pVACtools

pVACtools is a cancer immunotherapy tools suite consisting of the following tools:

pVACseq

A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a VCF file.

pVACbind

A cancer immunotherapy pipeline for identifying and prioritizing neoantigens from a FASTA file.

pVACfuse

A tool for detecting neoantigens resulting from gene fusions.

pVACsplice

A tool for detecting neoantigens resulting from splice site variants.

pVACvector

A tool designed to aid specifically in the construction of DNA-based cancer vaccines.

pVACview

An application based on R Shiny that assists users in reviewing, exploring and prioritizing neoantigens from the results of pVACtools processes for personalized cancer vaccine design.

pVACtools immunotherapy workflow

Contents

New in Version 5.1.0

This is a minor feature release. It adds the following features:

  • This update allows pVACvector to remove peptides in order to find a partial solution if a full solution cannot be found. The number of peptides permitted to be removed can be controlled by the --allow-n-peptide-exclusion parameter. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1168

  • This update adds functionalities to pVACvector to prevent the core neoantigen candidate from getting clipped. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1174

  • When only elution algorithms are chosen and no binding affinity algorithms, the pipelines will now output a warning message that no aggregated report can be created. by @ldhtnp in https://github.com/griffithlab/pVACtools/pull/1165

  • When creating the aggregated report, the Best Peptide for some variants may not match the aggregate inclusion criteria and no detail information would be available for this peptide when investigating the variant. This update ensures that the Best Peptide is always included in the metrics file and counted toward the Num Included Peptides count. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1177

  • The evaluation buttons in pVACview will now be colored green for Accept, red for Reject, and orange for Review to visually differentiate the different statuses. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1173

It also fixes the following problem(s):

  • This release removes two parameters from pVACvector: --aggregate-inclusion-binding-threshold and --aggregate-inclusion-count-limit which are not applicable to this pipeline. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1180

  • This release fixes various pVACview bugs. Specifically, it fixes a bug that would result in pVACview crashing when a variant with a Num Included Peptides of 0 was selected. It also fixes a bug where re-tiering the candidates before selecting evaluations would result in evaluations being associated with incorrect variants. Additionally, it fixes several deprecation warnings and typos. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1173

New in Version 5

This is a major version release. Please note that pVACtools 5.0 is not guaranteed to be backwards-compatible and certain changes could break old workflows.

New Tools

This release adds a new tool, pVACsplice, for prediction neoantigens from splice sites. Please see the full tool documentation for more information. by @mrichters in https://github.com/griffithlab/pVACtools/pull/911

New Features

  • This release refactors the pVACvector graph building algorithm in order to increase the probability for finding a solution and reduce the number of iterations needed before a solution is found. Please see the PR describtion for the full details. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1163

  • Add a new --aggregate-inclusion-count-limit parameter to set the maximum number of epitopes to include in the metrics.json detailed data for variants that have a large number of candidate neoantigens (e.g., frameshifts). by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1147

  • Add a new --biotypes parameter which defines a list of transcript consequence biotypes that the predictions from pVACseq and pVACsplice should be limited to. by @mrichters in https://github.com/griffithlab/pVACtools/pull/911

  • Add support for additional alleles that weren’t previously supported, includings ones for dog, mouse, and MHC class II. by @susannasiebert in https://github.com/griffithlab/pVACtools/pull/1148

Bugfixes

Past release notes can be found on our Release Notes page.

To stay up-to-date on the latest pVACtools releases please join our Mailing List.

Citations

Jasreet Hundal , Susanna Kiwala , Joshua McMichael, Chris Miller, Huiming Xia, Alex Wollam, Conner Liu, Sidi Zhao, Yang-Yang Feng, Aaron Graubert, Amber Wollam, Jonas Neichin, Megan Neveau, Jason Walker, William Gillanders, Elaine Mardis, Obi Griffith, Malachi Griffith. pVACtools: A Computational Toolkit to Identify and Visualize Cancer Neoantigens. Cancer Immunology Research. 2020 Mar;8(3):409-420. doi: 10.1158/2326-6066.CIR-19-0401. PMID: 31907209.

Jasreet Hundal, Susanna Kiwala, Yang-Yang Feng, Connor J. Liu, Ramaswamy Govindan, William C. Chapman, Ravindra Uppaluri, S. Joshua Swamidass, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. Accounting for proximal variants improves neoantigen prediction. Nature Genetics. 2018, DOI: 10.1038/s41588-018-0283-9. PMID: 30510237.

Jasreet Hundal, Beatriz M. Carreno, Allegra A. Petti, Gerald P. Linette, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. pVACseq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Medicine. 2016, 8:11, DOI: 10.1186/s13073-016-0264-5. PMID: 26825632.

Huiming Xia, My H. Hoang, Evelyn Schmidt, Susanna Kiwala, Joshua McMichael, Zachary L. Skidmore, Bryan Fisk, Jonathan J. Song, Jasreet Hundal, Thomas Mooney, Jason R. Walker, S. Peter Goedegebuure, Christopher A. Miller, William E. Gillanders, Obi L. Griffith, Malachi Griffith. pVACview: an interactive visualization tool for efficient neoantigen prioritization and selection. Genome Medicine. 2024, 16:132, DOI: 10.1186/s13073-024-01384-7. PMID: 39538339.

Source code

The pVACtools source code is available in GitHub.

License

This project is licensed under BSD 3-Clause Clear License.