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    Analytical validation of BRAF mutation testing from circulating free DNA using the amplification refractory mutation testing system.

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    Authors
    Aung, Kyaw Lwin
    Donald, E
    Ellison, G
    Bujac, S
    Fletcher, L
    Cantarini, M
    Brady, G
    Orr, M
    Clack, G
    Ranson, Malcolm R
    Dive, Caroline
    Hughes, A
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    Affiliation
    Clinical and Experimental Pharmacology Group, CRUK Manchester Institute, Manchester
    Issue Date
    2014-03-11
    
    Metadata
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    Abstract
    BRAF mutation testing from circulating free DNA (cfDNA) using the amplification refractory mutation testing system (ARMS) holds potential as a surrogate for tumor mutation testing. Robust assay validation is needed to establish the optimal clinical matrix for measurement and cfDNA-specific mutation calling criteria. Plasma- and serum-derived cfDNA samples from 221 advanced melanoma patients were analyzed for BRAF c.1799T>A (p.V600E) mutation using ARMS in two stages in a blinded fashion. cfDNA-specific mutation calling criteria were defined in stage 1 and validated in stage 2. cfDNA concentrations in serum and plasma, and the sensitivities and specificities of BRAF mutation detection in these two clinical matrices were compared. Sensitivity of BRAF c.1799T>A (p.V600E) mutation detection in cfDNA was increased by using mutation calling criteria optimized for cfDNA (these criteria were adjusted from those used for archival tumor biopsies) without compromising specificity. Sensitivity of BRAF mutation detection in serum was 44% (95% CI, 35% to 53%) and in plasma 52% (95% CI, 43% to 61%). Specificity was 96% (95% CI, 90% to 99%) in both matrices. Serum contains significantly higher total cfDNA than plasma, whereas the proportion of tumor-derived mutant DNA was significantly higher in plasma. Using mutation calling criteria optimized for cfDNA improves sensitivity of BRAF c.1799T>A (p.V600E) mutation detection. The proportion of tumor-derived cfDNA in plasma was significantly higher than in serum.
    Citation
    Analytical validation of BRAF mutation testing from circulating free DNA using the amplification refractory mutation testing system. 2014: J Mol Diagn
    Journal
    The Journal of Molecular Diagnostics
    URI
    http://hdl.handle.net/10541/315940
    DOI
    10.1016/j.jmoldx.2013.12.004
    PubMed ID
    24631158
    Type
    Article
    Language
    en
    ISSN
    1943-7811
    ae974a485f413a2113503eed53cd6c53
    10.1016/j.jmoldx.2013.12.004
    Scopus Count
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