| Title: |
Somatic point mutation calling in low cellularity tumors |
| Authors: |
Kassahn, KS; Holmes, O; Nones, K; Patch, AM; 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 |
| Contributors: |
Jordan, IK |
| Publisher Information: |
PUBLIC LIBRARY SCIENCE |
| Publication Year: |
2013 |
| Collection: |
The University of Melbourne: Digital Repository |
| Description: |
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. |
| Document Type: |
article in journal/newspaper |
| Language: |
English |
| ISSN: |
1932-6203 |
| Relation: |
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. ,. Pearson, J. V. (2013). Somatic point mutation calling in low cellularity tumors. Plos One, 8 (11), https://doi.org/10.1371/journal.pone.0074380.; https://hdl.handle.net/11343/261951 |
| Availability: |
https://hdl.handle.net/11343/261951 |
| Rights: |
https://creativecommons.org/licenses/by/4.0 ; CC BY |
| Accession Number: |
edsbas.5C3D6AD0 |
| Database: |
BASE |