Determinants of RNA quality from FFPE samples

PLoS One. 2007 Dec 5;2(12):e1261. doi: 10.1371/journal.pone.0001261.


The large archives of formalin-fixed paraffin-embedded (FFPE) tissue specimens that exist are a highly valuable source of sample material for molecular biological analysis, including gene expression profiling. However, current data on adverse effects of standard pathological practice on the usefulness of biomolecular analytes obtained from such archived specimens is largely anecdotal. Here, we present a systematic examination of the most relevant parameters for integrity and useability of RNA obtained from FFPE samples, including storage time and conditions, fixation time, and specimen size. The results are particularly relevant for any application relying on cDNA synthesis as an initial step of the procedure, such as RT-PCR, and microarray analysis.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Formaldehyde
  • Paraffin Embedding
  • RNA / isolation & purification
  • RNA / standards*
  • Rats
  • Rats, Wistar
  • Reverse Transcriptase Polymerase Chain Reaction
  • Specimen Handling
  • Tissue Fixation


  • Formaldehyde
  • RNA