Lise Lotte Hansen

Improved reproducibility in genome-wide DNA methylation analysis for PAXgene® fixed samples compared to restored FFPE DNA

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  • Gitte Brinch Andersen
  • Henrik Hager, Department of Pathology, Aarhus University Hospital, Nørrebrogade 45, DK-8000 Aarhus C, Denmark., Denmark
  • Lise Lotte Hansen
  • Jörg Tost, Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA - Institut de Génomique, 2 rue Gaston Crémieux, 91000 Evry, France. Electronic address:, France
Formalin fixation has been the standard method for conservation of clinical specimens for decades. However, a major drawback is the high degradation of nucleic acids, which complicates its use in genome-wide analyses. Unbiased identification of biomarkers, however, requires genome-wide studies, precluding the use of the valuable archives of specimens with long-term follow-up data. Therefore, restoration protocols for DNA from formalin-fixed and paraffin-embedded (FFPE) samples have been developed, although they are cost-intensive and time-consuming. An alternative to FFPE and snap-freezing is the PAXgene Tissue System, developed for simultaneous preservation of morphology, proteins, and nucleic acids. In the current study, we compared the performance of DNA from either PAXgene or formalin-fixed tissues to snap-frozen material for genome-wide DNA methylation analysis using the Illumina 450K BeadChip. Quantitative DNA methylation analysis demonstrated that the methylation profile in PAXgene-fixed tissues showed, in comparison with restored FFPE samples, a higher concordance with the profile detected in frozen samples. We demonstrate, for the first time, that DNA from PAXgene conserved tissue performs better compared with restored FFPE DNA in genome-wide DNA methylation analysis. In addition, DNA from PAXgene tissue can be directly used on the array without prior restoration, rendering the analytical process significantly more time- and cost-effective.
Original languageEnglish
JournalAnalytical Biochemistry
Pages (from-to)50-58
Number of pages9
Publication statusPublished - 29 Sep 2014

    Research areas

  • PAXgene DNA methylation Illumina 450K BeadChip FFPE DNA restoration Genome-wide methylation analysis

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