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Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
Published on: May 17, 2019
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TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis.
Jingcheng Wu1, Wenyi Zhao2, Binbin Zhou3
1Institute of Drug Metabolism and Pharmaceutical Analysis and Zhejiang Provincial Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China.
Genomics, Proteomics & Bioinformatics
|September 18, 2018
Summary
This study introduces TSNAdb, a comprehensive database of tumor-specific neoantigens. It aids in predicting immunotherapy response and identifying targets for cancer vaccines.
Area of Science:
- Immunology
- Genomics
- Bioinformatics
Background:
- Tumor-specific neoantigens are crucial biomarkers for predicting immune checkpoint blockade therapy efficacy.
- They also serve as potential targets for developing novel cancer immunotherapies.
Purpose of the Study:
- To develop a comprehensive tumor-specific neoantigen database (TSNAdb v1.0).
- To facilitate the discovery of shared neoantigens for cancer immunotherapy development.
Main Methods:
- Pan-cancer immunogenomic analysis of 7748 tumor samples from TCGA and TCIA.
- Prediction of neoantigen binding affinities using NetMHCpan v2.8/v4.0.
- Identification of shared neoantigens based on recurrent mutations and frequent HLA alleles.
Main Results:
- Detailed information on 3,707,562 potential neoantigens from mutant peptides and 1,146,961 from wild-type peptides.
- Identification of potential shared neoantigens across tumor patients.
- Development of a publicly accessible database (TSNAdb v1.0).
Conclusions:
- TSNAdb v1.0 provides a valuable resource for cancer immunotherapy research.
- The database aids in identifying neoantigen biomarkers and therapeutic targets.
- Facilitates the development of neoantigen-based cancer vaccines and therapies.
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