation et Analyse Statistique et Economique, University of Carthage , Tunis , Tunisia.

PMID: 27667992 PMCID: PMC5016520 DOI: 10.3389/fimmu.2016.00339

Abstract

There is a huge need for standardized analysis and statistical procedures in order to compare the complex immune repertoires of antigen receptors immunoglobulins (IG) and T cell receptors (TR) obtained by next generation sequencing (NGS). NGS technologies generate millions of nucleotide sequences and have led to the development of new tools. The IMGT/HighV-QUEST, available since 2010, is the first global web portal for the analysis of IG and TR high throughput sequences. IMGT/HighV-QUEST provides standardized outputs for the characterization of the "IMGT clonotype (AA)" (AA for amino acids) and their comparison in up to one million sequences. Standardized statistical procedures for "IMGT clonotype (AA)" diversity or expression comparisons have recently been described, however, no tool was yet available. IMGT/StatClonotype, a new IMGT(®) tool, evaluates and visualizes statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per V (variable), D (diversity), and J (joining) gene of a given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. IMGT/StatClonotype tool is incorporated in the R package "IMGTStatClonotype," with a user-friendly interface. IMGT/StatClonotype is downloadable at IMGT(®) for users to evaluate pairwise comparison of IG and TR NGS statistical output from IMGT/HighV-QUEST and to visualize, on their web browser, the statistical significance of IMGT clonotype (AA) diversity or expression, per gene, the comparative analysis of CDR-IMGT and the V-D-J associations, in immunoprofiles from normal or pathological immune responses.

Keywords: IMGT-ONTOLOGY; IMGT/HighV-QUEST; T cell receptor; antibody; immunoglobulin; immunoinformatics; next generation sequencing; statistical significance

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