Please use this identifier to cite or link to this item: http://hdl.handle.net/2440/97116
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Type: Journal article
Title: qpure: A tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles
Author: Song, S.
Nones, K.
Miller, D.
Harliwong, I.
Kassahn, K.
Pinese, M.
Pajic, M.
Gill, A.
Johns, A.
Anderson, M.
Holmes, O.
Leonard, C.
Taylor, D.
Wood, S.
Xu, Q.
Newell, F.
Cowley, M.
Wu, J.
Wilson, P.
Fink, L.
et al.
Citation: PLoS ONE, 2012; 7(9):e45835-1-e45835-7
Publisher: Public Library of Science
Issue Date: 2012
ISSN: 1932-6203
Statement of
Responsibility: 
Sarah Song, Katia Nones, David Miller, Ivon Harliwong, Karin S. Kassahn, Mark Pinese, Marina Pajic, Anthony J. Gill, Amber L. Johns, Matthew Anderson, Oliver Holmes, Conrad Leonard, Darrin Taylor, Scott Wood, Qinying Xu, Felicity Newell, Mark J. Cowley, Jianmin Wu, Peter Wilson, Lynn Fink, Andrew V. Biankin, Nic Waddell, Sean M. Grimmond, John V. Pearson
Abstract: Tumour cellularity, the relative proportion of tumour and normal cells in a sample, affects the sensitivity of mutation detection, copy number analysis, cancer gene expression and methylation profiling. Tumour cellularity is traditionally estimated by pathological review of sectioned specimens; however this method is both subjective and prone to error due to heterogeneity within lesions and cellularity differences between the sample viewed during pathological review and tissue used for research purposes. In this paper we describe a statistical model to estimate tumour cellularity from SNP array profiles of paired tumour and normal samples using shifts in SNP allele frequency at regions of loss of heterozygosity (LOH) in the tumour. We also provide qpure, a software implementation of the method. Our experiments showed that there is a medium correlation 0.42 (p-value = 0.0001) between tumor cellularity estimated by qpure and pathology review. Interestingly there is a high correlation 0.87 (p-value v 2.2e-16) between cellularity estimates by qpure and deep Ion Torrent sequencing of known somatic KRAS mutations; and a weaker correlation 0.32 (p-value = 0.004) between IonTorrent sequencing and pathology review. This suggests that qpure may be a more accurate predictor of tumour cellularity than pathology review. qpure can be downloaded from https://sourceforge.net/projects/qpure/.
Rights: © 2012 Song et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
RMID: 0030035711
DOI: 10.1371/journal.pone.0045835
Grant ID: http://purl.org/au-research/grants/nhmrc/631701
http://purl.org/au-research/grants/nhmrc/535903
http://purl.org/au-research/grants/nhmrc/427601
Appears in Collections:Molecular and Biomedical Science publications

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