Somatic point mutation calling in low cellularity tumors

Kassahn, K. S. et al. (2013) Somatic point mutation calling in low cellularity tumors. PLoS ONE, 8(11), e74380. (doi: 10.1371/journal.pone.0074380) (PMID:24250782) (PMCID:PMC3826759)

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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 ( 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.

Item Type:Articles
Glasgow Author(s) Enlighten ID:Biankin, Professor Andrew and Nourse, Dr Craig and Grimmond, Professor Sean and Chang, Professor David
Authors: Kassahn, K. S., Holmes, O., Nones, K., Patch, A.-M., Miller, D. K., Christ, A. N., Harliwong, I., Bruxner, T. J., Xu, Q., Anderson, M., Wood, S., Leonard, C., Taylor, D., Newell, F., Song, S., Idrisoglu, S., Nourse, C., Nourbakhsh, E., Manning, S., Wani, S., Steptoe, A., Pajic, M., Cowley, M. J., Pinese, M., Chang, D. K., Gill, A. J., Johns, A. L., Wu, J., Wilson, P. J., Fink, L., Biankin, A. V., Waddell, N., Grimmond, S. M., and Pearson, J. V.
College/School:College of Medical Veterinary and Life Sciences > School of Cancer Sciences
Journal Name:PLoS ONE
Publisher:Public Library of Science
ISSN (Online):1932-6203
Copyright Holders:Copyright © 2013 Kassahn et al.
First Published:First published in PLoS ONE 8(11): e74380
Publisher Policy:Reproduced under a Creative Commons License

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