ArticleBMC medical genomics2020
ProGeo-neo: a customized proteogenomic workflow for neoantigen prediction and selection.
Article in BMC medical genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers, 1 of them a synthesis that pooled it.
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Who cites it
23 citing papers in PubMed, 1 synthesis or guideline pooled it, 26 citations in OpenAlex.
- Transformers meets neoantigen detection: a systematic literature review.Journal of integrative bioinformatics · 2024Pooled it
- Artificial intelligence for translational personalized neoantigen cancer vaccine development.Journal of biomedical science · 2026Review
- SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data.Biology · 2026Article
- iPepGen: a modular, immunopeptidogenomic analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates.Genome biology · 2026Article
- Characterization of Tumor Antigens from Multi-omics Data: Computational Approaches and Resources.Genomics, proteomics & bioinformatics · 2025Review
- Computational methods and data resources for predicting tumor neoantigens.Briefings in bioinformatics · 2025Review
- Review
- OmniNeo: a multi-omics pipeline incorporating proteomics and AI selection for neoantigen optimization in tumor immunotherapy.Frontiers in immunology · 2025Article
- Phenotyping Tumor Heterogeneity through Proteogenomics: Study Models and Challenges.International journal of molecular sciences · 2024Review
- Neoantigen-targeted TCR-engineered T cell immunotherapy: current advances and challenges.Biomarker research · 2023Review
- Article
- Systems Biology Approaches for the Improvement of Oncolytic Virus-Based Immunotherapies.Cancers · 2023Review
- Article
- Article
- Prospects and challenges of cancer systems medicine: from genes to disease networks.Briefings in bioinformatics · 2022Review
- Single-Cell Sequencing Identifies the Heterogeneity of CD8+ T Cells and Novel Biomarker Genes in Hepatocellular Carcinoma.Journal of healthcare engineering · 2022Article
- dbPepNeo2.0: A Database for Human Tumor Neoantigen Peptides From Mass Spectrometry and TCR Recognition.Frontiers in immunology · 2022Article
- Computational cancer neoantigen prediction: current status and recent advances.Immuno-oncology technology · 2021Review
- Immunopeptidogenomics: Harnessing RNA-Seq to Illuminate the Dark Immunopeptidome.Molecular & cellular proteomics : MCP · 2021Article
- Protein-gene Expression Nexus: Comprehensive characterization of human cancer cell lines with proteogenomic analysis.Computational and structural biotechnology journal · 2021Article
Corrections and comments
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Authors and funding
10 authors at 6 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundNeoantigens can be differentially recognized by T cell receptor (TCR) as these sequences are derived from mutant proteins and are unique to the tumor. The discovery of neoantigens is the first key step for tumor-specific antigen (TSA) based immunotherapy. Based on high-throughput tumor genomic analysis, each missense mutation can potentially give rise to multiple neopeptides, resulting in a vast total number, but only a small percentage of these peptides may achieve immune-dominant status with a given major histocompatibility complex (MHC) class I allele. Specific identification of immunogenic candidate neoantigens is consequently a major challenge. Currently almost all neoantigen prediction tools are based on genomics data.
resultsHere we report the construction of proteogenomics prediction of neoantigen (ProGeo-neo) pipeline, which incorporates the following modules: mining tumor specific antigens from next-generation sequencing genomic and mRNA expression data, predicting the binding mutant peptides to class I MHC molecules by latest netMHCpan (v.4.0), verifying MHC-peptides by MaxQuant with mass spectrometry proteomics data searched against customized protein database, and checking potential immunogenicity of T-cell-recognization by additional screening methods. ProGeo-neo pipeline achieves proteogenomics strategy and the neopeptides identified were of much higher quality as compared to those identified using genomic data only.
conclusionsThe pipeline was constructed based on the genomics and proteomics data of Jurkat leukemia cell line but is generally applicable to other solid cancer research. With massively parallel sequencing and proteomics profiling increasing, this proteogenomics workflow should be useful for neoantigen oriented research and immunotherapy.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.