qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles
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; howe...
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| Format: | Online |
| Language: | English |
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Public Library of Science
2012
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457972/ |
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pubmed-3457972 |
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pubmed-34579722012-10-03 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. Pearson, John V. Research Article 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 (-value = 0.0001) between tumor cellularity estimated by qpure and pathology review. Interestingly there is a high correlation 0.87 (-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 (-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/. Public Library of Science 2012-09-25 /pmc/articles/PMC3457972/ /pubmed/23049875 http://dx.doi.org/10.1371/journal.pone.0045835 Text en © 2012 Song et al http://creativecommons.org/licenses/by/4.0/ 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 properly credited. |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| 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. |
| spellingShingle |
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. qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles |
| author_facet |
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. |
| author_sort |
Song, Sarah |
| title |
qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles |
| title_short |
qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles |
| title_full |
qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles |
| title_fullStr |
qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles |
| title_full_unstemmed |
qpure: A Tool to Estimate Tumor Cellularity from Genome-Wide Single-Nucleotide Polymorphism Profiles |
| title_sort |
qpure: a tool to estimate tumor cellularity from genome-wide single-nucleotide polymorphism profiles |
| description |
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 (-value = 0.0001) between tumor cellularity estimated by qpure and pathology review. Interestingly there is a high correlation 0.87 (-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 (-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/. |
| publisher |
Public Library of Science |
| publishDate |
2012 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457972/ |
| _version_ |
1611911729701191680 |