• Login
    View Item 
    •   Home
    • UA Faculty Research
    • UA Faculty Publications
    • View Item
    •   Home
    • UA Faculty Research
    • UA Faculty Publications
    • View Item
    JavaScript is disabled for your browser. Some features of this site may not work without it.

    Browse

    All of UA Campus RepositoryCommunitiesTitleAuthorsIssue DateSubmit DateSubjectsPublisherJournalThis CollectionTitleAuthorsIssue DateSubmit DateSubjectsPublisherJournal

    My Account

    LoginRegister

    About

    AboutUA Faculty PublicationsUA DissertationsUA Master's ThesesUA Honors ThesesUA PressUA YearbooksUA CatalogsUA Libraries

    Statistics

    Most Popular ItemsStatistics by CountryMost Popular Authors

    Sensitive and specific post-call filtering of genetic variants in xenograft and primary tumors

    • CSV
    • RefMan
    • EndNote
    • BibTex
    • RefWorks
    Thumbnail
    Name:
    mapex.pdf
    Size:
    846.8Kb
    Format:
    PDF
    Description:
    Final Accepted Manuscript
    Download
    Thumbnail
    Name:
    suppl.pdf
    Size:
    264.2Kb
    Format:
    PDF
    Description:
    Supplemental File
    Download
    Author
    Mannakee, Brian K
    Balaji, Uthra
    Witkiewicz, Agnieszka K
    Gutenkunst, Ryan N
    Knudsen, Erik S
    Affiliation
    Univ Arizona, Dept Epidemiol & Biostat, Mel & Enid Zuckerman Coll Publ Hlth
    Univ Arizona, Ctr Canc
    Univ Arizona, Dept Med
    Univ Arizona, Dept Pathol
    Univ Arizona, Dept Mol & Cellular Biol
    Issue Date
    2018-05-15
    
    Metadata
    Show full item record
    Publisher
    OXFORD UNIV PRESS
    Citation
    Brian 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/bty010
    Journal
    BIOINFORMATICS
    Rights
    © The Author(s) 2018. Published by Oxford University Press. All rights reserved.
    Collection Information
    This 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.
    Abstract
    Motivation: 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.
    Note
    12 month embargo; published online: 08 January 2018
    ISSN
    1367-4803
    1460-2059
    PubMed ID
    29325072
    DOI
    10.1093/bioinformatics/bty010
    Version
    Final accepted manuscript
    Sponsors
    National Science Foundation [DGE-1143953]; National Institutes of Health [R01CA211878-01, P30CA023074-36S2]
    Additional Links
    https://academic.oup.com/bioinformatics/article/34/10/1713/4792962
    ae974a485f413a2113503eed53cd6c53
    10.1093/bioinformatics/bty010
    Scopus Count
    Collections
    UA Faculty Publications

    entitlement

    Related articles

    • Consensus Genotyper for Exome Sequencing (CGES): improving the quality of exome variant genotypes.
    • Authors: Trubetskoy V, Rodriguez A, Dave U, Campbell N, Crawford EL, Cook EH, Sutcliffe JS, Foster I, Madduri R, Cox NJ, Davis LK
    • Issue date: 2015 Jan 15
    • WaveCNV: allele-specific copy number alterations in primary tumors and xenograft models from next-generation sequencing.
    • Authors: Holt C, Losic B, Pai D, Zhao Z, Trinh Q, Syam S, Arshadi N, Jang GH, Ali J, Beck T, McPherson J, Muthuswamy LB
    • Issue date: 2014 Mar 15
    • dv-trio: a family-based variant calling pipeline using DeepVariant.
    • Authors: Ip EKK, Hadinata C, Ho JWK, Giannoulatou E
    • Issue date: 2020 Jun 1
    • Using genotype array data to compare multi- and single-sample variant calls and improve variant call sets from deep coverage whole-genome sequencing data.
    • Authors: Shringarpure SS, Mathias RA, Hernandez RD, O'Connor TD, Szpiech ZA, Torres R, De La Vega FM, Bustamante CD, Barnes KC, Taub MA, CAAPA Consortium.
    • Issue date: 2017 Apr 15
    • SV2: accurate structural variation genotyping and de novo mutation detection from whole genomes.
    • Authors: Antaki D, Brandler WM, Sebat J
    • Issue date: 2018 May 15
    The University of Arizona Libraries | 1510 E. University Blvd. | Tucson, AZ 85721-0055
    Tel 520-621-6442 | repository@u.library.arizona.edu
    DSpace software copyright © 2002-2017  DuraSpace
    Quick Guide | Contact Us | Send Feedback
    Open Repository is a service operated by 
    Atmire NV
     

    Export search results

    The export option will allow you to export the current search results of the entered query to a file. Different formats are available for download. To export the items, click on the button corresponding with the preferred download format.

    By default, clicking on the export buttons will result in a download of the allowed maximum amount of items.

    To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export. The amount of items that can be exported at once is similarly restricted as the full export.

    After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.