The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis.
The past, present, and future of immune repertoire biology - the rise of next-generation repertoire analysis.
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DOI：
10.3389/fimmu.2013.00413
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发表时间：
2013-11-27
影响因子：
7.3
通讯作者：
Boudinot P
中科院分区：
文献类型：
--
作者：
Six A;Mariotti-Ferrandiz ME;Chaara W;Magadan S;Pham HP;Lefranc MP;Mora T;Thomas-Vaslin V;Walczak AM;Boudinot P
T细胞和B细胞库是淋巴细胞的集合，每种细胞的特征在于其抗原特异性受体。我们在这里回顾经典的技术和分析策略，以评估免疫球蛋白（IG）和T细胞受体（TR）的库的多样性，并描述在该领域的最新进展。首先，我们描述了在过去几十年中开发的广泛的可用方法学工具，每一种工具都回答了不同的问题，并显示出对库改变水平的逐步识别的互补性：通过流式细胞术进行的多样性的全球概述，用于鉴定IG反应性的蛋白质水平的IG库描述，IG/TR CDR 3谱分析策略，以及T/B细胞分化的相关分子定量或动力学。此外，我们还介绍了分子生物学工具的最新技术进展，通过下一代测序（NGS）可以更深入地分析IG/TR多样性，在短时间内提供IG/TR转录本的系统和全面测序。NGS提供了几个分析角度，如克隆型频率、CDR 3多样性、CDR 3序列分析、具有定量维度的V等位基因鉴定，因此需要开发高通量分析工具。在这条线上，我们讨论了最近的努力命名标准化和本体论的发展。然后，我们提出了各种可用的统计分析和建模方法开发方面的各个层次的多样性分析，并揭示了这些建模方法的日益复杂。最后，我们提供了一些例子，最近的数学建模策略和观点，说明了积极崛起的“下一代”的剧目分析。
T and B cell repertoires are collections of lymphocytes, each characterized by its antigen-specific 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 high-throughput 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.
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影响因子：
16.8
作者：
Bendall SC;Nolan GP;Roederer M;Chattopadhyay PK
通讯作者：
Chattopadhyay PK
影响因子：
56.9
作者：
Arstila, TP;Casrouge, A;Kourilsky, P
通讯作者：
Kourilsky, P
DOI：
10.1126/science.1198704
发表时间：
2011-05-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Bendall SC;Simonds EF;Qiu P;Amir el-AD;Krutzik PO;Finck R;Bruggner RV;Melamed R;Trejo A;Ornatsky OI;Balderas RS;Plevritis SK;Sachs K;Pe'er D;Tanner SD;Nolan GP
通讯作者：
Nolan GP
影响因子：
3
作者：
Bleakley, Kevin;Lefranc, Marie-Paule;Biau, Gerard
通讯作者：
Biau, Gerard
影响因子：
4.4
作者：
Bains, Iren;Thiebaut, Rodolphe;Callard, Robin
通讯作者：
Callard, Robin