Related Experiment Video

Updated: Dec 27, 2025

Predictive Immune Modeling of Solid Tumors
08:50

Predictive Immune Modeling of Solid Tumors

Published on: February 25, 2020

7.4K

OpenVax: An Open-Source Computational Pipeline for Cancer Neoantigen Prediction

Julia Kodysh1, Alex Rubinsteyn2

  • 1Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. julia@openvax.org.

Methods in Molecular Biology (Clifton, N.J.)
|March 4, 2020
PubMed

Insights

OpenVax is a computational workflow for identifying cancer mutations and predicting neoantigens for personalized cancer vaccines. This pipeline analyzes tumor/normal sequencing data and is used in ongoing clinical trials.

Area of Science:

  • Computational biology
  • Immunogenomics
  • Cancer immunotherapy

Background:

  • Personalized cancer vaccines require accurate identification of tumor-specific mutations and neoantigens.
  • Computational tools are essential for analyzing complex genomic data in cancer research.

Purpose of the Study:

  • To describe the installation and usage of OpenVax, a computational workflow for personalized cancer vaccine development.
  • To guide users in interpreting the results generated by the OpenVax pipeline.

Main Methods:

  • OpenVax is a Dockerized, end-to-end computational pipeline.
  • It processes raw tumor and normal sequencing data.
  • The workflow includes somatic variant identification and neoantigen prediction.

Main Results:

  • OpenVax successfully identifies somatic variants and predicts neoantigens.
  • The workflow is currently implemented in three active clinical trials.
  • Detailed instructions for installation, usage, and result interpretation are provided.

Conclusions:

  • OpenVax provides a robust computational framework for personalized cancer vaccine design.
  • The workflow facilitates the integration of genomic data into clinical applications for cancer immunotherapy.
  • The described methods enable researchers and clinicians to utilize OpenVax effectively.
Keywords:
Bioinformatics pipelineCancer vaccineDockerImmunoinformaticsNGSNeoantigen

More Related Videos

Enrich and Expand Rare Antigen-specific T Cells with Magnetic Nanoparticles09:28

Enrich and Expand Rare Antigen-specific T Cells with Magnetic Nanoparticles

Published on: November 17, 2018

11.9K
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization03:08

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

825

Related Concept Videos

Cancer Vaccines01:30

Cancer Vaccines

Cancer treatment vaccines are a rapidly evolving field that offers a promising approach to immunotherapy. Unlike traditional vaccines that prevent diseases, cancer treatment vaccines are designed to treat existing cancers by stimulating the immune system to recognize and attack cancer cells.
Cancer vaccines come in two categories: preventive (prophylactic) and treatment (active). Preventive vaccines, such as the Human Papillomavirus (HPV) vaccine, protect against viruses that cause certain...
880
Adaptive Mechanisms in Cancer Cells02:53

Adaptive Mechanisms in Cancer Cells

Cancer cells accumulate genetic changes at an abnormally rapid rate due to the defects in the DNA repair mechanisms. From an evolutionary perspective, such genetic instability is advantageous for cancer development. Mutant cell lines accumulate a series of beneficial mutations that contribute to their progression into cancer.
Some of the advantages that cancer cells have on normal cells include - enhanced ability to divide without terminally differentiating, induce new blood vessel formation,...
6.8K
Mouse Models of Cancer Study02:43

Mouse Models of Cancer Study

Mice have long served as models for studying human biology and pathology because of their phylogenetic and physiological similarity with humans. They are also easy to maintain and breed in the laboratory, and hence, many inbred strains are now available for research. Studies on mice have contributed immeasurably to our understanding of cancer biology.
The development of transgenic, knockout, and knock-in mice has led to an exponential increase in their use as model organisms in research,...
6.3K
Tumor Immunotherapy01:27

Tumor Immunotherapy

Immunotherapy is a treatment that boosts or manipulates the immune system to fight diseases, including cancer. For instance, by stimulating an immune response through vaccinations against viruses that cause cancers, like hepatitis B virus and human papillomavirus, these diseases can be prevented. Nonetheless, some cancer cells can avoid the immune system due to their rapid mutation and division. The immune response to many cancers involves three phases: elimination, equilibrium, and escape.
1.7K
Cancer Survival Analysis01:21

Cancer Survival Analysis

Cancer survival analysis focuses on quantifying and interpreting the time from a key starting point, such as diagnosis or the initiation of treatment, to a specific endpoint, such as remission or death. This analysis provides critical insights into treatment effectiveness and factors that influence patient outcomes, helping to shape clinical decisions and guide prognostic evaluations. A cornerstone of oncology research, survival analysis tackles the challenges of skewed, non-normally...
594
Cancer-Critical Genes I: Proto-oncogenes01:33

Cancer-Critical Genes I: Proto-oncogenes

Genes usually encode proteins necessary for the proper functioning of a healthy cell. Mutations can often cause changes to the gene expression pattern, thereby altering the phenotype.
When the function of certain critical genes, especially those involved in cell cycle regulation and cell growth signaling cascades, gets disrupted, it upsets the cell cycle progression. Such cells with unchecked cell cycles start proliferating uncontrollably and eventually develop into tumors.
Such genes that act...
11.0K