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Related Experiment Video

Updated: Sep 12, 2025

Analyzing Tumor and Tissue Distribution of Target Antigen Specific Therapeutic Antibody
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Predicting Tumor Antigens Using the LENS Workflow Through RAFT.

Steven P Vensko Ii1, Dante Bortone2, Benjamin G Vincent2

  • 1Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA. steven.vensko@med.unc.edu.

Methods in Molecular Biology (Clifton, N.J.)
|August 8, 2025
PubMed
Summary

Predicting tumor antigens for personalized cancer vaccines and T cell therapies is challenging. This study introduces RAFT and LENS, a flexible bioinformatics framework and modular workflow for accurate neoantigen prediction.

Keywords:
BioinformaticsImmuno-oncologyNeoantigenNeoantigen workflowTumor antigenTumor-associated antigen

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Area of Science:

  • Oncology
  • Immunology
  • Bioinformatics

Background:

  • Tumor antigens are key targets for personalized cancer immunotherapies, including vaccination and T cell receptor-engineered T cell (TCR-T) therapy.
  • Accurate prediction of these tumor antigens is computationally challenging, requiring adaptable tools and methods.

Purpose of the Study:

  • To present RAFT, a framework for reproducible bioinformatics.
  • To introduce LENS, a modular workflow for neoantigen prediction.
  • To provide guidance on installing, running, and customizing LENS.

Main Methods:

  • Development of the RAFT bioinformatics framework.
  • Implementation of the LENS neoantigen prediction workflow.
  • Detailed instructions for LENS setup and adaptation.

Main Results:

  • A functional and reproducible bioinformatics framework (RAFT).
  • A modular and adaptable neoantigen prediction workflow (LENS).
  • Comprehensive documentation for LENS utilization.

Conclusions:

  • RAFT and LENS offer a flexible and reproducible solution for neoantigen prediction.
  • The LENS workflow facilitates personalized cancer immunotherapy development.
  • Customizable bioinformatics tools are crucial for advancing cancer research.