PT - JOURNAL ARTICLE AU - Patrick Danaher AU - Sarah Warren AU - Lucas Dennis AU - Leonard D’Amico AU - Andrew White AU - Mary L. Disis AU - Melissa A. Geller AU - Kunle Odunsi AU - Joseph Beechem AU - Steven P. Fling TI - Gene expression markers of Tumor Infiltrating Leukocytes AID - 10.1101/068940 DP - 2016 Jan 01 TA - bioRxiv PG - 068940 4099 - http://biorxiv.org/content/early/2016/08/11/068940.short 4100 - http://biorxiv.org/content/early/2016/08/11/068940.full AB - Background Assays of the abundance of immune cell populations in the tumor microenvironment promise to inform immune oncology research and the choice of immunotherapy for individual patients. We propose to measure the intratumoral abundance of various immune cells populations with gene expression. In contrast to IHC and flow cytometry, gene expression assays yield high information content from a clinically practical workflow. Previous studies of gene expression in purified immune cells have reported hundreds of genes showing enrichment in a single cell type, but the utility of these genes in tumor samples is unknown. We describe a novel statistical method for using co-expression patterns in large tumor gene expression datasets to validate previously reported candidate cell type marker genes, and we use this method to winnow previously published gene lists down to a subset of high confidence marker genes.Methods We use co-expression patterns in 9986 samples from The Cancer Genome Atlas (TCGA) to validate previously reported cell type marker genes. We compare immune cell scores derived from these genes to measurements from flow cytometry and immunohistochemistry. We characterize the reproducibility of our cell scores in replicate runs of RNA extracted from FFPE tumor tissue.Results We identify a list of 60 marker genes whose expression levels quantify 14 immune cell populations. Cell type scores calculated from these genes are concordant with flow cytometry and IHC readings, show high reproducibility in replicate RNA samples from FFPE tissue, and reveal an intricate picture of the immune infiltrate in TCGA. Most genes previously reported to be enriched in a single cell type have co-expression patterns inconsistent with cell type specificity.Conclusions Due to their concise gene set, computational simplicity and utility in tumor samples, these cell type gene signatures may be useful in future discovery research and clinical trials to understand how tumors and therapeutic intervention shape the immune response.