Inferring tumour purity and stromal and immune cell admixture from expression data

Kosuke Yoshihara, Maria Shahmoradgoli, Emmanuel Martínez, Rahulsimham Vegesna, Hoon Kim, Wandaliz Torres-Garcia, Victor Treviño, Hui Shen, Peter W. Laird, Douglas A. Levine, Scott L. Carter, Gad Getz, Katherine Stemke-Hale, Gordon Mills, Roel G.W. Verhaak

Research output: Contribution to journalArticle

406 Citations (Scopus)

Abstract

Infiltrating stromal and immune cells form the major fraction of normal cells in tumour tissue and not only perturb the tumour signal in molecular studies but also have an important role in cancer biology. Here we describe 'Estimation of STromal and Immune cells in MAlignant Tumours using Expression data' (ESTIMATE)-a method that uses gene expression signatures to infer the fraction of stromal and immune cells in tumour samples. ESTIMATE scores correlate with DNA copy number-based tumour purity across samples from 11 different tumour types, profiled on Agilent, Affymetrix platforms or based on RNA sequencing and available through The Cancer Genome Atlas. The prediction accuracy is further corroborated using 3,809 transcriptional profiles available elsewhere in the public domain. The ESTIMATE method allows consideration of tumour-associated normal cells in genomic and transcriptomic studies. An R-library is available on https://sourceforge.net/projects/estimateproject/.

Original languageEnglish (US)
Article number2612
JournalNature Communications
Volume4
DOIs
StatePublished - Oct 21 2013
Externally publishedYes

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Stromal Cells
admixtures
Tumors
purity
tumors
cells
Neoplasms
cancer
sequencing
genome
gene expression
RNA Sequence Analysis
biology
Gene expression
Atlases
Public Sector
Transcriptome
deoxyribonucleic acid
platforms
Genes

ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Yoshihara, K., Shahmoradgoli, M., Martínez, E., Vegesna, R., Kim, H., Torres-Garcia, W., ... Verhaak, R. G. W. (2013). Inferring tumour purity and stromal and immune cell admixture from expression data. Nature Communications, 4, [2612]. https://doi.org/10.1038/ncomms3612

Inferring tumour purity and stromal and immune cell admixture from expression data. / Yoshihara, Kosuke; Shahmoradgoli, Maria; Martínez, Emmanuel; Vegesna, Rahulsimham; Kim, Hoon; Torres-Garcia, Wandaliz; Treviño, Victor; Shen, Hui; Laird, Peter W.; Levine, Douglas A.; Carter, Scott L.; Getz, Gad; Stemke-Hale, Katherine; Mills, Gordon; Verhaak, Roel G.W.

In: Nature Communications, Vol. 4, 2612, 21.10.2013.

Research output: Contribution to journalArticle

Yoshihara, K, Shahmoradgoli, M, Martínez, E, Vegesna, R, Kim, H, Torres-Garcia, W, Treviño, V, Shen, H, Laird, PW, Levine, DA, Carter, SL, Getz, G, Stemke-Hale, K, Mills, G & Verhaak, RGW 2013, 'Inferring tumour purity and stromal and immune cell admixture from expression data', Nature Communications, vol. 4, 2612. https://doi.org/10.1038/ncomms3612
Yoshihara K, Shahmoradgoli M, Martínez E, Vegesna R, Kim H, Torres-Garcia W et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nature Communications. 2013 Oct 21;4. 2612. https://doi.org/10.1038/ncomms3612
Yoshihara, Kosuke ; Shahmoradgoli, Maria ; Martínez, Emmanuel ; Vegesna, Rahulsimham ; Kim, Hoon ; Torres-Garcia, Wandaliz ; Treviño, Victor ; Shen, Hui ; Laird, Peter W. ; Levine, Douglas A. ; Carter, Scott L. ; Getz, Gad ; Stemke-Hale, Katherine ; Mills, Gordon ; Verhaak, Roel G.W. / Inferring tumour purity and stromal and immune cell admixture from expression data. In: Nature Communications. 2013 ; Vol. 4.
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