TY - JOUR
T1 - Inferring tumour purity and stromal and immune cell admixture from expression data
AU - Yoshihara, Kosuke
AU - Shahmoradgoli, Maria
AU - Martínez, Emmanuel
AU - Vegesna, Rahulsimham
AU - Kim, Hoon
AU - Torres-Garcia, Wandaliz
AU - Treviño, Victor
AU - Shen, Hui
AU - Laird, Peter W.
AU - Levine, Douglas A.
AU - Carter, Scott L.
AU - Getz, Gad
AU - Stemke-Hale, Katherine
AU - Mills, Gordon B.
AU - Verhaak, Roel G.W.
N1 - Funding Information:
We gratefully acknowledge the contributions from the TCGA Research Network and its TCGA Pan-Cancer Analysis Working Group (contributing consortium members are listed in Supplementary Note 1). The TCGA Pan-Cancer Analysis Working Group is coordinated by J.M. Stuart, C. Sander and I. Shmulevich. This work was supported in part by the U.S. National Cancer Institute (grant number CA143883 to The University of Texas MD Anderson Genome Data Analysis Centre). We thank Dr W.K. Alfred Yung and Dr Erik Sulman for providing the glioma stem-like cell expression data set.
PY - 2013
Y1 - 2013
N2 - 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/.
AB - 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/.
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U2 - 10.1038/ncomms3612
DO - 10.1038/ncomms3612
M3 - Article
C2 - 24113773
AN - SCOPUS:84885673911
SN - 2041-1723
VL - 4
JO - Nature Communications
JF - Nature Communications
M1 - 2612
ER -