ProGeo-Neo v2.0: A One-Stop Software for Neoantigen Prediction and Filtering Based on the Proteogenomics Strategy

Genes

Yuyu Li¹  Chunyu Liu¹  Manman Lu¹  Lanming Chen¹  Lu Xie¹  Yong Lin²  Zhenhao Liu³  Linfeng Xu³  Xiaoxiu Tan³  Jian Ouyang³  Yu Zhang³  Xingxing Jian³ 

[1] College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China;School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200093, China;Shanghai-MOST Key Laboratory of Health and Disease Genomics, Institute for Genome and Bioinformatics, Shanghai Institute for Biomedical and Pharmaceutical Technologies, 779 Old Humin Road, Shanghai 200237, China;

关键词: bioinformatics;    neoantigen;    proteogenomic;    tumor immunotherapy;   

DOI  :  10.3390/genes13050783

来源: DOAJ

【 摘 要 】

A proteogenomics-based neoantigen prediction pipeline, namely ProGeo-neo, was previously developed by our team to predict neoantigens, allowing the identification of class-I major histocompatibility complex (MHC) binding peptides based on single-nucleotide variation (SNV) mutations. To improve it, we here present an updated pipeline, i.e., ProGeo-neo v2.0, in which a one-stop software solution was proposed to identify neoantigens based on the paired tumor-normal whole genome sequencing (WGS)/whole exome sequencing (WES) data in FASTQ format. Preferably, in ProGeo-neo v2.0, several new features are provided. In addition to the identification of MHC-I neoantigens, the new version supports the prediction of MHC class II-restricted neoantigens, i.e., peptides up to 30-mer in length. Moreover, the source of neoantigens has been expanded, allowing more candidate neoantigens to be identified, such as in-frame insertion-deletion (indels) mutations, frameshift mutations, and gene fusion analysis. In addition, we propose two more efficient screening approaches, including an in-group authentic neoantigen peptides database and two more stringent thresholds. The range of candidate peptides was effectively narrowed down to those that are more likely to elicit an immune response, providing a more meaningful reference for subsequent experimental validation. Compared to ProGeo-neo, the ProGeo-neo v2.0 performed well based on the same dataset, including updated functionality and improved accuracy.

【 授权许可】

Unknown