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.

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 Release 3.1.0

This release adds the following new features:

  • When running the pipelines with the --netmhc-stab flag enabled, the NetMHCstab allele column now also reports the distance of the NetMHCstabpan allele when that allele is not identical to the HLA Allele of the original result.

  • When running the pipelines with a set of individual class II alleles, the pipeline now also auto-generates valid combinations of these alleles so that users no longer need to explicitly provide these combinations.

This release also fixes the following problem(s):

  • Some class I alleles are not supported by NetMHCstabpan and will lead to an error when attempt to make predictions with them. This release will skip such alleles for the stability prediction step.

  • For very large result sets the filtering steps would stall or be killed because the steps would run out of memory. This release fixes this issue.

  • This release adds better handling of timeout errors while running NetMHCstabpan and/or NetChop.

New in Version 3.1

This version adds the following features, outlined below. Please note that pVACtools 3.0 is not backwards-compatible and certain changes will break old workflows.

Breaking Changes

  • The pVACapi and pVACviz tools have been removed. They have been replaced by the pVACview tool.

  • The package namespace has been updated. The files will now be installed underneath a pvactools directory in your python package installation path.

  • The aggregated report format has been updated. The headers have been updated for clarity. An additional column Allele Expr has been added, representing RNA expression * RNA VAF. For more information see all_epitopes.aggregated.tsv Report Columns.

  • pVACfuse no longer supports inputs from Integrate NEO. Only AGFusion inputs will be supported going forward.

  • The format of the pVACfuse all_epitopes and filtered reports has been updated to remove columns that aren’t applicable for the tool. Please see the documentation for the pVACfuse Prediction Algorithms Supporting Percentile Information for more information.

New Features

  • This release adds a new tool, pVACview. pVACview is an R Shiny application that allows for that visualization of the pVACseq aggregated report file to review, explore, and prioritize the different neoantigen candidates predicted by pVACseq.

  • The 3.0 release adds several improvements to the reference proteome similarity step:

    • Users can now run the reference proteome similarity step with a standalone Protein BLAST installation. To use a standalone BLASTp installation, provide the installation path using the --blastp-path parameter. The supported Protein BLAST databases are refseq_select_prot and refseq_protein. Please reference the Installing BLAST documentation for further instructions.

    • When running the reference proteome similarity step using the NCBI Protein BLAST API, users can now pick between the refseq_select_prot and refseq_protein databases.

    • Parallelization has been added to the reference proteome similarity step. When running this step as part of the pVACseq, pVACfuse, or pVACbind pipelines, the existing --t parameter will also be used to set the number of parallel threads in this step.

  • This release adds standalone commands to run stability predictions, cleavage site predictions, and the reference proteome similarity step on the output of the pVACseq, pVACfuse, and pVACbind pipelines.

Minor Updates

  • Previously, when running NetChop for cleavage site predictions, predictions were made for each epitope individually. However, these predictions will differ if additional flanking amino acids are provided and will be stable with 9 or more flanking amino acids. We updated this step to make predictions with 9 flanking amino acids around each epitope to generate stable predictions.

  • This release adds a --species option to the valid_alleles commands to filter alleles on a species of interest.

  • This release adds a --pass-only flag to the pvacseq generate_protein_fasta commands to only process VCF entries that do not have a FILTER set.

  • This release adds a new parameter --tumor-purity. This parameter indicates the fraction of tumor cells in the tumor sample and is used during aggregate report creation for a simple estimation whether variants are subclonal or clonal based on VAF.

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.

Source code

The pVACtools source code is available in GitHub.

License

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