title: Improved reproducibility in genome-wide DNA methylation analysis for PAXgene-fixed samples compared with restored formalin-fixed and paraffin-embedded DNA.
abstract: 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.
authors.affiliation: Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark; Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, 91000 Evry, France.
authors.forename: Gitte Brinch
authors.initials: GB
authors.lastname: Andersen
authors.affiliation: Department of Pathology, Aarhus University Hospital, DK-8000 Aarhus C, Denmark.
authors.forename: Henrik
authors.initials: H
authors.lastname: Hager
authors.affiliation: Department of Biomedicine, Aarhus University, DK-8000 Aarhus C, Denmark.
authors.forename: Lise Lotte
authors.initials: LL
authors.lastname: Hansen
authors.affiliation: Laboratory for Epigenetics and Environment, Centre National de Génotypage, CEA-Institut de Génomique, 91000 Evry, France. Electronic address: tost@cng.fr.
authors.forename: Jörg
authors.initials: J
authors.lastname: Tost
mesh_terms: D000230:Adenocarcinoma / Q000737:chemistry; D000077192:Adenocarcinoma of Lung; D018899:CpG Islands; D004247:DNA / Q000032:analysis* / Q000737:chemistry*; D019175:DNA Methylation; D004273:DNA, Neoplasm / Q000032:analysis / Q000737:chemistry; D005557:Formaldehyde; D015894:Genome, Human; D006801:Humans; D008168:Lung / Q000737:chemistry; D008175:Lung Neoplasms / Q000737:chemistry; D016612:Paraffin Embedding; D015203:Reproducibility of Results; D016707:Tissue Fixation
chemical_list: D004273:DNA, Neoplasm; D005557:Formaldehyde; D004247:DNA
keywords: DNA methylation; DNA restoration; FFPE; Genome-wide methylation analysis; Illumina 450K BeadChip; PAXgene