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Kagan, J., Srivastava, S., Barker, P. E., Belinsky, S. A. & Cairns, P. Towards clinical application of methylated DNA sequences as cancer biomarkers: a joint NCI's EDRN & NIST workshop on standards, methods, assays, reagents and tools (SMART). Cancer Res. 67, 4545-4549

Cancer Biomarkers Research Group, Division of Cancer Prevention, National Cancer Institute, NIH, Bethesda, Maryland, USA.
Cancer Research (Impact Factor: 9.28). 06/2007; 67(10):4545-9. DOI: 10.1158/0008-5472.CAN-06-2888
Source: PubMed

ABSTRACT The workshop report, entitled Towards Clinical Application of Methylated DNA Sequences as Cancer Biomarkers: A Joint National Cancer Institute's Early Detection Research Network and National Institute of Standards and Technology Workshop, presents a summary of the main issues, current challenges, outcomes, and recommendations toward application of methylated DNA sequences as cancer biomarkers.

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    • "A well-designed epidemiologic study is needed to evaluate the validity of a putative methylation-based biomarker. Strategies to validate biomarkers were well established in the community of the Early Detection Research Network (EDRN).71,72 The researchers developed a 5-phase strategy for identifying cancer biomarkers. "
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    ABSTRACT: Aberrant DNA methylation is associated with cancer development and progression. There are several types of specimens from which DNA methylation pattern can be measured and evaluated as an indicator of disease status (from normal biological process to pathologic condition) and even of pharmacologic response to therapy. Blood-based specimens such as cell-free circulating nucleic acid and DNA extracted from leukocytes in peripheral blood may be a potential source of noninvasive cancer biomarkers. In this article, we describe the characteristics of blood-based DNA methylation from different biological sources, detection methods, and the factors affecting DNA methylation. We provide a comprehensive literature review of blood-based DNA methylation as a cancer biomarker and focus on the study of DNA methylation using peripheral blood leukocytes. Although DNA methylation patterns measured in peripheral blood have great potential to be useful and informative biomarkers of cancer risk and prognosis, large systematic and unbiased prospective studies that consider biological plausibility and data analysis issues will be needed in order to develop a clinically feasible blood-based assay.
    Journal of Epidemiology 08/2012; 22(5):384-94. DOI:10.2188/jea.JE20120003 · 2.86 Impact Factor
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    • "However, some issues remain to be solved in the future. For example, few methylated genes have been identified in ESCC by a single group, with the methylation frequency of some TSGs varying widely in different labs, probably due to different patient cohorts or detection methods[75]. With the use of genome-wide epigenomic approaches[76], the more reliable identification of methylated genes or gene panels might improve the early detection and prognosis of ESCC in future. "
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    ABSTRACT: Esophageal squamous cell carcinoma (ESCC) is a prevalent and fatal cancer in China and other Asian countries. Epigenetic silencing of key tumor suppressor genes (TSGs) is critical to ESCC initiation and progression. Recently, many novel TSGs silenced by promoter methylation have been identified in ESCC, and these genes further serve as potential tumor markers for high-risk group stratification, early detection, and prognosis prediction. This review summarizes recent discoveries on aberrant promoter methylation of TSGs in ESCC, providing better understanding of the role of disrupted epigenetic regulation in tumorigenesis and insight into diagnostic and prognostic biomarkers for this malignancy.
    Chinese journal of cancer 05/2012; 32(1). DOI:10.5732/cjc.011.10381 · 2.16 Impact Factor
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    • "Thus, even when extraction methods dedicated to FFPE tissue were used, problems occurred with bisulfite conversion. The importance of successful bisulfite conversion was underlined by a panel of experts who reported that incomplete conversion of DNA was the major cause of false-positive results in methylation analysis [29]. We chose not to evaluate the results of the methylation levels obtained from FFPE DNA extracted using the classical method because the number of unsatisfactory conversions was too high, but it was clear that poor bisulfite conversion led to overestimation of methylation (Additional file 3: Figure 1). "
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    ABSTRACT: In colorectal carcinoma, extensive gene promoter hypermethylation is called the CpG island methylator phenotype (CIMP). Explaining why studies on CIMP and survival yield conflicting results is essential. Most experiments to measure DNA methylation rely on the sodium bisulfite conversion of unmethylated cytosines into uracils. No study has evaluated the performance of bisulfite conversion and methylation levels from matched cryo-preserved and Formalin-Fixed Paraffin Embedded (FFPE) samples using pyrosequencing. Couples of matched cryo-preserved and FFPE samples from 40 colon adenocarcinomas were analyzed. Rates of bisulfite conversion and levels of methylation of LINE-1, MLH1 and MGMT markers were measured. For the reproducibility of bisulfite conversion, the mean of bisulfite-to-bisulfite standard deviation (SD) was 1.3%. The mean of run-to-run SD of PCR/pyrosequencing was 0.9%. Of the 40 DNA couples, only 67.5%, 55.0%, and 57.5% of FFPE DNA were interpretable for LINE-1, MLH1, and MGMT markers, respectively, after the first analysis. On frozen samples the proportion of well converted samples was 95.0%, 97.4% and 87.2% respectively. For DNA showing a total bisulfite conversion, 8 couples (27.6%) for LINE-1, 4 couples (15.4%) for MLH1 and 8 couples (25.8%) for MGMT displayed significant differences in methylation levels. Frozen samples gave reproducible results for bisulfite conversion and reliable methylation levels. FFPE samples gave unsatisfactory and non reproducible bisulfite conversions leading to random results for methylation levels. The use of FFPE collections to assess DNA methylation by bisulfite methods must not be recommended. This can partly explain the conflicting results on the prognosis of CIMP colon cancers.
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