Center of Growth, Metabolism and Aging, Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.
Animal Disease Prevention and Food Safety Key Laboratory of Sichuan Province, Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, Chengdu, China.
Curr Protoc. 2024 Feb;4(2):e1002. doi: 10.1002/cpz1.1002.
The widespread application of high-throughput sequencing technology has generated massive sequences of B-cell receptor (BCR) immune repertoires. Computational analysis of these data has gained significant attention due to the increasing importance of immunotherapy and precision medicine. It not only reveals the diversity and dynamic changes in immune responses, contributing to the study of associated diseases, but also provides valuable information for immunodiagnostics and drug development. Recently, we introduced a BCR-specific multiple sequence alignment (MSA) method along with a comprehensive platform software called Abalign, which stands out as an excellent choice for analyzing BCR immune repertoires due to its unique high-throughput processing capability. It offers ultra-fast MSA functionality and a wide range of analytical features, including BCR/antibody extraction, clonal grouping, lineage tree construction, mutation profiling, diversity statistics, VJ gene assignment, antibody humanization, and more. Importantly, users can perform these analyses using the graphical user interface without any programming skills or scripts. In this article, we present a series of protocols that integrate Abalign's analysis modules into a cohesive workflow. This step-by-step workflow provides detailed instructions for software installation, data preparation, and comprehensive analysis of BCR immune repertoires. This workflow facilitates the efficient acquisition of comprehensive results in profiling BCR immune repertoires, offering insights into the impacts of infectious diseases, allergies, autoimmune disorders, tumor immunology, and antibody drugs. Abalign is freely available at http://cao.labshare.cn/abalign/. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Resource preparation Basic Protocol 2: Analyzing BCR immune repertoires Support Protocol 1: Aiding antibody humanization Support Protocol 2: Constructing B-cell lineage trees Alternate Protocol: Running with Linux command line Basic Protocol 3: Comparing BCR immune repertoires.
高通量测序技术的广泛应用产生了大量的 B 细胞受体 (BCR) 免疫受体库序列。由于免疫疗法和精准医学的重要性日益增加，对这些数据的计算分析引起了广泛关注。它不仅揭示了免疫反应的多样性和动态变化，有助于相关疾病的研究，而且为免疫诊断和药物开发提供了有价值的信息。最近，我们引入了一种 BCR 特异性的多重序列比对 (MSA) 方法以及一个名为 Abalign 的综合平台软件，由于其独特的高通量处理能力，它是分析 BCR 免疫受体库的绝佳选择。它提供了超快的 MSA 功能和广泛的分析功能，包括 BCR/抗体提取、克隆分组、谱系树构建、突变分析、多样性统计、VJ 基因分配、抗体人源化等。重要的是，用户可以使用图形用户界面执行这些分析，而无需任何编程技能或脚本。在本文中，我们提出了一系列将 Abalign 的分析模块集成到一个连贯工作流程中的协议。这个逐步工作流程为软件安装、数据准备和 BCR 免疫受体库的全面分析提供了详细的说明。这个工作流程有助于高效获取 BCR 免疫受体库分析的全面结果，深入了解传染病、过敏、自身免疫性疾病、肿瘤免疫学和抗体药物的影响。Aalign 可在 http://cao.labshare.cn/abalign/ 免费获得。© 2024 Wiley Periodicals LLC. 基础方案 1：资源准备 基础方案 2：分析 BCR 免疫受体库 支持方案 1：辅助抗体人源化 支持方案 2：构建 B 细胞谱系树 可选方案：使用 Linux 命令行运行 基础方案 3：比较 BCR 免疫受体库
