Journal
GENOME MEDICINE
Volume 11, Issue -, Pages -Publisher
BMC
DOI: 10.1186/s13073-019-0638-6
Keywords
Cancer immunology; Immunotherapy; Deconvolution; RNA-seq; Immune contexture
Categories
Funding
- European Union's Horizon 2020 research and innovation program [633592]
- Austrian Cancer Aid/Tyrol [17003]
- Austrian Science Fund (FWF) [T 974-B30, I3291, I3978, TRR 241]
- Vienna Science and Technology Fund [LS16-025]
- European Research Council [786295]
- Fight Colorectal Cancer-Michael's Mission-AACR Fellowship
- Alpe d'HuZes/KWF Bas Mulder Award [UL2015-7664]
- Vanderbilt-Incyte Research Alliance Program Grant
- Breast Cancer Specialized Program of Research Excellence (SPORE) [P50 CA098131]
- [R00CA181491]
- [K23CA204726]
- Austrian Science Fund (FWF) [I3291] Funding Source: Austrian Science Fund (FWF)
- European Research Council (ERC) [786295] Funding Source: European Research Council (ERC)
- H2020 Societal Challenges Programme [633592] Funding Source: H2020 Societal Challenges Programme
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We introduce quanTIseq, a method to quantify the fractions of ten immune cell types from bulk RNA-sequencing data. quanTIseq was extensively validated in blood and tumor samples using simulated, flow cytometry, and immunohistochemistry data.quanTIseq analysis of 8000 tumor samples revealed that cytotoxic T cell infiltration is more strongly associated with the activation of the CXCR3/CXCL9 axis than with mutational load and that deconvolution-based cell scores have prognostic value in several solid cancers. Finally, we used quanTIseq to show how kinase inhibitors modulate the immune contexture and to reveal immune-cell types that underlie differential patients' responses to checkpoint blockers.Availability: quanTIseq is available at http://icbi.at/quantiseq.
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