University Library
  • Login
A gateway to Melbourne's research publications
Minerva Access is the University's Institutional Repository. It aims to collect, preserve, and showcase the intellectual output of staff and students of the University of Melbourne for a global audience.
View Item 
  • Minerva Access
  • Medicine, Dentistry & Health Sciences
  • Medical Biology
  • Medical Biology - Research Publications
  • View Item
  • Minerva Access
  • Medicine, Dentistry & Health Sciences
  • Medical Biology
  • Medical Biology - Research Publications
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

    HYSYS: have you swapped your samples?

    Thumbnail
    Download
    Published version (133.7Kb)

    Citations
    Scopus
    Web of Science
    Altmetric
    2
    2
    Author
    Schroder, J; Corbin, V; Papenfuss, AT
    Date
    2017-02-15
    Source Title
    Bioinformatics
    Publisher
    OXFORD UNIV PRESS
    University of Melbourne Author/s
    Schroeder, Jan; Corbin, Vincent; Papenfuss, Anthony
    Affiliation
    Medical Biology (W.E.H.I.)
    Computing and Information Systems
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Schroder, J., Corbin, V. & Papenfuss, A. T. (2017). HYSYS: have you swapped your samples?. BIOINFORMATICS, 33 (4), pp.596-598. https://doi.org/10.1093/bioinformatics/btw685.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/257891
    DOI
    10.1093/bioinformatics/btw685
    Abstract
    Motivation: The application of a genomics assay to samples from a cohort is a frequently applied experimental design in cancer genomics studies. The collection and analysis of cancer sequencing data in the clinical setting is an elaborate process that may involve consenting patients, obtaining possibly-multiple DNA samples, sequencing and analysis. Many of these steps are manual. At any stage mistakes can occur that cause a DNA sample to be labelled incorrectly. However, there is a paucity of methods in the literature to identify such swaps specifically in cancer studies. Results: Here, we introduce a simple method, HYSYS, to estimate the relatedness of samples and test for sample swaps and contamination. The test uses the concordance of homozygous SNPs between samples. The method is motivated by the observation that homozygous germline population variants rarely change in the disease and are not affected by loss of heterozygosity. Our tools include visualization and a testing framework to flag possible sample swaps. We demonstrate the utility of this approach on a small cohort. Availability and Implementation: http://github.com/PapenfussLab/HaveYouSwappedYourSamples. Contact: papenfuss@wehi.edu.au. Supplementary information: Supplementary data are available at Bioinformatics online.

    Export Reference in RIS Format     

    Endnote

    • Click on "Export Reference in RIS Format" and choose "open with... Endnote".

    Refworks

    • Click on "Export Reference in RIS Format". Login to Refworks, go to References => Import References


    Collections
    • Minerva Elements Records [45770]
    • Computing and Information Systems - Research Publications [1456]
    • Medical Biology - Research Publications [865]
    Minerva AccessDepositing Your Work (for University of Melbourne Staff and Students)NewsFAQs

    BrowseCommunities & CollectionsBy Issue DateAuthorsTitlesSubjectsThis CollectionBy Issue DateAuthorsTitlesSubjects
    My AccountLoginRegister
    StatisticsMost Popular ItemsStatistics by CountryMost Popular Authors