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.
New in version 4.0.1¶
This version fixes compatibility issues with the new IEDB Analysis Resource v2.15 that was released on October 3rd 2016. Since pVAC-Seq uses the IEDB RESTful web interface, the new IEDB Analysis Resource version is being used natively. As a result, pVAC-Seq output for the NetMHC prediction algorithm is now NetMHC version 4.0. Some other changes in the output format from IEDB led to compatibility issues that are fixed in this new pVAC-Seq release.
This release also fixes an error with bam-readcount input files that occurs when a variant does not have a bam readcount entry.
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.