TY - JOUR T1 - Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data JF - bioRxiv DO - 10.1101/117788 SP - 117788 AU - Julien Racle AU - Kaat de Jonge AU - Petra Baumgaertner AU - Daniel E. Speiser AU - David Gfeller Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/03/17/117788.abstract N2 - Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene expression data. Our method integrates novel gene expression profiles from circulating and tumor infiltrating cells for each major immune cell type, cell-type specific mRNA content and the ability to model uncharacterized, and possibly highly variable, cell types. Feasibility is demonstrated by validation with flow cytometry, immunohistochemistry and single-cell RNA-Seq analyses of human melanoma and colorectal tumor specimens. Altogether, our work not only improves accuracy but also broadens the scope of absolute cell fraction predictions from tumor gene expression data, and provides a unique novel experimental benchmark for immunogenomics analyses in cancer research.EPICacronym for our method to "Estimate the Proportion of Immune and Cancer cells"GEOGene Expression OmnibusIHCimmunohistochemistryPCAprincipal component analysisRMSEroot mean squared errorTCGAThe Cancer Genome Atlas ER -