Please use this identifier to cite or link to this item: https://hdl.handle.net/2440/94921
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Type: Journal article
Title: Somatic point mutation calling in low cellularity tumors
Author: Kassahn, K.
Holmes, O.
Nones, K.
Patch, A.
Miller, D.
Christ, A.
Harliwong, I.
Bruxner, T.
Xu, Q.
Anderson, M.
Wood, S.
Leonard, C.
Taylor, D.
Newell, F.
Song, S.
Idrisoglu, S.
Nourse, C.
Nourbakhsh, E.
Manning, S.
Wani, S.
et al.
Citation: PLoS One, 2013; 8(11):e74380-1-e74380-10
Publisher: Public Library of Science
Issue Date: 2013
ISSN: 1932-6203
1932-6203
Editor: Jordan, I.
Statement of
Responsibility: 
Karin S. Kassahn, Oliver Holmes, Katia Nones, Ann-Marie Patch, David K. Miller, Angelika N. Christ, Ivon Harliwong, Timothy J. Bruxner, Qinying Xu, Matthew Anderson, Scott Wood, Conrad Leonard, Darrin Taylor, Felicity Newell, Sarah Song, Senel Idrisoglu, Craig Nourse, Ehsan Nourbakhsh, Suzanne Manning, Shivangi Wani, Anita Steptoe, Marina Pajic, Mark J. Cowley, Mark Pinese, David K. Chang, Anthony J. Gill, Amber L. Johns, Jianmin Wu, Peter J. Wilson, Lynn Fink, Andrew V. Biankin, Nicola Waddell, Sean M. Grimmond, John V. Pearson
Abstract: Somatic mutation calling from next-generation sequencing data remains a challenge due to the difficulties of distinguishing true somatic events from artifacts arising from PCR, sequencing errors or mis-mapping. Tumor cellularity or purity, sub-clonality and copy number changes also confound the identification of true somatic events against a background of germline variants. We have developed a heuristic strategy and software (http://www.qcmg.org/bioinformatics/qsnp/) for somatic mutation calling in samples with low tumor content and we show the superior sensitivity and precision of our approach using a previously sequenced cell line, a series of tumor/normal admixtures, and 3,253 putative somatic SNVs verified on an orthogonal platform.
Rights: © 2013 Kassahn 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.
DOI: 10.1371/journal.pone.0074380
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