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pVACtools: a computational toolkit to identify and visualize cancer neoantigens

View ORCID ProfileJasreet Hundal, Susanna Kiwala, Joshua McMichael, Christopher A. Miller, Alexander T. Wollam, Huiming Xia, Connor J. Liu, Sidi Zhao, Yang-Yang Feng, Aaron P. Graubert, Amber Z. Wollam, Jonas Neichin, Megan Neveau, Jason Walker, William E Gillanders, Elaine R. Mardis, View ORCID ProfileObi L. Griffith, View ORCID ProfileMalachi Griffith
doi: https://doi.org/10.1101/501817
Jasreet Hundal
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Susanna Kiwala
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Joshua McMichael
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Christopher A. Miller
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
2Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
4Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
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Alexander T. Wollam
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Huiming Xia
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Connor J. Liu
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Sidi Zhao
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Yang-Yang Feng
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Aaron P. Graubert
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Amber Z. Wollam
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Jonas Neichin
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Megan Neveau
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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Jason Walker
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
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William E Gillanders
4Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
5Department of Surgery, Washington University School of Medicine, St. Louis, MO, USA
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Elaine R. Mardis
3Institute for Genomic Medicine, Nationwide Children’s Hospital, 575 Children’s Crossroad, Columbus OH, USA
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Obi L. Griffith
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
2Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
4Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
6Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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  • For correspondence: obigriffith@wustl.edu mgriffit@wustl.edu
Malachi Griffith
1McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA
2Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, MO, USA
4Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO, USA
6Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
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  • ORCID record for Malachi Griffith
  • For correspondence: obigriffith@wustl.edu mgriffit@wustl.edu
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Abstract

Identification of neoantigens is a critical step in predicting response to checkpoint blockade therapy and design of personalized cancer vaccines. We have developed an in silico sequence analysis toolkit - pVACtools, to facilitate comprehensive neoantigen characterization. pVACtools supports a modular workflow consisting of tools for neoantigen prediction from somatic alterations (pVACseq and pVACfuse), prioritization and selection using a graphical web-based interface (pVACviz) and design of DNA vector-based vaccines (pVACvector) and synthetic long peptide vaccines. pVACtools is available at pvactools.org.

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Posted May 29, 2019.
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pVACtools: a computational toolkit to identify and visualize cancer neoantigens
Jasreet Hundal, Susanna Kiwala, Joshua McMichael, Christopher A. Miller, Alexander T. Wollam, Huiming Xia, Connor J. Liu, Sidi Zhao, Yang-Yang Feng, Aaron P. Graubert, Amber Z. Wollam, Jonas Neichin, Megan Neveau, Jason Walker, William E Gillanders, Elaine R. Mardis, Obi L. Griffith, Malachi Griffith
bioRxiv 501817; doi: https://doi.org/10.1101/501817
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pVACtools: a computational toolkit to identify and visualize cancer neoantigens
Jasreet Hundal, Susanna Kiwala, Joshua McMichael, Christopher A. Miller, Alexander T. Wollam, Huiming Xia, Connor J. Liu, Sidi Zhao, Yang-Yang Feng, Aaron P. Graubert, Amber Z. Wollam, Jonas Neichin, Megan Neveau, Jason Walker, William E Gillanders, Elaine R. Mardis, Obi L. Griffith, Malachi Griffith
bioRxiv 501817; doi: https://doi.org/10.1101/501817

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