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 F. Hansen

Research output: Contribution to journalArticlepeer-review

22 Scopus citations

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
Pages (from-to)8864-8870
Number of pages7
JournalACS Nano
Volume11
Issue number9
DOIs
StatePublished - 26 Sep 2017

Keywords

  • DNA array
  • GMR biosensor
  • melanoma
  • melting curve
  • methylation
  • mutation

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