Simultaneous Profiling of DNA Mutation and Methylation by Melting Analysis Using Magnetoresistive Biosensor Array

Giovanni Rizzi, Jung-Rok Lee, Christina Dahl, Per Guldberg, Martin Dufva, Shan X. Wang, Mikkel Fougt Hansen

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    Abstract

    Epigenetic modifications, in particular DNA methylation, are gaining increasing interest as complementary information to DNA mutations for cancer diagnostics and prognostics. We introduce a method to simultaneously profile DNA mutation and methylation events for an array of sites with single site specificity. Genomic (mutation) or bisulphite-treated (methylation) DNA is amplified using nondiscriminatory primers, and the amplicons are then hybridized to a giant magnetoresistive (GMR) biosensor array followed by melting curve measurements. The GMR biosensor platform offers scalable multiplexed detection of DNA hybridization, which is insensitive to temperature variation. The melting curve approach further enhances the assay specificity and tolerance to variations in probe length. We demonstrate the utility of this method by simultaneously profiling five mutation and four methylation sites in human melanoma cell lines. The method correctly identified all mutation and methylation events and further provided quantitative assessment of methylation density validated by bisulphite pyrosequencing.
    Original languageEnglish
    JournalA C S Nano
    Volume11
    Issue number9
    Pages (from-to)8864-8870
    Number of pages7
    ISSN1936-0851
    DOIs
    Publication statusPublished - 2017

    Keywords

    • DNA array
    • Mutation
    • Methylation
    • GMR biosensor
    • Melanoma
    • Melting curve

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