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
  • Sir Peter MacCallum Department of Oncology
  • Sir Peter MacCallum Department of Oncology - Research Publications
  • View Item
  • Minerva Access
  • Medicine, Dentistry & Health Sciences
  • Sir Peter MacCallum Department of Oncology
  • Sir Peter MacCallum Department of Oncology - Research Publications
  • View Item
JavaScript is disabled for your browser. Some features of this site may not work without it.

    A community effort to create standards for evaluating tumor subclonal reconstruction

    Thumbnail
    Citations
    Scopus
    Web of Science
    Altmetric
    7
    4
    Author
    Salcedo, A; Tarabichi, M; Espiritu, SMG; Deshwar, AG; David, M; Wilson, NM; Dentro, S; Wintersinger, JA; Liu, LY; Ko, M; ...
    Date
    2020-01-01
    Source Title
    Nature Biotechnology
    Publisher
    NATURE RESEARCH
    University of Melbourne Author/s
    Cmero, Marek
    Affiliation
    Sir Peter MacCallum Department of Oncology
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Salcedo, A., Tarabichi, M., Espiritu, S. M. G., Deshwar, A. G., David, M., Wilson, N. M., Dentro, S., Wintersinger, J. A., Liu, L. Y., Ko, M., Sivanandan, S., Zhang, H., Zhu, K., Ou Yang, T. -H., Chilton, J. M., Buchanan, A., Lalansingh, C. M., P'ng, C., Anghel, C. V. ,... Zhu, H. (2020). A community effort to create standards for evaluating tumor subclonal reconstruction. NATURE BIOTECHNOLOGY, 38 (1), pp.97-+. https://doi.org/10.1038/s41587-019-0364-z.
    Access Status
    Access this item via the Open Access location
    URI
    http://hdl.handle.net/11343/254011
    DOI
    10.1038/s41587-019-0364-z
    Open Access URL
    http://europepmc.org/articles/pmc6956735?pdf=render
    Abstract
    Tumor DNA sequencing data can be interpreted by computational methods that analyze genomic heterogeneity to infer evolutionary dynamics. A growing number of studies have used these approaches to link cancer evolution with clinical progression and response to therapy. Although the inference of tumor phylogenies is rapidly becoming standard practice in cancer genome analyses, standards for evaluating them are lacking. To address this need, we systematically assess methods for reconstructing tumor subclonality. First, we elucidate the main algorithmic problems in subclonal reconstruction and develop quantitative metrics for evaluating them. Then we simulate realistic tumor genomes that harbor all known clonal and subclonal mutation types and processes. Finally, we benchmark 580 tumor reconstructions, varying tumor read depth, tumor type and somatic variant detection. Our analysis provides a baseline for the establishment of gold-standard methods to analyze tumor heterogeneity.

    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 [45689]
    • Sir Peter MacCallum Department of Oncology - Research Publications [728]
    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