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Formalin-fixed, paraffin-embedded samples are a common method for the storage of specimens for disease research. They are an important resource for time-based studies because they can be stored indefinitely at room temperature. DNA and RNA can also be recovered over very long periods (decades) since the time the original sample was produced. FFPE is a widespread form of sample storage so there are vast archives of specimens available that users can select from.

One of the challenges with FFPE tissue blocks is that it can be difficult to extract information from them because severe damage and decay as well as molecular or biological changes can occur throughout the treatment and storage of these samples. Additionally, Formalin is toxic and the process of paraffin-embedding can take a long time. They are typically not suited for molecular analysis and there are no standard protocols for FFPE preparation so there’s no guarantee each sample was prepared the same.

There have been many recently published discoveries of gene variations, gene expression profiling changes, and protein biomarkers found with FFPE tissues.