title: The influence of DNA degradation in formalin-fixed, paraffin-embedded (FFPE) tissue on locus-specific methylation assessment by MS-HRM.
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.
authors.affiliation: Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Build. 1230, DK-8000 Aarhus C, Denmark. Electronic address: iben@biomed.au.dk.
authors.forename: Iben
authors.initials: I
authors.lastname: Daugaard
authors.affiliation: Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Build. 1230, DK-8000 Aarhus C, Denmark.
authors.forename: Tina E
authors.initials: TE
authors.lastname: Kjeldsen
authors.affiliation: Department of Pathology, Aarhus University Hospital, Nørrebrogade 45, DK-8000 Aarhus C, Denmark.
authors.forename: Henrik
authors.initials: H
authors.lastname: Hager
authors.affiliation: Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Build. 1230, DK-8000 Aarhus C, Denmark.
authors.forename: Lise Lotte
authors.initials: LL
authors.lastname: Hansen
authors.affiliation: 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.
authors.forename: Tomasz K
authors.initials: TK
authors.lastname: Wojdacz
mesh_terms: D002289:Carcinoma, Non-Small-Cell Lung / Q000235:genetics*; D019175:DNA Methylation / Q000235:genetics*; D004273:DNA, Neoplasm / Q000032:analysis* / Q000378:metabolism; D005557:Formaldehyde; D005821:Genetic Techniques; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics*; D016612:Paraffin Embedding; D016133:Polymerase Chain Reaction; D016707:Tissue Fixation
chemical_list: D004273:DNA, Neoplasm; D005557:Formaldehyde
keywords: Biomarker; Formalin fixed paraffin embedded (FFPE); MS-HRM; Methylation