FFPE

FFPE stands for formalin-fixed, paraffin-embedded, a widely used method for preserving and embedding tissue specimens for histology and long-term storage. In this process, tissue is fixed in neutral buffered formalin to stabilize structure by cross-linking proteins. After fixation, the sample undergoes dehydration through graded alcohols, clearing with a solvent such as xylene, and infiltration with molten paraffin, which solidifies to form a block suitable for sectioning.

Thin sections, typically 4-5 microns, are cut from FFPE blocks and mounted on glass slides. Before staining or molecular testing, sections are deparaffinized and rehydrated. FFPE tissues support routine hematoxylin and eosin staining, as well as immunohistochemistry and in situ hybridization. They also serve as a valuable source for retrospective molecular analyses, including DNA, RNA, and protein assays, when appropriate extraction and retrieval protocols are used.

Advantages of FFPE include robust morphological preservation, stability at room temperature, and the ability to archive samples for decades. This enables longitudinal diagnostic workups and retrospective research. Limitations arise from formaldehyde-induced cross-links, which can fragment nucleic acids and hinder antigenicity; fixation time and decalcification procedures can further affect molecular test performance. Special pre-analytical and extraction methods are often required to obtain usable DNA, RNA, or proteins from FFPE tissue.

Safety considerations are important, as formalin is hazardous. FFPE remains the standard method in diagnostic pathology and a foundational resource for translational and clinical research.