Strategies for Validation and Testing of DNA Methylation Biomarkers

Abstract

DNA methylation is a stable covalent epigenetic modification of primarily CpG dinucleotides that has recently gained considerable attention for its use as a biomarker in different clinical settings, including disease diagnosis, prognosis and therapeutic response prediction. Although the advent of genome-wide DNA methylation profiling in primary disease tissue has provided a manifold resource for biomarker development, only a tiny fraction of DNA methylation-based assays have reached clinical testing. Here, we provide a critical overview of different analytical methods that are suitable for biomarker validation, including general study design considerations, which might help to streamline epigenetic marker development. Furthermore, we highlight some of the recent marker validation studies and established markers that are currently commercially available for assisting in clinical management of different cancers.

Keywords::

• assay validation
• biomarker
• bisulfite-deamination
• circulating free DNA
• deep sequencing
• DNA methylation
• MALDI
• qPCR
• pyrosequencing

Financial & competing interests disclosure

Work on this review was among others supported by the framework of CTMM, the Center for Translational Molecular Medicine, project DeCoDe (grant 03O-101), the European Community FP7 program (FP7 project number 202047 ‘RESOLVE,’ and FP7 project no. ‘277849 EURHEALTHAGEING) and the Austrian funding agencies OeNB Anniversary Fund and TECNET. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Additional information

Funding

Work on this review was among others supported by the framework of CTMM, the Center for Translational Molecular Medicine, project DeCoDe (grant 03O-101), the European Community FP7 program (FP7 project number 202047 ‘RESOLVE,’ and FP7 project no. ‘277849 EURHEALTHAGEING) and the Austrian funding agencies OeNB Anniversary Fund and TECNET. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.