@article{e249b2135be0475d82cf58f09d9f4bb9,
title = "Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration",
abstract = "Transcriptome deconvolution in cancer and other heterogeneous tissues remains challenging. Available methods lack the ability to estimate both component-specific proportions and expression profiles for individual samples. We present DeMixT, a new tool to deconvolve high-dimensional data from mixtures of more than two components. DeMixT implements an iterated conditional mode algorithm and a novel gene-set-based component merging approach to improve accuracy. In a series of experimental validation studies and application to TCGA data, DeMixT showed high accuracy. Improved deconvolution is an important step toward linking tumor transcriptomic data with clinical outcomes. An R package, scripts, and data are available: https://github.com/wwylab/DeMixTallmaterials. Computational Bioinformatics; Cancer; Transcriptomics",
keywords = "Cancer, Computational Bioinformatics, Transcriptomics",
author = "Zeya Wang and Shaolong Cao and Morris, {Jeffrey S.} and Jaeil Ahn and Rongjie Liu and Svitlana Tyekucheva and Fan Gao and Bo Li and Wei Lu and Ximing Tang and Wistuba, {Ignacio I.} and Michaela Bowden and Lorelei Mucci and Massimo Loda and Giovanni Parmigiani and Holmes, {Chris C.} and Wenyi Wang",
note = "Funding Information: Z.W. and W.W. are supported by the U.S. National Cancer Institute through grant numbers R01CA174206 , R01 CA183793 , and P30 CA016672 . W.W. is supported by U.S. National Cancer Institute 2R01 CA158113 . Z.W. and J.S.M. are supported by NIH grants R01 CA178744 and P30 CA016672 and NSF grant 1550088 . J.S.M. is supported by U.S. NSF 1550088 and the MD Anderson Colorectal Cancer Moonshot. S.C., J.A., X.T., and I.I.W. are supported by NIH grant 1R01CA183793 . X.T. and I.I.W. are supported by The University of Texas Lung Specialized Programs of Research Excellence grant P50CA70907 . S.T. is supported by NIH grant R01 CA174206 and Prostate Cancer Foundation Challenge Award. G.P. is supported by NIH grants 5R01 CA174206-05 and 4P30CA006516-51 . M.L. is supported by NIH grants RO1CA131945 , R01CA187918 , DoD PC130716 , P50 CA90381 and the Prostate Cancer Foundation, United States . ",
year = "2018",
month = nov,
day = "30",
doi = "10.1016/j.isci.2018.10.028",
language = "English (US)",
volume = "9",
pages = "451--460",
journal = "iScience",
issn = "2589-0042",
publisher = "Elsevier Inc.",
}