Frontiers in Immunology (Aug 2021)
RAPID: A Rep-Seq Dataset Analysis Platform With an Integrated Antibody Database
- Yanfang Zhang,
- Yanfang Zhang,
- Yanfang Zhang,
- Yanfang Zhang,
- Yanfang Zhang,
- Tianjian Chen,
- Huikun Zeng,
- Huikun Zeng,
- Huikun Zeng,
- Huikun Zeng,
- Huikun Zeng,
- Xiujia Yang,
- Xiujia Yang,
- Xiujia Yang,
- Xiujia Yang,
- Xiujia Yang,
- Qingxian Xu,
- Yanxia Zhang,
- Yanxia Zhang,
- Yuan Chen,
- Minhui Wang,
- Minhui Wang,
- Minhui Wang,
- Yan Zhu,
- Yan Zhu,
- Chunhong Lan,
- Chunhong Lan,
- Qilong Wang,
- Haipei Tang,
- Yan Zhang,
- Chengrui Wang,
- Wenxi Xie,
- Wenxi Xie,
- Cuiyu Ma,
- Cuiyu Ma,
- Junjie Guan,
- Junjie Guan,
- Shixin Guo,
- Sen Chen,
- Wei Yang,
- Lai Wei,
- Jian Ren,
- Xueqing Yu,
- Xueqing Yu,
- Zhenhai Zhang,
- Zhenhai Zhang,
- Zhenhai Zhang,
- Zhenhai Zhang,
- Zhenhai Zhang
Affiliations
- Yanfang Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Yanfang Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Yanfang Zhang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Yanfang Zhang
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
- Yanfang Zhang
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Tianjian Chen
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Huikun Zeng
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Huikun Zeng
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Huikun Zeng
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Huikun Zeng
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
- Huikun Zeng
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Xiujia Yang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Xiujia Yang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Xiujia Yang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Xiujia Yang
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
- Xiujia Yang
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Qingxian Xu
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Yanxia Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Yanxia Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Yuan Chen
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Minhui Wang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Minhui Wang
- Department of Nephrology, Hainan General Hospital, Haikou, China
- Minhui Wang
- Hainan Affiliated Hospital of Hainan Medical College, Haikou, China
- Yan Zhu
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Yan Zhu
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Chunhong Lan
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Chunhong Lan
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Qilong Wang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Haipei Tang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Yan Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Chengrui Wang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Wenxi Xie
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Wenxi Xie
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Cuiyu Ma
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Cuiyu Ma
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Junjie Guan
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Junjie Guan
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Shixin Guo
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Sen Chen
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Wei Yang
- 0Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Lai Wei
- State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-Sen University, Guangzhou, China
- Jian Ren
- State Key Laboratory of Oncology in South China, Cancer Center, Collaborative Innovation Center for Cancer Medicine, School of Life Sciences, Sun Yat-sen University, Guangzhou, China
- Xueqing Yu
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Xueqing Yu
- 1Division of Nephrology, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Zhenhai Zhang
- State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Zhenhai Zhang
- Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China
- Zhenhai Zhang
- Center for Precision Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- Zhenhai Zhang
- Key Laboratory of Mental Health of the Ministry of Education, Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou, China
- Zhenhai Zhang
- Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China
- DOI
- https://doi.org/10.3389/fimmu.2021.717496
- Journal volume & issue
-
Vol. 12
Abstract
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.
Keywords
