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User THOMAS-VASLIN
title The past, present, and future of immune repertoire biology – the rise of next-generation repertoire analysis.
Authors Six , Mariotti-Ferrandiz ME, Chaara W, Magadan S, Pham H-P, Lefranc M-P, Mora T, Thomas-Vaslin V, Walczak AM and Boudinot P
Source Front. Immunol. 4:413. doi: 10.3389/fimmu.2013.00413 http://www.frontiersin.org/t_cell_biology/10.3389/fimmu.2013.00413/abstracthttp://www.frontiersin.org/t_cell_biology/10.3389/fimmu.2013.00413/abstract" class="wiki wikinew">?
Year 2013
Type Journal
Type of publication ISC-PIF scholar

Optional Infos

Abstract T and B cell repertoires are collections of lymphocytes, each characterized by its antigenspecific
receptor.We review here classical technologies and analysis strategies developed
to assess immunoglobulin (IG) and T cell receptor (TR) repertoire diversity, and describe
recent advances in the field. First, we describe the broad range of available methodological
tools developed in the past decades, each of which answering different questions
and showing complementarity for progressive identification of the level of repertoire alterations:
global overview of the diversity by flow cytometry, IG repertoire descriptions at the
protein level for the identification of IG reactivities, IG/TR CDR3 spectratyping strategies,
and related molecular quantification or dynamics of T/B cell differentiation. Additionally,
we introduce the recent technological advances in molecular biology tools allowing deeper
analysis of IG/TR diversity by next-generation sequencing (NGS), offering systematic and
comprehensive sequencing of IG/TR transcripts in a short amount of time. NGS provides
several angles of analysis such as clonotype frequency, CDR3 diversity, CDR3 sequence
analysis, V allele identification with a quantitative dimension, therefore requiring highthroughput
analysis tools development. In this line, we discuss the recent efforts made
for nomenclature standardization and ontology development. We then present the variety
of available statistical analysis and modeling approaches developed with regards to
the various levels of diversity analysis, and reveal the increasing sophistication of those
modeling approaches. To conclude, we provide some examples of recent mathematical
modeling strategies and perspectives that illustrate the active rise of a “next-generation”
of repertoire analysis.
Keywords: diversity analysis, immune receptors, next-generation sequencing, modeling, statistics, gene nomenclature,
B cell repertoire,T cell repertoire
Created Wednesday 02 April, 2014 19:43:05


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