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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...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
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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 |
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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 |
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