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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.
  • Zhang Y; State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
  • Chen T; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
  • Zeng H; Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
  • Yang X; 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.
  • Xu Q; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
  • Zhang Y; 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.
  • Chen Y; State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
  • Wang M; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
  • Zhu Y; Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
  • Lan C; 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.
  • Wang Q; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
  • Tang H; State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
  • Zhang Y; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
  • Wang C; Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
  • Xie W; 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.
  • Ma C; Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
  • Guan J; 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.
  • Guo S; State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
  • Chen S; Department of Bioinformatics, School of Basic Medical Sciences, Southern Medical University, Guangzhou, China.
  • Yang W; Center for Precision Medicine, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou, China.
  • Wei L; State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
  • Ren J; Department of Nephrology, Hainan General Hospital, Haikou, China.
  • Yu X; Hainan Affiliated Hospital of Hainan Medical College, Haikou, China.
  • Zhang Z; State Key Laboratory of Organ Failure Research, National Clinical Research, Center for Kidney Disease, Division of Nephrology, Nanfang Hospital, Southern Medical University, Guangzhou, China.
Front Immunol ; 12: 717496, 2021.
Article in English | MEDLINE | ID: covidwho-1512035
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.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Computational Biology / Databases, Genetic / Antibodies Type of study: Prognostic study Limits: Humans Language: English Journal: Front Immunol Year: 2021 Document Type: Article Affiliation country: Fimmu.2021.717496

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Computational Biology / Databases, Genetic / Antibodies Type of study: Prognostic study Limits: Humans Language: English Journal: Front Immunol Year: 2021 Document Type: Article Affiliation country: Fimmu.2021.717496