A critical evaluation of the PAXgene tissue fixation system: Morphology, immunohistochemistry, molecular biology, and proteomics

William Mathieson, Nathalie Marcon, Laurent Antunes, David A. Ashford, Fay Betsou, Sonia G. Frasquilho, Olga A. Kofanova, Siobhan C. McKay, Stephan Pericleous, Colleen Smith, Kristian M. Unger, Constanze Zeller, Geraldine A. Thomas*

*Corresponding author for this work

Research output: Contribution to journalArticleResearchpeer-review

37 Citations (Scopus)


Objectives: To evaluate the PAXgene tissue fixation system. Methods: Clinical biospecimens (n=46) were divided into PAXgene-fixed paraffin-embedded (PFPE), formalin-fixed paraffin-embedded (FFPE), and fresh-frozen (FF) blocks. PFPE and FFPE sections were compared for histology (H&E staining) and immunohistochemistry (14 antibodies) using tissue microarrays. PFPE, FFPE, and FF samples were compared in terms of RNA quality (RNA integrity number, polymerase chain reaction [PCR] amplicon length, and quantitative reverse transcription PCR), DNA quality (gel electrophoresis and methylation profiling) and protein quality (liquid chromatography-mass spectrometry [LC-MS/MS]). Results: PFPE protocol optimization was required in most cases and is described. RNA extracted from PFPE sections was considerably less degraded than that from FFPE sections but more degraded than that from FF blocks. Genomic-length DNA was extracted from PFPE and FF biospecimens, and methylation profiling showed PFPE and FF biospecimens to be almost indistinguishable. Only degraded DNA was extracted from FFPE biospecimens. PFPE sections yielded peptides that were slightly less amenable to LC-MS/MS analysis than FFPE sections, but FF gave slightly better results. Conclusions: While it cannot be envisaged that PAXgene will replace formalin in a routine clinical setting, for specific projects or immunodiagnostics involving biospecimens destined for immunohistochemical or histologic staining and DNA or RNA analyses, PAXgene is a viable option.

Original languageEnglish
Pages (from-to)25-40
Number of pages16
JournalAmerican Journal of Clinical Pathology
Issue number1
Publication statusPublished - 1 Jul 2016


  • DNA
  • FFPE
  • Formalin
  • Method validation
  • PFPE
  • Protein
  • RNA
  • Tissue microarray


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