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In Silico Prediction of Tumor Neoantigens with TIminer

  • Alexander Kirchmair
  • Francesca FinotelloEmail author
Protocol
  • 246 Downloads
Part of the Methods in Molecular Biology book series (MIMB, volume 2120)

Abstract

Tumor neoantigens are at the core of immunological tumor control and response to immunotherapy. In silico prediction of tumor neoantigens from next-generation sequencing (NGS) data is possible but requires the assembly of complex, multistep computational pipelines and extensive data preprocessing. Using public data from two cancer cell lines, here we show how TIminer, a framework to perform immunogenomics analyses, can be easily used to assemble and run customized pipelines to predict cancer neoantigens from multisample NGS data.

Key words

Neoantigen prediction HLA typing Gene expression Cancer immunology Immuno-oncology 

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  1. 1.Biocenter, Institute of BioinformaticsMedical University of InnsbruckInnsbruckAustria

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