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Somatic point mutation calling in low cellularity tumors

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.

Type Journal
ISBN 1932-6203 (Electronic) 1932-6203 (Linking)
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.; Pearson, J. V.;
Publisher Name PLoS ONE
Published Date 2013-12-01 00:00:00
Published Volume 8
Published Issue 11
Published Pages e74380
Status Published In-print
OpenAccess Link https://publications.gimr.garvan.org.au/download.php?12148_12686/journal.pone.0074380.pdf