This study systematically analyzes the impact of tumor purity on genomic data analysis across 21 cancer types from the Cancer Genome Atlas (TCGA). Tumor purity, defined as the proportion of cancer cells in a sample, is influenced by both intrinsic and extrinsic factors. The authors used four different methods to estimate tumor purity and found high concordance among DNA, RNA, and methylation-based methods but lower correlation with immunohistochemistry (IHC) estimates. They observed significant associations between tumor purity and mutational burden, as well as with clinical features such as histological subtype and tumor grade. The study highlights the confounding effect of tumor purity on various bioinformatics analyses, including co-expression networks, molecular subtyping, and differential expression analysis. Adjusting for tumor purity in these analyses revealed novel pathways and genes, particularly those related to T-cell activation, which are important for immunotherapy. The findings underscore the importance of accounting for tumor purity in future cancer research and clinical applications.This study systematically analyzes the impact of tumor purity on genomic data analysis across 21 cancer types from the Cancer Genome Atlas (TCGA). Tumor purity, defined as the proportion of cancer cells in a sample, is influenced by both intrinsic and extrinsic factors. The authors used four different methods to estimate tumor purity and found high concordance among DNA, RNA, and methylation-based methods but lower correlation with immunohistochemistry (IHC) estimates. They observed significant associations between tumor purity and mutational burden, as well as with clinical features such as histological subtype and tumor grade. The study highlights the confounding effect of tumor purity on various bioinformatics analyses, including co-expression networks, molecular subtyping, and differential expression analysis. Adjusting for tumor purity in these analyses revealed novel pathways and genes, particularly those related to T-cell activation, which are important for immunotherapy. The findings underscore the importance of accounting for tumor purity in future cancer research and clinical applications.