Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration

Zeya Wang, Shaolong Cao, Jeffrey S. Morris, Jaeil Ahn, Rongjie Liu, Svitlana Tyekucheva, Fan Gao, Bo Li, Wei Lu, Ximing Tang, Ignacio I. Wistuba, Michaela Bowden, Lorelei Mucci, Massimo Loda, Giovanni Parmigiani, Chris C. Holmes, Wenyi Wang

Research output: Contribution to journalArticle

2 Citations (Scopus)

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

Original languageEnglish (US)
Pages (from-to)451-460
Number of pages10
JournalFood Science and Human Wellness
Volume9
DOIs
StatePublished - Nov 30 2018
Externally publishedYes

Fingerprint

Transcriptome
transcriptome
transcriptomics
neoplasms
Neoplasms
Validation Studies
Computational Biology
bioinformatics
sampling
Genes
genes
methodology

Keywords

  • Cancer
  • Computational Bioinformatics
  • Transcriptomics

ASJC Scopus subject areas

  • Food Science
  • General

Cite this

Wang, Z., Cao, S., Morris, J. S., Ahn, J., Liu, R., Tyekucheva, S., ... Wang, W. (2018). Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration. Food Science and Human Wellness, 9, 451-460. https://doi.org/10.1016/j.isci.2018.10.028

Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration. / Wang, Zeya; Cao, Shaolong; Morris, Jeffrey S.; Ahn, Jaeil; Liu, Rongjie; Tyekucheva, Svitlana; Gao, Fan; Li, Bo; Lu, Wei; Tang, Ximing; Wistuba, Ignacio I.; Bowden, Michaela; Mucci, Lorelei; Loda, Massimo; Parmigiani, Giovanni; Holmes, Chris C.; Wang, Wenyi.

In: Food Science and Human Wellness, Vol. 9, 30.11.2018, p. 451-460.

Research output: Contribution to journalArticle

Wang, Z, Cao, S, Morris, JS, Ahn, J, Liu, R, Tyekucheva, S, Gao, F, Li, B, Lu, W, Tang, X, Wistuba, II, Bowden, M, Mucci, L, Loda, M, Parmigiani, G, Holmes, CC & Wang, W 2018, 'Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration', Food Science and Human Wellness, vol. 9, pp. 451-460. https://doi.org/10.1016/j.isci.2018.10.028
Wang, Zeya ; Cao, Shaolong ; Morris, Jeffrey S. ; Ahn, Jaeil ; Liu, Rongjie ; Tyekucheva, Svitlana ; Gao, Fan ; Li, Bo ; Lu, Wei ; Tang, Ximing ; Wistuba, Ignacio I. ; Bowden, Michaela ; Mucci, Lorelei ; Loda, Massimo ; Parmigiani, Giovanni ; Holmes, Chris C. ; Wang, Wenyi. / Transcriptome Deconvolution of Heterogeneous Tumor Samples with Immune Infiltration. In: Food Science and Human Wellness. 2018 ; Vol. 9. pp. 451-460.
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