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Review
. 2019 Dec;20(12):724-746.
doi: 10.1038/s41576-019-0166-7. Epub 2019 Sep 12.

Next-generation computational tools for interrogating cancer immunity

Francesca Finotello  1 , Dietmar Rieder  1 , Hubert Hackl  1 , Zlatko Trajanoski  2
Affiliations
Review

Next-generation computational tools for interrogating cancer immunity

Francesca Finotello et al. Nat Rev Genet. 2019 Dec.

Abstract

The remarkable success of cancer therapies with immune checkpoint blockers is revolutionizing oncology and has sparked intensive basic and translational research into the mechanisms of cancer-immune cell interactions. In parallel, numerous novel cutting-edge technologies for comprehensive molecular and cellular characterization of cancer immunity have been developed, including single-cell sequencing, mass cytometry and multiplexed spatial cellular phenotyping. In order to process, analyse and visualize multidimensional data sets generated by these technologies, computational methods and software tools are required. Here, we review computational tools for interrogating cancer immunity, discuss advantages and limitations of the various methods and provide guidelines to assist in method selection.

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References

    1. Tang, J. et al. Trial watch: the clinical trial landscape for PD1/PDL1 immune checkpoint inhibitors. Nat. Rev. Drug Discov. 17, 854–855 (2018). - PubMed - PMC
    1. Charoentong, P. et al. Pan-cancer immunogenomic analyses reveal genotype–immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 18, 248–262 (2017). - PubMed
    1. Thorsson, V. et al. The immune landscape of cancer. Immunity 48, 812–830.e14 (2018). - PubMed - PMC
    1. Hackl, H., Charoentong, P., Finotello, F. & Trajanoski, Z. Computational genomics tools for dissecting tumour–immune cell interactions. Nat. Rev. Genet. 17, 441 (2016). - PubMed
    1. Chen, D. S. & Mellman, I. Oncology meets immunology: the cancer-immunity cycle. Immunity 39, 1–10 (2013). - PubMed

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