A computational analysis pipeline for neoepitope discovery toward cancer vaccines

Name: Nattachart Techajaroonjit

Organization : Mahidol University. Faculty of Science

Name: Nattawadee Panyain

Organization : Mahidol University. Faculty of Science

Name: Suradej Hongeng

Organization : Mahidol University. Faculty of Medicine Ramathibodi Hospital

Name: Vorthon Sawaswong

Organization : Mahidol University. Faculty of Science

Name: Patompon Wongtrakoongate

Organization : Mahidol University. Faculty of Science

Email : patompon.won@mahidol.edu

keyword: Neoantigens

LCSH: Cancer -- Genetic aspects

LCSH: Tumor antigens

LCSH: Immunotherapy

LCSH: Major histocompatibility complex

Abstract: Cancers arise from genetic alterations and clonal evolution, creating a unique profile for each patient. These genetic alterations enable tumors to produce unique peptides beyond normal cells, which can be presented by major histocompatibility complexes (MHC), and recognized by T-cell receptors to trigger tumor-specific immune responses. These peptides could be used as neoantigens or neoepitopes for personalized cancer therapeutics which can activate the patient’s immune system against cancer. However, not all mutated peptides are presented on MHC and can activate the immune response. The prediction of effective neoantigen is still challenging and needs to be improved. This study adopts and evaluates the bioinformatics workflow to predict neoantigens using next-generation sequencing (NGS) data. The multi-step process involves variant calling, MHC-binding prediction, and filtration. The state-of-the-art tools including NetMHCpan 4.0 and IEDB evaluate these mutant peptides for MHC binding affinity, and RNA expression levels filter the top candidates. The study demonstrates the promising neoantigen prediction pipeline which can identify the potential immunogenic neoantigens with statistically significantly reduced tumor growth. Future efforts will focus on experimentally validating predicted neoantigens to prove and enhance the accuracy of these predictions

King Mongkut's University of Technology North Bangkok. Central Library

Address: BANGKOK

Email: library@kmutnb.ac.th

Created: 2025

Modified: 2025-10-29

Issued: 2025-10-29

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BibliograpyCitation : In The Chemical Society of Thailand under the Patronage of Professor Dr. Her Royal Highness Princess Chulabhorn Krom Phra Srisavangavadhana and Suranaree University of Technology. Institute of Science. School of Chemistry. Pure and Applied Chemistry International Conference 2025 (PACCON 2025) (pp.765-770). Bangkok : The Chemical Society of Thailand under the Patronage of Professor Dr. Her Royal Highness Princess Chulabhorn Krom Phra Srisavangavadhana in association with the School of Chemistry, Institute of Science, Suranaree University of Technology, 2025

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