Somatic Point Mutation Calling in Low Cellularity Tumors
- Kassahn, KS
- Holmes, O
- Nones, K
- Patch, A-M
- Miller, DK
- Christ, AN
- Harliwong, I
- Bruxner, TJ
- 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, MJ
- Pinese, M
- Chang, DK
- Gill, AJ
- Johns, AL
- Wu, J
- Wilson, PJ
- Fink, L
- Biankin, AV
- Waddell, N
- Grimmond, SM
- Pearson, JV
Publication date
November 2013
DOI Publisher
Public Library of Science (PLoS) Journal
PLoS ONEAbstract
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
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