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Updated: Feb 18, 2026
Predictive Immune Modeling of Solid Tumors
Published on: February 25, 2020
Impact of Tumor Purity on Immune Gene Expression and Clustering Analyses across Multiple Cancer Types
Je-Keun Rhee1,2, Yu Chae Jung3, Kyu Ryung Kim1,2
1Department of Medical Informatics, College of Medicine, The Catholic University of Korea, Seoul, Korea.
Abstract:
Surgical archives of tumor specimens are often impure. The presence of RNA transcripts from nontumor cells, such as immune and stromal cells, can impede analyses of cancer expression profiles. To systematically analyze the impact of tumor purity, the gene expression profiles and tumor purities were obtained for 7,794 tumor specimens across 21 tumor types (available in The Cancer Genome Atlas consortium). First, we observed that genes with roles in immunity and oxidative phosphorylation were significantly inversely correlated and correlated with the tumor purity, respectively. The expression of genes implicated in immunotherapy and specific immune cell genes, along with the abundance of immune cell infiltrates, was substantially inversely correlated with tumor purity. This relationship may explain the correlation between immune gene expression and mutation burden, highlighting the need to account for tumor purity in the evaluation of expression markers obtained from bulk tumor transcriptome data. Second, examination of cluster membership of gene pairs, with or without controlling for tumor purity, revealed that tumor purity may have a substantial impact on gene clustering across tumor types. Third, feature genes for molecular taxonomy were analyzed for correlation with tumor purity, and for some tumor types, feature genes representing the mesenchymal and classical subtypes were inversely correlated and correlated with tumor purity, respectively. Our findings indicate that tumor purity is an important confounder in evaluating the correlation between gene expression and clinicopathologic features such as mutation burden, as well as gene clustering and molecular taxonomy. Cancer Immunol Res; 6(1); 87-97. ©2017 AACR.
Insights
Tumor purity significantly impacts cancer gene expression analysis. Accounting for non-tumor cell RNA is crucial for accurate cancer profiling and understanding immune gene expression correlations.
Area of Science:
- Cancer genomics
- Transcriptomics
- Bioinformatics
Background:
- Tumor specimens often contain non-tumor cells (immune, stromal), leading to impure RNA samples.
- This impurity can interfere with the analysis of cancer gene expression profiles.
- Understanding the impact of tumor purity is essential for accurate interpretation of cancer transcriptome data.
Purpose of the Study:
- To systematically analyze the influence of tumor purity on gene expression profiles across various cancer types.
- To investigate the relationship between tumor purity and immune gene expression, mutation burden, and molecular subtypes.
- To highlight the importance of accounting for tumor purity in bulk transcriptome data analysis.
Main Methods:
- Utilized gene expression profiles and tumor purity data from 7,794 tumor specimens across 21 tumor types from The Cancer Genome Atlas (TCGA).
- Performed correlation analyses between tumor purity and gene expression, focusing on immune and oxidative phosphorylation pathways.
- Examined the impact of tumor purity on gene clustering and the correlation of subtype-specific feature genes with purity.
Main Results:
- Immunity-related genes were inversely correlated with tumor purity, while oxidative phosphorylation genes were positively correlated.
- Immune cell infiltration and expression of immunotherapy-related genes showed a substantial inverse correlation with tumor purity.
- Tumor purity significantly affected gene clustering and the correlation of molecular subtype markers (e.g., mesenchymal, classical) with purity.
Conclusions:
- Tumor purity is a critical confounder in the analysis of bulk tumor transcriptome data.
- Adjusting for tumor purity is necessary for accurate evaluation of gene expression markers, mutation burden correlations, and molecular taxonomy.
- These findings underscore the need to consider tumor purity for robust cancer expression profiling and biomarker discovery.
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