Biobanking pp 269-278 | Cite as

Microtomy: Cutting Formalin-Fixed, Paraffin-Embedded Sections

  • Joanne SyEmail author
  • Lee-Cyn Ang
Part of the Methods in Molecular Biology book series (MIMB, volume 1897)


Formalin-fixed, paraffin-embedded tissue (FFPE) still plays an important role in biobanking, since it is comparatively easy to obtain and store in comparison to fresh frozen tissue. They are stored as paraffin or FFPE blocks. Unstained slides derived from FFPE blocks may be used for hematoxylin and eosin histology, special stains, immunohistochemistry, and chromogenic or fluorescent in situ hybridization. In addition, tissue scraped off FFPE slides or from scrolls of FFPE tissue may be used for molecular or proteomic analyses. Hematoxylin and eosin staining of FFPE sections reviewed by a pathologist are highly valuable to ensure the presence of adequate lesional cells for molecular and other analyses. Therefore, proper microtomy technique is essential in the preparation of formalin-fixed, paraffin-embedded tissue for biobanking purposes. Here we describe the process of cutting paraffin embedded sections using a rotary microtome. We also highlight the possible pitfalls that may arise and discuss how to avoid them.

Key words

Microtomy Formalin-fixed Paraffin sections FFPE 


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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2019

Authors and Affiliations

  1. 1.Department of Anatomical Pathology, Concord Repatriation General HospitalUniversity of SydneyConcordAustralia
  2. 2.Department of Pathology (Neuropathology) and Laboratory MedicineUniversity Hospital – London Health Sciences Centre, Western UniversityOntario, LondonCanada

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