Cargando…

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

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...

Descripción completa

Detalles Bibliográficos
Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8414647/
https://www.ncbi.nlm.nih.gov/pubmed/34484220
http://dx.doi.org/10.3389/fimmu.2021.717496
_version_ 1783747821684391936
author 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
author_facet 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
author_sort Zhang, Yanfang
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8414647
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-84146472021-09-04 RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database 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 Front Immunol Immunology 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. Frontiers Media S.A. 2021-08-13 /pmc/articles/PMC8414647/ /pubmed/34484220 http://dx.doi.org/10.3389/fimmu.2021.717496 Text en Copyright © 2021 Zhang, Chen, Zeng, Yang, Xu, Zhang, Chen, Wang, Zhu, Lan, Wang, Tang, Zhang, Wang, Xie, Ma, Guan, Guo, Chen, Yang, Wei, Ren, Yu and Zhang https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Immunology
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
RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database
title RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database
title_full RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database
title_fullStr RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database
title_full_unstemmed RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database
title_short RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database
title_sort rapid: a rep-seq dataset analysis platform with an integrated antibody database
topic Immunology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8414647/
https://www.ncbi.nlm.nih.gov/pubmed/34484220
http://dx.doi.org/10.3389/fimmu.2021.717496
work_keys_str_mv AT zhangyanfang rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT chentianjian rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT zenghuikun rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT yangxiujia rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT xuqingxian rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT zhangyanxia rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT chenyuan rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT wangminhui rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT zhuyan rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT lanchunhong rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT wangqilong rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT tanghaipei rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT zhangyan rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT wangchengrui rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT xiewenxi rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT macuiyu rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT guanjunjie rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT guoshixin rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT chensen rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT yangwei rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT weilai rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT renjian rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT yuxueqing rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase
AT zhangzhenhai rapidarepseqdatasetanalysisplatformwithanintegratedantibodydatabase