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Exp Mol Pathol. 2015 Dec;99(3):632-40. doi: 10.1016/j.yexmp.2015.11.007. Epub 2015 Nov 6.

The influence of DNA degradation in formalin-fixed, paraffin-embedded (FFPE) tissue on locus-specific methylation assessment by MS-HRM.

Author information

1
Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Build. 1230, DK-8000 Aarhus C, Denmark. Electronic address: iben@biomed.au.dk.
2
Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Build. 1230, DK-8000 Aarhus C, Denmark.
3
Department of Pathology, Aarhus University Hospital, Nørrebrogade 45, DK-8000 Aarhus C, Denmark.
4
Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Build. 1230, DK-8000 Aarhus C, Denmark; Aarhus Institute of Advanced Studies, Høegh-Guldbergs Gade 6B, DK-8000 Aarhus C, Denmark.

Abstract

Readily accessible formalin-fixed paraffin embedded (FFPE) tissues are a highly valuable source of genetic material for molecular analyses in both research and in vitro diagnostics but frequently genetic material in those samples is highly degraded. With locus-specific methylation changes being widely investigated for use as biomarkers in various aspects of clinical disease management, we aimed to evaluate to what extent standard laboratory procedures can approximate the quality of the DNA extracted from FFPE samples prior to methylation analyses. DNA quality in 107 FFPE non-small cell lung cancer (NSCLC) samples was evaluated using spectrophotometry and gel electrophoresis. Subsequently, the quality assessment results were correlated with the results of locus specific methylation assessment with methylation sensitive high resolution melting (MS-HRM). The correlation of template quality with PCR amplification performance and HRM based methylation detection indicated a significant influence of DNA quality on PCR amplification but not on methylation assessment. In conclusion, standard laboratory procedures fairly well approximate DNA degradation of FFPE samples and DNA degradation does not seem to considerably affect locus-specific methylation assessment by MS-HRM.

KEYWORDS:

Biomarker; Formalin fixed paraffin embedded (FFPE); MS-HRM; Methylation

PMID:
26551081
DOI:
10.1016/j.yexmp.2015.11.007
[Indexed for MEDLINE]

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