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An algorithm to quantify intratumor heterogeneity based on alterations of gene expression profiles.
- Source :
-
Communications biology [Commun Biol] 2020 Sep 11; Vol. 3 (1), pp. 505. Date of Electronic Publication: 2020 Sep 11. - Publication Year :
- 2020
-
Abstract
- Intratumor heterogeneity (ITH) is a biomarker of tumor progression, metastasis, and immune evasion. Previous studies evaluated ITH mostly based on DNA alterations. Here, we developed a new algorithm (DEPTH) for quantifying ITH based on mRNA alterations in the tumor. DEPTH scores displayed significant correlations with ITH-associated features (genomic instability, tumor advancement, unfavorable prognosis, immunosuppression, and drug response). Compared to DNA-based ITH scores (EXPANDS, PhyloWGS, MATH, and ABSOLUTE), DEPTH scores had stronger correlations with antitumor immune signatures, cell proliferation, stemness, tumor advancement, survival prognosis, and drug response. Compared to two other mRNA-based ITH scores (tITH and sITH), DEPTH scores showed stronger and more consistent associations with genomic instability, unfavorable tumor phenotypes and clinical features, and drug response. We further validated the reliability and robustness of DEPTH in 50 other datasets. In conclusion, DEPTH may provide new insights into tumor biology and potential clinical implications for cancer prognosis and treatment.
- Subjects :
- Algorithms
Biomarkers, Tumor genetics
Cell Proliferation genetics
Disease-Free Survival
Female
Gene Expression Regulation, Neoplastic genetics
Humans
Kaplan-Meier Estimate
Male
Middle Aged
Mutation genetics
Neoplasms genetics
Neoplasms pathology
DNA Copy Number Variations genetics
Genetic Heterogeneity
Neoplasms epidemiology
Prognosis
Transcriptome genetics
Subjects
Details
- Language :
- English
- ISSN :
- 2399-3642
- Volume :
- 3
- Issue :
- 1
- Database :
- MEDLINE
- Journal :
- Communications biology
- Publication Type :
- Academic Journal
- Accession number :
- 32917965
- Full Text :
- https://doi.org/10.1038/s42003-020-01230-7