Formalin-fixed paraffin-embedded (FFPE) tissue samples stored in pathology departments worldwide are an invaluable source for diagnostic purposes when fresh clinical material is not available, as well as for retrospective molecular and epidemiologic studies for which prospective collection is not possible (Campos PF et al. 2012). The method was developed in the late 19th century.
FFPE
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DefinitionThis section has been translated automatically.
FFPE is the acronym for "Formalin-Fixed, Paraffin-Embedded". FFPE is an abbreviation for the currently common method of embedding organic tissue samples in kerosene so that they can be prepared for histological examination. Tissue samples prepared in this way can be preserved for a long time (years to decades).
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The introduction of state-of-the-art nucleic acid sequencing technologies has sparked great interest in the use of historical FFPE samples stored in biobanks, as they offer promising opportunities to extract new information from these valuable samples. However, formalin fixation chemically alters the DNA, which can lead to incorrect sequences or misinterpretations during further processing and data analysis (Steiert TA et al. 2023). Such DNA damage can be compensated for even if small amounts (50 ng) of fragmented FFPE DNA (DNA integrity number 2.0) are used, which cannot be amplified well (Steiert TA et al. 2023 ). In the meantime, methods for the detection of HPV DNA/RNA in FFPE tissue samples have also been described that can increase their integrity and/or amplifiability and lead to satisfactory detection methods (Kocjan BJ et al. 2016).
LiteratureThis section has been translated automatically.
- Campos PF et al. (2012) DNA extraction from formalin-fixed material. Methods Mol Biol 840:81-85.
- Kocjan BJ et al. (2016) Detection of alpha human papillomaviruses in archival formalin-fixed, paraffin-embedded (FFPE) tissue specimens. J Clin Virol 76 Suppl 1:88-97.
- Nirmalan NJ et al. (2008) Mining the archival formalin-fixed paraffin-embedded tissue proteome: opportunities and challenges. Mol Biosyst 4:712-720
- Steiert TA et al. (2023) A critical spotlight on the paradigms of FFPE-DNA sequencing. Nucleic Acids Res 51:7143-7162.