Deep Mining of Human Antibody Repertoires: Concepts, Methodologies, and Applications,Small Methods

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Deep Mining of Human Antibody Repertoires: Concepts, Methodologies, and Applications
Small Methods ( IF 10.7 ) Pub Date : 2020-09-02 , DOI: 10.1002/smtd.202000451
Xiaolong Tian ₁ , Cheng Li ₁ , Yanling Wu ₁ , Tianlei Ying ₁

Affiliation

The ability of the human adaptive immune system to respond to antigens relies upon the tremendous diversity of T cell receptors (TCR) and B cell receptors (BCR). The entirety of an individual's BCRs, often referred to as an antibody repertoire, shapes the humoral immune system. Therefore, technologies to identify and characterize antibody repertoires are critical for understanding fundamental aspects of the development and maintenance of the humoral immune system. Recently, innovative methodologies and technologies devoted to high‐throughput sequencing of antibody repertoires (Ig‐Seq) have broadened the understanding of humoral immunity. This review provides an overview of the Ig‐Seq pipeline from sample collection, library preparation, and sequencing, to data cleaning, sequence alignment, and high‐level processing. Conventional and current strategies used in Ig‐Seq are introduced in detail, including bulk BCR sequencing, heavy and light chain paired sequencing combined with proteomic or single B cell sequencing approaches, antigen‐specific single B cell sequencing, and single‐molecule sequencing. Applications of Ig‐Seq are also discussed, including antibody diversity measurement, signatures associated with different populations, novel findings involved in the antibody repertoire development, and strategies of functional antibody discovery from antibody repertoires. Finally, the pitfalls and opportunities in the deep mining of antibody repertoires are discussed.

中文翻译：

人体抗体库的深度挖掘：概念，方法和应用

人类适应性免疫系统对抗原作出反应的能力取决于T细胞受体（TCR）和B细胞受体（BCR）的巨大多样性。个体的整个BCR（通常称为抗体库）决定着体液免疫系统。因此，鉴定和表征抗体库的技术对于理解体液免疫系统的发育和维持的基本方面至关重要。最近，致力于抗体库高通量测序（Ig-Seq）的创新方法和技术拓宽了对体液免疫的理解。这篇综述概述了Ig-Seq管道，从样品收集，文库制备和测序到数据清洗，序列比对和高级处理。详细介绍了Ig-Seq中使用的常规和当前策略，包括批量BCR测序，结合蛋白质组学或单B细胞测序方法的重链和轻链配对测序，抗原特异性单B细胞测序和单分子测序。还讨论了Ig-Seq的应用，包括抗体多样性测量，与不同人群相关的特征，涉及抗体库开发的新发现以及从抗体库中发现功能性抗体的策略。最后，讨论了抗体库的深度挖掘中的陷阱和机会。抗原特异性单B细胞测序和单分子测序。还讨论了Ig-Seq的应用，包括抗体多样性测量，与不同人群相关的特征，涉及抗体库开发的新发现以及从抗体库中发现功能性抗体的策略。最后，讨论了抗体库的深度挖掘中的陷阱和机会。抗原特异性单B细胞测序和单分子测序。还讨论了Ig-Seq的应用，包括抗体多样性测量，与不同人群相关的特征，涉及抗体库开发的新发现以及从抗体库中发现功能性抗体的策略。最后，讨论了抗体库的深度挖掘中的陷阱和机会。

更新日期：2020-10-07

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