qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles

Song, Sarah, Nones, Katia, Miller, David, Harliwong, Ivon, Kassahn, Karin S., Pinese, Mark, Pajic, Marina, Gill, Anthony J., Johns, Amber L., Anderson, Matthew, Holmes, Oliver, Leonard, Conrad, Taylor, Darrin, Wood, Scott, Xu, Qinying, Newell, Felicity, Cowley, Mark J., Wu, Jianmin, Wilson, Peter, Fink, Lynn, Biankin, Andrew V., Waddell, Nic, Grimmond, Sean M. and Pearson, John V. (2012) qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles. PLoS One, 7 9: e45835.1-e45835.7. doi:10.1371/journal.pone.0045835

Author Song, Sarah
Nones, Katia
Miller, David
Harliwong, Ivon
Kassahn, Karin S.
Pinese, Mark
Pajic, Marina
Gill, Anthony J.
Johns, Amber L.
Anderson, Matthew
Holmes, Oliver
Leonard, Conrad
Taylor, Darrin
Wood, Scott
Xu, Qinying
Newell, Felicity
Cowley, Mark J.
Wu, Jianmin
Wilson, Peter
Fink, Lynn
Biankin, Andrew V.
Waddell, Nic
Grimmond, Sean M.
Pearson, John V.
Total Author Count Override 24
Title qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2012-09
Sub-type Article (original research)
DOI 10.1371/journal.pone.0045835
Open Access Status DOI
Volume 7
Issue 9
Start page e45835.1
End page e45835.7
Total pages 7
Place of publication San Francisco, CA, United States
Publisher Public Library of Science
Collection year 2013
Language eng
Formatted 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 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/.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ
Additional Notes Article # e45835

Document type: Journal Article
Sub-type: Article (original research)
Collections: UQ Centre for Clinical Research Publications
Official 2013 Collection
Institute for Molecular Bioscience - Publications
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Citation counts: TR Web of Science Citation Count  Cited 29 times in Thomson Reuters Web of Science Article | Citations
Scopus Citation Count Cited 35 times in Scopus Article | Citations
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Created: Wed, 26 Sep 2012, 15:56:29 EST by Dr Sarah Song on behalf of Institute for Molecular Bioscience