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EPIC: A Tool to Estimate the Proportions of Different Cell Types from Bulk Gene Expression Data

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Bioinformatics for Cancer Immunotherapy

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2120))

Abstract

Gene expression profiling is nowadays routinely performed on clinically relevant samples (e.g., from tumor specimens). Such measurements are often obtained from bulk samples containing a mixture of cell types. Knowledge of the proportions of these cell types is crucial as they are key determinants of the disease evolution and response to treatment. Moreover, heterogeneity in cell type proportions across samples is an important confounding factor in downstream analyses.

Many tools have been developed to estimate the proportion of the different cell types from bulk gene expression data. Here, we provide guidelines and examples on how to use these tools, with a special focus on our recent computational method EPIC (Estimating the Proportions of Immune and Cancer cells). EPIC includes RNA-seq-based gene expression reference profiles from immune cells and other nonmalignant cell types found in tumors. EPIC can additionally manage user-defined gene expression reference profiles. Some unique features of EPIC include the ability to account for an uncharacterized cell type, the introduction of a renormalization step to account for different mRNA content in each cell type, and the use of single-cell RNA-seq data to derive biologically relevant reference gene expression profiles. EPIC is available as a web application (http://epic.gfellerlab.org) and as an R-package (https://github.com/GfellerLab/EPIC).

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Author information

Authors and Affiliations

  1. Department of Oncology UNIL CHUV, Ludwig Institute for Cancer Research, University of Lausanne, Lausanne, Switzerland

    Julien Racle & David Gfeller

  2. Swiss Institute of Bioinformatics (SIB), Lausanne, Switzerland

    Julien Racle & David Gfeller

Authors
  1. Julien Racle
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  2. David Gfeller
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Corresponding author

Correspondence to David Gfeller .

Editor information

Editors and Affiliations

  1. Mainz, Germany

    Sebastian Boegel

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Racle, J., Gfeller, D. (2020). EPIC: A Tool to Estimate the Proportions of Different Cell Types from Bulk Gene Expression Data. In: Boegel, S. (eds) Bioinformatics for Cancer Immunotherapy. Methods in Molecular Biology, vol 2120. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0327-7_17

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  • DOI: https://doi.org/10.1007/978-1-0716-0327-7_17

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-0326-0

  • Online ISBN: 978-1-0716-0327-7

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