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dc.contributor.authorMannakee, Brian K*
dc.contributor.authorBalaji, Uthra*
dc.contributor.authorWitkiewicz, Agnieszka K*
dc.contributor.authorGutenkunst, Ryan N*
dc.contributor.authorKnudsen, Erik S*
dc.date.accessioned2018-07-16T21:42:26Z
dc.date.available2018-07-16T21:42:26Z
dc.date.issued2018-05-15
dc.identifier.citationBrian K Mannakee, Uthra Balaji, Agnieszka K Witkiewicz, Ryan N Gutenkunst, Erik S Knudsen; Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors, Bioinformatics, Volume 34, Issue 10, 15 May 2018, Pages 1713–1718, https://doi.org/10.1093/bioinformatics/bty010en_US
dc.identifier.issn1367-4803
dc.identifier.issn1460-2059
dc.identifier.pmid29325072
dc.identifier.doi10.1093/bioinformatics/bty010
dc.identifier.urihttp://hdl.handle.net/10150/628238
dc.description.abstractMotivation: Tumor genome sequencing offers great promise for guiding research and therapy, but spurious variant calls can arise from multiple sources. Mouse contamination can generate many spurious calls when sequencing patient-derived xenografts. Paralogous genome sequences can also generate spurious calls when sequencing any tumor. We developed a BLAST-based algorithm, Mouse And Paralog EXterminator (MAPEX), to identify and filter out spurious calls from both these sources. Results: When calling variants from xenografts, MAPEX has similar sensitivity and specificity to more complex algorithms. When applied to any tumor, MAPEX also automatically flags calls that potentially arise from paralogous sequences. Our implementation, mapexr, runs quickly and easily on a desktop computer. MAPEX is thus a useful addition to almost any pipeline for calling genetic variants in tumors.en_US
dc.description.sponsorshipNational Science Foundation [DGE-1143953]; National Institutes of Health [R01CA211878-01, P30CA023074-36S2]en_US
dc.language.isoenen_US
dc.publisherOXFORD UNIV PRESSen_US
dc.relation.urlhttps://academic.oup.com/bioinformatics/article/34/10/1713/4792962en_US
dc.rights© The Author(s) 2018. Published by Oxford University Press. All rights reserved.en_US
dc.titleSensitive and specific post-call filtering of genetic variants in xenograft and primary tumorsen_US
dc.typeArticleen_US
dc.contributor.departmentUniv Arizona, Dept Epidemiol & Biostat, Mel & Enid Zuckerman Coll Publ Hlthen_US
dc.contributor.departmentUniv Arizona, Ctr Cancen_US
dc.contributor.departmentUniv Arizona, Dept Meden_US
dc.contributor.departmentUniv Arizona, Dept Patholen_US
dc.contributor.departmentUniv Arizona, Dept Mol & Cellular Biolen_US
dc.identifier.journalBIOINFORMATICSen_US
dc.description.note12 month embargo; published online: 08 January 2018en_US
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.en_US
dc.eprint.versionFinal accepted manuscripten_US
dc.source.journaltitleBioinformatics
dc.source.volume34
dc.source.issue10
dc.source.beginpage1713
dc.source.endpage1718


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