The DOI matches its Crossref record; 19 of the 19 references it cites were found in a registry or an index.
Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data
Open accessAbstract
Immune cells infiltrating tumors can have important impact on tumor progression and response to therapy. We present an efficient algorithm to simultaneously estimate the fraction of cancer and immune cell types from bulk tumor gene expression data. Our method integrates novel gene expression profiles from each major non-malignant cell type found in tumors, renormalization based on cell-type-specific mRNA content, and the ability to consider uncharacterized and possibly highly variable cell types. Feasibility is demonstrated by validation with flow cytometry, immunohistochemistry and single-cell RNA-Seq analyses of human melanoma and colorectal tumor specimens. Altogether, our work not only improves accuracy but also broadens the scope of absolute cell fraction predictions from tumor gene expression data, and provides a unique novel experimental benchmark for immunogenomics analyses in cancer research (http://epic.gfellerlab.org).
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Cited by
Finotello, F., Mayer, C., Plattner, C., Laschober, G., Rieder, D., Hackl, H., Krogsdam, A., Loncova, Z., Posch, W., Wilflingseder, D., et al. (2019) · Genome Medicine · doi:10.1186/s13073-019-0638-6 · Cited by 1,542
Neoantigen-directed immune escape in lung cancer evolution
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Benchmarking of cell type deconvolution pipelines for transcriptomics data
Avila Cobos, F., Alquicira-Hernandez, J., Powell, J. E., Mestdagh, P., & De Preter, K. (2020) · Nature Communications · doi:10.1038/s41467-020-19015-1 · Cited by 446
Melanoma plasticity and phenotypic diversity: therapeutic barriers and opportunities
Rambow, F., Marine, J.-C., & Goding, C. R. (2019) · Genes & Development · doi:10.1101/gad.329771.119 · Cited by 325
Xu, Y., Su, G.-H., Ma, D., Xiao, Y., Shao, Z.-M., & Jiang, Y.-Z. (2021) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-021-00729-7 · Cited by 163
Metadata
- Authors
- Racle, J., de Jonge, K., Baumgaertner, P., Speiser, D. E., & Gfeller, D.
- Venue
- eLife
- Publisher
- eLife Sciences Publications, Ltd
- Published
- 2017-11-13
- Volume
- 6
- ISSN
- 2050-084X (ISSN-L)
- OpenAlex
- W2600132724
- Cited by
- 1,384
- References
- 19
- FWCI
- 12.42
- Type
- journal article
- Language
- en
- Open access
- gold
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- Racle, J., de Jonge, K., Baumgaertner, P., Speiser, D. E., & Gfeller, D. (2017). Simultaneous enumeration of cancer and immune cell types from bulk tumor gene expression data. eLife. https://doi.org/10.7554/elife.26476
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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