Sensitive Detection of DNA Methylation

Abstract

In recent years, many molecular biomarkers have been discovered that are capable of distinguishing tumors from normal tissue. Among the different types of markers, DNA methylation markers stand out for their potential to provide a unique combination of specificity, sensitivity, high information content, and applicability to a wide variety of clinical specimens. Methylation markers are particularly suited for situations where sensitive detection is necessary, such as when tumor DNA is either scarce or diluted by excess normal DNA. One of the most widely used methods for measuring methylation levels, methylation-specific PCR (MSP), has been proved to be a very effective tool in situations requiring sensitive detection. The addition of fluorogenic probes makes these assays more informative, quantitative, and suitable for a clinical format. The field of sensitive detection is not limited to MSP; hence, an alternative methylation-sensitive amplification is discussed. PCR-based methylation assays have been applied to the detection of tumor DNA in a variety of body fluids, including serum, plasma, urine, sputum, and lavage fluids. In many cases, the sensitivity and specificity of these detection assays has been impressive, but important technological issues remain in areas such as sample preparation, assay design, and marker selection. Once these technical concerns have been addressed, the sensitive detection of methylation will provide a powerful diagnostic and prognostic tool, especially for the early detection of preneoplastic and neoplastic lesions.

Prognostic DNA Methylation Biomarkers in Ovarian Cancer

“…Epigenetically modified DNA, however, offers potential advantages over other markers, in that it is well associated with tumor progression and several sensitive, high-throughput assays are now widely available (19). DNA is also more stable than RNA, and methylation biomarkers have been established as present in patient serum and other body fluids (20).…”

“…However, methylation signatures may offer advantages over expression signatures, for reasons described above. Additionally, methylated DNA has been shown as present in serum (20,28); it will thus be important to determine whether any of our markers might also be present in body fluids and could thus be used to monitor disease status noninvasively.…”

Screening of Differential Promoter Hypermethylated Genes in Primary Oral Squamous Cell Carcinoma

“…It can be applied for distinguishing unmethylated from the methylated cytosine residues. As few as 1 to 10 tumour cells among 104 normal cells in clinical samples could be detected (Cottrell and Laird, 2003). It is a sensitive but not quantitative technique for the methylation level (Herman et al, 1996;Towle et al, 2012).…”

Status of p16<SUP>INK4a</SUP> and E-Cadherin Gene Promoter Methylation in Moroccan Patients With Cervical Carcinoma

“…It has become increasingly apparent that DNA hypermethylation with subsequent epigenetic silencing of tumor suppressor genes (TSGs) through chromatin remodeling is associated with loss of function, which may constitute the second hit of the "two hit" hypothesis, providing a selective advantage during carcinogenesis (8,9,12). Moreover, genes that are frequently aberrantly methylated in specific tumors have been used as molecular targets for the detection of neoplastic cells in body fluids such as urine and plasma (13,14). p16…”