Publications
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 |
| Published Volume | 8 |
| Published Issue | 11 |
| Published Pages | e74380 |
| Status | Published in-print |
| OpenAccess link to author's accepted manuscript version | https://publications.gimr.garvan.org.au/open-access/12148 |