2014
DOI: 10.1186/1868-7083-6-22
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Quantitative methodology is critical for assessing DNA methylation and impacts on correlation with patient outcome

Abstract: BackgroundDNA hypermethylation is reported as a frequent event and prognostic marker in head and neck squamous cell carcinomas (HNSCC). Methylation has been commonly assessed with non-quantitative methodologies, such as methylation-specific PCR (MSP). We investigated previously reported hypermethylated genes with quantitative methodology in oral tongue squamous cell carcinomas (OTSCC).ResultsThe methylation status of 12 genes in 115 OTSCC samples was assessed by one or more of three quantitative analyses: meth… Show more

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Cited by 20 publications
(25 citation statements)
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“…In the current study, we detected ID4 methylation in a large cohort of myeloid malignancies using RQ-MSP, a rapid and precise methodology in detecting DNA methylation [37]. Increased ID4 methylation level was frequently occurred in patients with MDS, AML and BC-CML.…”
Section: Discussionmentioning
confidence: 93%
“…In the current study, we detected ID4 methylation in a large cohort of myeloid malignancies using RQ-MSP, a rapid and precise methodology in detecting DNA methylation [37]. Increased ID4 methylation level was frequently occurred in patients with MDS, AML and BC-CML.…”
Section: Discussionmentioning
confidence: 93%
“…EpigenDx performed pyro-sequencing on the PSQ96 HS System (Qiagen) following the manufacturer’s instructions, using custom assays and a gradient of controls with known methylation levels. This allowed for the quantification of the absolute percent methylation [ 58 ] of each CpG at specific loci using QCpG software (Qiagen). The absolute percent methylation at each assayed cytosine was averaged among ethanol-exposed (n = 3) and control (n = 3) samples and compared using a Student’s t-test.…”
Section: Methodsmentioning
confidence: 99%
“…This allowed for the quantification of the absolute percent methylation [34] of each CpG at select loci using QCpG software (Qiagen). The sequencing reads also allowed for the analysis of SNPs known to be within or close to the CpGs of the 450K probes.…”
Section: Confirmation By Pyrosequencingmentioning
confidence: 99%