Comprehensive evaluation of transcriptome-based cell-type quantification methods for immuno-oncology
Technical University of Munich · Innsbruck Medical University · +7 more institutions
Abstract
MOTIVATION: The composition and density of immune cells in the tumor microenvironment (TME) profoundly influence tumor progression and success of anti-cancer therapies. Flow cytometry, immunohistochemistry staining or single-cell sequencing are often unavailable such that we rely on computational methods to estimate the immune-cell composition from bulk RNA-sequencing (RNA-seq) data. Various methods have been proposed recently, yet their capabilities and limitations have not been evaluated systematically. A general guideline leading the research community through cell type deconvolution is missing. RESULTS: We developed a systematic approach for benchmarking such computational methods and assessed the accuracy…
Citation impact
- FWCI
- 38.02
- Percentile
- 100%
- References
- 37
Authors
8- GSGregor SturmCorresponding
Technical University of Munich
- FFFrancesca Finotello
Innsbruck Medical University, Universität Innsbruck
- FPFlorent Petitprez
Inserm, Université Paris Cité, Sorbonne Université, Centre de Recherche des Cordeliers, La Ligue Contre le Cancer
- JDJitao David Zhang
Roche (Switzerland)
- JBJan Baumbach
Technical University of Munich
Topics & keywords
- Transcriptome
- Precision oncology
- Computational biology
- Computer science
- Medicine
- Internal medicine
- Biology
- Cancer