Factors in tissue handling and processing that impact RNA obtained from formalin-fixed, paraffin-embedded tissue

Joon Yong Chung, Till Braunschweig, Reginald Williams, Natalie Guerrero, Karl M. Hoffmann, Mijung Kwon, Young K. Song, Steven K. Libutti, Stephen M. Hewitt

Research output: Contribution to journalArticlepeer-review

117 Scopus citations


Formalin-fixed, paraffin-embedded (FFPE) tissue is the most common specimen available for molecular assays on tissue after diagnostic histopathological examination. RNA from FFPE tissue suffers from strand breakage and cross-linking. Despite excellent extraction methods, RNA quality from FFPE material remains variable. To address the RNA quality factors within FFPE tissues, we studied RNA quality, isolating individual elements of the tissue fixation and processing including length of fixation in formalin and the type of buffer incorporated in the fixative. We examined the impact of the length of the tissue processing cycle as well. The optimal fixation period of 12-24 hr in phosphate-buffered formalin resulted in better-quality RNA. Longer tissue processing times were associated with higher quality RNA. We determined that the middle region of gene suffers less damage by these processes as shown by real-time quantitative RT-PCR. These data provide key information for the development of methods of analysis of gene expression in archival FFPE tissues and contribute to the establishment of objective standards for the processing and handling of tissue in surgical pathology. This manuscript contains online supplemental material at http://www.jhc.org. Please visit this article online to view these materials.

Original languageEnglish (US)
Pages (from-to)1033-1042
Number of pages10
JournalJournal of Histochemistry and Cytochemistry
Issue number11
StatePublished - Nov 2008
Externally publishedYes


  • Formalin fixed
  • Gene expression
  • Paraffin embedded
  • RNA integrity
  • Real-time RT-PCR
  • Tissue fixation and processing

ASJC Scopus subject areas

  • Anatomy
  • Histology


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