pVAC-Seq

pVAC-Seq is a cancer immunotherapy pipeline for the identification of personalized Variant Antigens by Cancer Sequencing (pVAC-Seq) that integrates tumor mutation and expression data (DNA- and RNA-Seq). It enables cancer immunotherapy research by using massively parallel sequence data to predicting tumor-specific mutant peptides (neoantigens) that can elicit anti-tumor T cell immunity. It is being used in studies of checkpoint therapy response and to identify targets for cancer vaccines and adoptive T cell therapies. For more general information, see the manuscript published in Genome Medicine.

• Features
• Installation
  • Installing IEDB binding prediction tools (optional)
    • MHC Class I
    • MHC Class II
• Prerequisites
  • VEP
  • Optional Preprocessing
    • bam-readcount
    • Cufflinks
• Usage
• Filtering Commands
  • Binding Filter
  • Coverage Filter
• Additional Commands
  • Download Example Data
  • Install VEP Plugin
  • List Valid Alleles
  • Documentation For Configuration Files
• Optional Downstream Analysis Tools
  • Generate Protein Fasta
• Contact

New in version 4.0.6

This version updates the IEDB RESTful API URL to the new target announced in IEDB Analysis Resource v2.15.1.

This release introduces a change in how invalid alleles are handeled. Previously, the pipeline would throw a fatal error. The pipeline will now proceed but invalid alleles will be skipped.

This version also has improved error handling around calling standalone IEDB installations.

Citation

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

License

This project is licensed under NPOSL-3.0.