Neo-Pred:全变异来源的肿瘤新生抗原检测流程OA

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.