NeoHunter:Flexible software for systematically detecting neoantigens from sequencing data

作     者：Tianxing Ma Zetong Zhao Haochen Li Lei Wei Xuegong Zhang Tianxing Ma;Zetong Zhao;Haochen Li;Lei Wei;Xuegong Zhang

作者机构：MOE Key Lab of BioinformaticsBioinformatics Division of BNRIST and Department of AutomationTsinghua UniversityBeijingChina School of MedicineTsinghua UniversityBeijingChina School of Life SciencesTsinghua UniversityBeijingChina 

出 版 物：《Quantitative Biology》 (定量生物学（英文版）)

年 卷 期：2024年第12卷第1期

页      面：70-84页

核心收录：

学科分类：1004[医学-公共卫生与预防医学(可授医学、理学学位)] 100401[医学-流行病与卫生统计学] 10[医学] 

基　　金：National Key R&D Program of China,Grant/Award Number:2021YFF1200900 National Natural Science Foundation of China,Grant/Award Numbers:61721003,62250005,62103227 

主　　题：cancer vaccine molecular alteration neoantigen neoantigen prioritization 

摘      要：Complicated molecular alterations in tumors generate various mutant *** of these mutant peptides can be presented to the cell surface and then elicit immune responses,and such mutant peptides are called *** detection of neoantigens could help to design personalized cancer *** some computational frameworks for neoantigen detection have been proposed,most of them can only detect SNV-and indel-derived *** addition,current frameworks adopt oversimplified neoantigen prioritization *** factors hinder the comprehensive and effective detection of *** developed NeoHunter,flexible software to systematically detect and prioritize neoantigens from sequencing data in different *** can detect not only SNV-and indel-derived neoantigens but also gene fusion-and aberrant splicing-derived *** supports both direct and indirect immunogenicity evaluation strategies to prioritize candidate *** strategies utilize binding characteristics,existing biological big data,and T-cell receptor specificity to ensure accurate detection and *** applied NeoHunter to the TESLA dataset,cohorts of melanoma and non-small cell lung cancer *** achieved high performance across the TESLA cancer patients and detected 79%(27 out of 34)of validated neoantigens in ***-and indel-derived neoantigens accounted for 90%of the top 100 candidate neoantigens while neoantigens from aberrant splicing accounted for 9%.Gene fusion-derived neoantigens were detected in one *** is a powerful tool to‘catch all’neoantigens and is available for free academic use on Github(XuegongLab/NeoHunter).