Genome-wide methylation profiling in archival formalin-fixed paraffin-embedded tissue samples

Area of Science:

• Epigenetics
• Molecular Pathology
• Biomarker Discovery

Background:

• Genome-scale DNA methylation measurement technologies are advancing.
• DNA methylation holds potential as a clinical biomarker.
• Archival formalin-fixed paraffin-embedded (FFPE) specimens are valuable resources.

Purpose of the Study:

• To adapt a commercial bisulfite epigenotyping assay for genome-wide methylation profiling.
• To demonstrate the feasibility of using archival FFPE pathology specimens for this analysis.
• To guide biomarker discovery experiments for identifying DNA methylation signatures.

Main Methods:

• Adaptation of a commercial bisulfite epigenotyping assay.
• Application to archival formalin-fixed paraffin-embedded (FFPE) pathology specimens.
• Step-by-step protocol for genome-wide methylation profiling and biomarker discovery.

Main Results:

• Successful genome-wide DNA methylation profiling in archival FFPE specimens.
• Demonstration of a methodology for identifying phenotype-correlated DNA methylation signatures.
• Establishment of a workflow for biomarker discovery using routine pathology samples.

Conclusions:

• The adapted assay is suitable for genome-wide DNA methylation analysis in archival FFPE tissues.
• This approach increases the clinical utility of DNA methylation as a biomarker.
• The methodology facilitates the discovery of novel methylation-based biomarkers from readily available pathology specimens.