Inferring Tumour Purity and Stromal and Immune Cell Admixture from Expression Data

Overview

Journal Nat Commun

Specialty Biology

Date 2013 Oct 12

PMID 24113773

Citations 5102

Authors

Kosuke Yoshihara

Maria Shahmoradgoli

Emmanuel Martinez

Rahulsimham Vegesna

Hoon Kim

Wandaliz Torres-Garcia

Victor Trevino

Hui Shen

Peter W Laird

Douglas A Levine

Scott L Carter

Gad Getz

Katherine Stemke-Hale

Gordon B Mills

Roel G W Verhaak

Affiliations

Soon will be listed here.

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/.

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