Somatic Point Mutation Calling in Low Cellularity Tumors
Somatic Point Mutation Calling in Low Cellularity Tumors
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Author / Creator
Kassahn, Karin S. , Holmes, Oliver , Nones, Katia , Patch, Ann-Marie , Miller, David K. , Christ, Angelika N. , Harliwong, Ivon , Bruxner, Timothy J. , Xu, Qinying , Anderson, Matthew , Wood, Scott , Leonard, Conrad , Taylor, Darrin , Newell, Felicity , Song, Sarah , Idrisoglu, Senel , Nourse, Craig , Nourbakhsh, Ehsan , Manning, Suzanne , Wani, Shivangi , Steptoe, Anita , Pajic, Marina , Cowley, Mark J. , Pinese, Mark , Chang, David K. , Gill, Anthony J. , Johns, Amber L. , Wu, Jianmin , Wilson, Peter J. , Fink, Lynn , Biankin, Andrew V. , Waddell, Nicola , Grimmond, Sean M. and Pearson, John V.
Publisher
United States: Public Library of Science
Journal title
Language
English
Formats
Publication information
Publisher
United States: Public Library of Science
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More information
Scope and Contents
Contents
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....
Alternative Titles
Full title
Somatic Point Mutation Calling in Low Cellularity Tumors
Authors, Artists and Contributors
Author / Creator
Holmes, Oliver
Nones, Katia
Patch, Ann-Marie
Miller, David K.
Christ, Angelika N.
Harliwong, Ivon
Bruxner, Timothy J.
Xu, Qinying
Anderson, Matthew
Wood, Scott
Leonard, Conrad
Taylor, Darrin
Newell, Felicity
Song, Sarah
Idrisoglu, Senel
Nourse, Craig
Nourbakhsh, Ehsan
Manning, Suzanne
Wani, Shivangi
Steptoe, Anita
Pajic, Marina
Cowley, Mark J.
Pinese, Mark
Chang, David K.
Gill, Anthony J.
Johns, Amber L.
Wu, Jianmin
Wilson, Peter J.
Fink, Lynn
Biankin, Andrew V.
Waddell, Nicola
Grimmond, Sean M.
Pearson, John V.
Identifiers
Primary Identifiers
Record Identifier
TN_cdi_plos_journals_1449481604
Permalink
https://devfeature-collection.sl.nsw.gov.au/record/TN_cdi_plos_journals_1449481604
Other Identifiers
ISSN
1932-6203
E-ISSN
1932-6203
DOI
10.1371/journal.pone.0074380
