Related Experiment Video
Updated: Jul 6, 2026
Detection of Cell-Free DNA in Blood Plasma Samples of Cancer Patients
Published on: September 9, 2020
Bioinformatic Discovery of Tumor-Specific Neoantigens Arising from Chimeric RNAs
Samir Lalani1, Sehajroop Gadh1, Hui Li2,3
1Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, 22903, USA.
Abstract:
Cancer vaccines inducing immunogenic responses to tumor-specific neoantigens are rapidly emerging into a new frontier of cancer therapy. Chimeric RNAs encoding fusion proteins are a rich source of novel neoantigens. Here, we present a straightforward bioinformatic pipeline to identify immunogenic peptides produced from chimeric RNAs. We apply a bespoke script to identify fusion-specific peptide regions from chimeric transcript predictions and leverage the netMHCpan program to identify immunogenic peptides. In this paper, we provide a guide for installation and running of the program as well as discuss the rationale behind its design.
Insights
This study introduces a bioinformatic pipeline to find cancer neoantigens from chimeric RNAs, aiding the development of novel cancer vaccines. The method identifies immunogenic peptides for improved cancer immunotherapy.
Area of Science:
- Oncology
- Immunology
- Bioinformatics
Background:
- Cancer vaccines targeting tumor-specific neoantigens represent a significant advancement in cancer therapy.
- Chimeric RNAs are a promising source for generating novel neoantigens.
Purpose of the Study:
- To present a straightforward bioinformatic pipeline for identifying immunogenic peptides derived from chimeric RNAs.
- To facilitate the discovery of novel neoantigens for cancer vaccine development.
Main Methods:
- A bespoke script was developed to identify fusion-specific peptide regions from chimeric transcript predictions.
- The netMHCpan program was utilized to predict the immunogenicity of identified peptides.
Main Results:
- The pipeline successfully identifies potential immunogenic peptides from chimeric RNA sequences.
- The study provides a practical guide for the implementation and application of the developed pipeline.
Conclusions:
- The presented bioinformatic pipeline offers a valuable tool for discovering neoantigens from chimeric RNAs.
- This approach supports the advancement of neoantigen-based cancer vaccines and immunotherapies.
