RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database

• Published in: Frontiers in immunology Vol. 12; p. 717496
• Main Authors: Zhang, Yanfang, Chen, Tianjian, Zeng, Huikun, Yang, Xiujia, Xu, Qingxian, Zhang, Yanxia, Chen, Yuan, Wang, Minhui, Zhu, Yan, Lan, Chunhong, Wang, Qilong, Tang, Haipei, Zhang, Yan, Wang, Chengrui, Xie, Wenxi, Ma, Cuiyu, Guan, Junjie, Guo, Shixin, Chen, Sen, Yang, Wei, Wei, Lai, Ren, Jian, Yu, Xueqing, Zhang, Zhenhai
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 13.08.2021
• Subjects: Antibodies - genetics; antibody annotation; antibody database; comparative analysis; Computational Biology - methods; Databases, Genetic; Humans; Immunology; public clone; Rep-Seq; Software; Web Browser; comparative analysis; public clone; antibody annotation; Rep-Seq; antibody database
• ISSN: 1664-3224; 1664-3224
• DOI: 10.3389/fimmu.2021.717496

The antibody repertoire is a critical component of the adaptive immune system and is believed to reflect an individual’s immune history and current immune status. Delineating the antibody repertoire has advanced our understanding of humoral immunity, facilitated antibody discovery, and showed great potential for improving the diagnosis and treatment of disease. However, no tool to date has effectively integrated big Rep-seq data and prior knowledge of functional antibodies to elucidate the remarkably diverse antibody repertoire. We developed a Rep-seq dataset Analysis Platform with an Integrated antibody Database (RAPID; https://rapid.zzhlab.org/ ), a free and web-based tool that allows researchers to process and analyse Rep-seq datasets. RAPID consolidates 521 WHO-recognized therapeutic antibodies, 88,059 antigen- or disease-specific antibodies, and 306 million clones extracted from 2,449 human IGH Rep-seq datasets generated from individuals with 29 different health conditions. RAPID also integrates a standardized Rep-seq dataset analysis pipeline to enable users to upload and analyse their datasets. In the process, users can also select set of existing repertoires for comparison. RAPID automatically annotates clones based on integrated therapeutic and known antibodies, and users can easily query antibodies or repertoires based on sequence or optional keywords. With its powerful analysis functions and rich set of antibody and antibody repertoire information, RAPID will benefit researchers in adaptive immune studies.