生物信息学2026，Vol.24Issue(1)：95-100,6.DOI:10.12113/202504006
Neo-Pred:全变异来源的肿瘤新生抗原检测流程
Neo-Pred:A comprehensive workflow for detecting tumor neoantigens from all types of mutation sources
摘要
Abstract
Neoantigens derived from somatic mutations have emerged as ideal targets for activating anti-tumor T-cell responses due to their high tumor specificity,strong immunogenicity,and absence of expression in normal tissues.Current bioinformatics tools remain limited in comprehensively detecting neoantigens originating from diverse genomic variations.To address this challenge,we developed Neo-Pred,a tumor neoantigen detection pipeline based on the Snakemake workflow management system.This pipeline processes high-throughput sequencing data to identify neoantigens derived from multiple variant types,including single nucleotide variants(SNVs),insertions-deletions(InDels),gene fusions,and alternative splicing.When evaluated on the benchmark dataset from the Tumor Neoantigen Screening Consortium,Neo-Pred demonstrated superior performance with an Area Under the Precision-Recall Curve(AUPRC)of 0.71(mean AUPRC:0.221 for all teams;0.540 for the top-performing team).This represents a performance improvement of 31.5%to 221.3%,highlighting its leading-edge detection capabilities.The implementation of Singularity containerization and modular architecture ensures remarkable stability,portability,and dynamic scalability.These technical advancements establish Neo-Pred as a cutting-edge solution for neoantigen detection,providing critical support for precision cancer immunotherapy research.关键词
新生抗原/单核苷酸突变/基因融合/可变剪接/流程Key words
Neoantigen/Single nucleotide variant/Gene fusion/Alternative splicing/Workflow分类
医药卫生引用本文复制引用
杜航,唐景玲,周玲,杨远..Neo-Pred:全变异来源的肿瘤新生抗原检测流程[J].生物信息学,2026,24(1):95-100,6.基金项目
国家自然科学基金(No.82260584) （No.82260584）
贵州省科技厅项目(No.黔科合支撑[2022]一般193、黔科合基础-ZK[2023]一般359、黔科合支撑[2023]一般373) （No.黔科合支撑[2022]一般193、黔科合基础-ZK[2023]一般359、黔科合支撑[2023]一般373）
贵州医科大学附属医院2024年国家自然科学基金培育计划(地区基金)(No.gyfynsfc[2024]-21). （地区基金）
