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

被引：6686

作者：

Yoshihara, Kosuke ^{[1
,2
]}

Shahmoradgoli, Maria ^{[3
]}

Martinez, Emmanuel ^{[1
,4
]}

Vegesna, Rahulsimham ^{[1
]}

Kim, Hoon ^{[1
]}

Torres-Garcia, Wandaliz ^{[1
]}

Trevino, Victor ^{[4
]}

Shen, Hui ^{[5
]}

Laird, Peter W. ^{[5
]}

Levine, Douglas A. ^{[6
]}

Carter, Scott L. ^{[7
]}

Getz, Gad ^{[7
]}

Stemke-Hale, Katherine ^{[3
]}

Mills, Gordon B. ^{[3
]}

Verhaak, Roel G. W. ^{[1
]}

机构：

[1] Univ Texas MD Anderson Canc Ctr, Dept Bioinformat & Computat Biol, Houston, TX 77030 USA

[2] Niigata Univ, Grad Sch Med & Dent Sci, Dept Obstet & Gynecol, Niigata 9518510, Japan

[3] Univ Texas MD Anderson Canc Ctr, Dept Syst Biol, Houston, TX 77030 USA

[4] Tecnol Monterrey, Catedra Bioinformat, Monterrey 64849, Nuevo Leon, Mexico

[5] Univ So Calif, USC Epigenome Ctr, Los Angeles, CA 90033 USA

[6] Mem Sloan Kettering Canc Ctr, Dept Surg, Gynecol Serv, New York, NY 10065 USA

[7] Broad Inst Harvard & MIT, Cambridge, MA 02142 USA

来源：

NATURE COMMUNICATIONS | 2013年 / 4卷

关键词：

GENE-EXPRESSION; MOLECULAR SUBTYPES; BREAST-CANCER; T-CELLS; SURVIVAL; MICROENVIRONMENT; DIFFERENTIATION; QUANTIFICATION; PREDICTION; SIGNATURE;

D O I：

10.1038/ncomms3612

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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/.

引用

页数：11

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