Breaking analytical barriers for fragmented samples: Revolutionizing FFPE samples in DNA methylation biomarker discovery

FFPE (Formalin-Fixed Paraffin-Embedded) tissue is a widely used sample type, as this tissue preparation method which involves tissue fixation, dehydration, clearing, and embedding, allows for long-term preservation of samples, maintenance of cellular morphology, and enabling of retrospective studies with archived samples. Samples have been stored in this form for decades and are essential in cancer research and diagnosis by providing a valuable resource for studying tumor biology, identifying potential therapeutic targets, and validating new diagnostic methods and treatments. In this application note, Zymo Research shows that while bisulfite converting FFPE DNA can be challenging due to the degraded nature of the sample, careful optimization of protocols and considerations for the compromised DNA quality can enable successful analysis of DNA methylation patterns in these valuable samples. Proper handling and analysis of bisulfite-converted FFPE DNA can provide critical insights into epigenetic changes associated with cancer and other diseases.