DIY: Visualizing the immune landscape of tumors using transcriptome and methylome data

The importance of the immune system in combating many different types of malignancies has been firmly established. Indeed, the success of immune checkpoint-blocking antibodies in cancer treatment has focused the attention of many researchers on the tumor immune microenvironment. As one consequence, the analysis of the number, type, and activation status of tumor-infiltrating leukocytes (TILs) has become an area of great interest. Detailed knowledge of the immunological profile of a given tumor has the potential to predict patient response to therapy and overall survival. This chapter is intended to summarize the steps necessary for basic comparative analysis of the infiltration and activation status of immune cells in various human solid tumors, using freely available data obtained from The Cancer Genome Atlas (TCGA).