Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy

doi:10.1093/database/baad041

	Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy
	Wu, Tao1,2,3 ; Chen, Jing1 ; Diao, Kaixuan1 ; Wang, Guangshuai1 ; Wang, Jinyu1 ; Yao, Huizi1 ; Liu, Xue-Song1,4
	2023-06-13
发表期刊	DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (IF:3.4[JCR-2023],4.2[5-Year])
ISSN	1758-0463
卷号	2023
发表状态	已发表
DOI	10.1093/database/baad041
摘要	Neoantigens derived from somatic deoxyribonucleic acid alterations are ideal cancer-specific targets. However, integrated platform for neoantigen discovery is urgently needed. Recently, many scattered experimental evidences suggest that some neoantigens are immunogenic, and comprehensive collection of these experimentally validated neoantigens is still lacking. Here, we have integrated the commonly used tools in the current neoantigen discovery process to form a comprehensive web-based analysis platform. To identify experimental evidences supporting the immunogenicity of neoantigens, we performed comprehensive literature search and constructed the database. The collection of public neoantigens was obtained by using comprehensive features to filter the potential neoantigens from recurrent driver mutations. Importantly, we constructed a graph neural network (GNN) model (Immuno-GNN) using an attention mechanism to consider the spatial interactions between human leukocyte antigen and antigenic peptides for neoantigen immunogenicity prediction. The new easy-to-use R/Shiny web-based neoantigen database and discovery platform, Neodb, contains currently the largest number of experimentally validated neoantigens. In addition to validated neoantigen, Neodb also includes three additional modules for facilitating neoantigen prediction and analysis, including 'Tools' module (comprehensive neoantigen prediction tools); 'Driver-Neo' module (collection of public neoantigens derived from recurrent mutations) and 'Immuno-GNN' module (a novel immunogenicity prediction tool based on a GNN). Immuno-GNN shows improved performance compared with known methods and also represents the first application of GNN model in neoantigen immunogenicity prediction. The construction of Neodb will facilitate the study of neoantigen immunogenicity and the clinical application of neoantigen-based cancer immunotherapy.
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收录类别	SCI
语种	英语
资助项目	Shanghai Science and Technology Commission[21ZR144-2400] ; National Natural Science Foundation of China[31771373]
WOS研究方向	Mathematical & Computational Biology
WOS类目	Mathematical & Computational Biology
WOS记录号	WOS:001009888500001
出版者	OXFORD UNIV PRESS
引用统计	正在获取...
文献类型	期刊论文
条目标识符	https://kms.shanghaitech.edu.cn/handle/2MSLDSTB/316416
专题	生命科学与技术学院生命科学与技术学院_PI研究组_刘雪松组生命科学与技术学院_硕士生生命科学与技术学院_博士生
通讯作者	Liu, Xue-Song
作者单位	1.ShanghaiTech Univ, Sch Life Sci & Technol, 93 Middle Huaxia Rd, Shanghai 201203, Peoples R China 2.Chinese Acad Sci, Shanghai Inst Biochem & Cell Biol, 20 Yue Yang Rd, Shanghai 200031, Peoples R China 3.Univ Chinese Acad Sci, Yanqihu East Rd, Beijing 101408, Peoples R China 4.Shanghai Clin Res & Trial Ctr, 599 Keyuan Rd, Pudong New Area, Shanghai 201203, Peoples R China
第一作者单位	生命科学与技术学院
通讯作者单位	生命科学与技术学院
第一作者的第一单位	生命科学与技术学院
推荐引用方式 GB/T 7714	Wu, Tao,Chen, Jing,Diao, Kaixuan,et al. Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy[J]. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION,2023,2023.
APA	Wu, Tao.,Chen, Jing.,Diao, Kaixuan.,Wang, Guangshuai.,Wang, Jinyu.,...&Liu, Xue-Song.(2023).Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy.DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION,2023.
MLA	Wu, Tao,et al."Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy".DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2023(2023).