Show simple item record

dc.contributor.authorDe Chiara Prada, Loretta 
dc.contributor.authorLeiro Fernandez, Virginia
dc.contributor.authorRodríguez Girondo, Mar
dc.contributor.authorValverde Pérez, Diana 
dc.contributor.authorBotana Rial, María Isabel
dc.contributor.authorFernández Villar, Alberto
dc.date.accessioned2021-03-22T12:12:41Z
dc.date.available2021-03-22T12:12:41Z
dc.date.issued2020-12-03
dc.identifier.citationInternational Journal of Molecular Sciences, 21(23): 9242 (2020)spa
dc.identifier.issn14220067
dc.identifier.urihttp://hdl.handle.net/11093/1886
dc.description.abstractDifferent methodological approaches are available to assess DNA methylation biomarkers. In this study, we evaluated two sodium bisulfite conversion-dependent methods, namely pyrosequencing and methylation-specific qPCR (MS-qPCR), with the aim of measuring the closeness of agreement of methylation values between these two methods and its effect when setting a cut-off. Methylation of tumor suppressor gene p16/INK4A was evaluated in 80 lung cancer patients from which cytological lymph node samples were obtained. Cluster analyses were used to establish methylated and unmethylated groups for each method. Agreement and concordance between pyrosequencing and MS-qPCR was evaluated with Pearson’s correlation, Bland–Altman, Cohen’s kappa index and ROC curve analyses. Based on these analyses, cut-offs were derived for MS-qPCR. An acceptable correlation (Pearson’s R2 = 0.738) was found between pyrosequencing (PYRmean) and MS-qPCR (NMP; normalized methylation percentage), providing similar clinical results when categorizing data as binary using cluster analysis. Compared to pyrosequencing, MS-qPCR tended to underestimate methylation for values between 0 and 15%, while for methylation >30% overestimation was observed. The estimated cut-off for MS-qPCR data based on cluster analysis, kappa-index agreement and ROC curve analysis were much lower than that derived from pyrosequencing. In conclusion, our results indicate that independently of the approach used for estimating the cut-off, the methylation percentage obtained through MS-qPCR is lower than that calculated for pyrosequencing. These differences in data and therefore in the cut-off should be examined when using methylation biomarkers in the clinical practice.spa
dc.description.sponsorshipXunta de Galicia | Ref. 09CSA053905PRspa
dc.description.sponsorshipInstituto Carlos III | Ref. PI09 / 90385spa
dc.language.isoengspa
dc.publisherInternational Journal of Molecular Sciencesspa
dc.rightsCreative Commons Attribution (CC BY) license
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.titleComparison of bisulfite pyrosequencing and methylation-specific qPCR for methylation assessmentspa
dc.typearticlespa
dc.rights.accessRightsopenAccessspa
dc.identifier.doi10.3390/ijms21239242
dc.identifier.editorhttps://www.mdpi.com/1422-0067/21/23/9242spa
dc.publisher.departamentoBioquímica, xenética e inmunoloxíaspa
dc.publisher.grupoinvestigacionXenómica e Biomedicinaspa
dc.subject.unesco3201.01 Oncologíaspa
dc.subject.unesco2410.07 Genética Humanaspa
dc.subject.unesco3201.02 Genética Clínicaspa
dc.date.updated2021-03-22T09:49:17Z
dc.computerCitationpub_title=International Journal of Molecular Sciences|volume=21|journal_number=23|start_pag=9242|end_pag=spa


Files in this item

[PDF]

    Show simple item record

    Creative Commons Attribution
(CC BY) license
    Except where otherwise noted, this item's license is described as Creative Commons Attribution (CC BY) license