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    A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing

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    Author
    Alioto, TS; Buchhalter, I; Derdak, S; Hutter, B; Eldridge, MD; Hovig, E; Heisler, LE; Beck, TA; Simpson, JT; Tonon, L; ...
    Date
    2015-12-01
    Source Title
    Nature Communications
    Publisher
    NATURE PUBLISHING GROUP
    University of Melbourne Author/s
    ANDERSON, CHARLOTTE; Grimmond, Sean
    Affiliation
    Centre for Cancer Research
    Metadata
    Show full item record
    Document Type
    Journal Article
    Citations
    Alioto, T. S., Buchhalter, I., Derdak, S., Hutter, B., Eldridge, M. D., Hovig, E., Heisler, L. E., Beck, T. A., Simpson, J. T., Tonon, L., Sertier, A. -S., Patch, A. -M., Jaeger, N., Ginsbach, P., Drews, R., Paramasivam, N., Kabbe, R., Chotewutmontri, S., Diessl, N. ,... Gut, I. G. (2015). A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. NATURE COMMUNICATIONS, 6 (1), https://doi.org/10.1038/ncomms10001.
    Access Status
    Open Access
    URI
    http://hdl.handle.net/11343/258047
    DOI
    10.1038/ncomms10001
    Abstract
    As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.

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