Somatic point mutation calling in low cellularity tumors.
oleh: 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
| Format: | Article |
|---|---|
| Diterbitkan: | Public Library of Science (PLoS) 2013-01-01 |
Deskripsi
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.