dbPepNeo2.0：一个基于质谱和 TCR 识别的人类肿瘤新抗原肽数据库。
dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition.
机构信息
College of Food Science and Technology, Shanghai Ocean University, Shanghai, China.
Shanghai-Ministry of Science and Technology (MOST) Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China.
出版信息
Front Immunol. 2022 Apr 13;13:855976. doi: 10.3389/fimmu.2022.855976. eCollection 2022.
Neoantigens are widely reported to induce T-cell response and lead to tumor regression, indicating a promising potential to immunotherapy. Previously, we constructed an open-access database, i.e., dbPepNeo, providing a systematic resource for human tumor neoantigens to storage and query. In order to expand data volume and application scope, we updated dbPepNeo to version 2.0 (http://www.biostatistics.online/dbPepNeo2). Here, we provide about 801 high-confidence (HC) neoantigens (increased by 170%) and 842,289 low-confidence (LC) HLA immunopeptidomes (increased by 107%). Notably, 55 class II HC neoantigens and 630 neoantigen-reactive T-cell receptor-β (TCRβ) sequences were firstly included. Besides, two new analytical tools are developed, DeepCNN-Ineo and BLASTdb. DeepCNN-Ineo predicts the immunogenicity of class I neoantigens, and BLASTdb performs local alignments to look for sequence similarities in dbPepNeo2.0. Meanwhile, the web features and interface have been greatly improved and enhanced.
新抗原被广泛报道能诱导 T 细胞反应，导致肿瘤消退，这表明其在免疫治疗方面有很大的潜力。此前，我们构建了一个开放获取的数据库，即 dbPepNeo，为人类肿瘤新抗原的存储和查询提供了一个系统的资源。为了扩大数据量和应用范围，我们将 dbPepNeo 更新到了 2.0 版本（http://www.biostatistics.online/dbPepNeo2）。在这里，我们提供了大约 801 个高可信度（HC）新抗原（增加了 170%）和 842,289 个低可信度（LC）HLA 免疫肽组（增加了 107%）。值得注意的是，首次纳入了 55 个 II 类 HC 新抗原和 630 个新抗原反应性 T 细胞受体-β（TCRβ）序列。此外，还开发了两个新的分析工具，即 DeepCNN-Ineo 和 BLASTdb。DeepCNN-Ineo 预测了 I 类新抗原的免疫原性，BLASTdb 则在 dbPepNeo2.0 中进行局部比对，以寻找序列相似性。同时，网站的功能和界面得到了极大的改进和增强。
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