A qPCR technology for direct quantification of methylation in untreated DNA

Kamilla Bendixen*, Maria Mindegaard, Samantha Epistolio, Giulia Dazio, Francesco Marchi, Paolo Spina, Eva C. Arnspang, Mette Sørensen, Ulf Bech Christensen, Milo Frattini, Rasmus Kofoed Petersen

*Kontaktforfatter

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Abstract

DNA methylation is important for gene expression and alterations in DNA methylation are involved in the development and progression of cancer and other major diseases. Analysis of DNA methylation patterns has until now been dependent on either a chemical or an enzymatic pre-treatment, which are both time consuming procedures and potentially biased due to incomplete treatment. We present a qPCR technology, EpiDirect®, that allows for direct PCR quantification of DNA methylations using untreated DNA. EpiDirect® is based on the ability of Intercalating Nucleic Acids (INA®) to differentiate between methylated and unmethylated cytosines in a special primer design. With this technology, we develop an assay to analyze the methylation status of a region of the MGMT promoter used in treatment selection and prognosis of glioblastoma patients. We compare the assay to two bisulfite-relying, methyl-specific PCR assays in a study involving 42 brain tumor FFPE samples, revealing high sensitivity, specificity, and the clinical utility of the method.

OriginalsprogEngelsk
Artikelnummer5153
TidsskriftNature Communications
Vol/bind14
Udgave nummer1
Antal sider11
ISSN2041-1723
DOI
StatusUdgivet - aug. 2023

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© 2023. Springer Nature Limited.

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