Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection

Kristensen, Lasse Sommer; Mikeska, Thomas; Krypuy, Michael; Dobrovic, Alexander

doi:10.1093/nar/gkn113

Cited by 162 publications

(163 citation statements)

References 42 publications

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“…The MSP and MSRA detection rates were identical (16.6%) in six normal controls (1/6 cases). The COBRA method is a semi-quantitative detection method that, as a result of the use of bisulfite restriction enzyme, may display methylation frequencies at a specific enzyme locus (CGCG), thereby yielding false-negative results (Eads et al, 2000;Kristensen et al, 2008). Thus, the use of COBRA was regarded as an exclusion criterion, and four QMSP studies in the meta-analysis were excluded when the control group utilized NRTs to improve the reliability of the analysis results.…”

Section: Discussionmentioning

confidence: 99%

Association between RASSF1A promoter methylation and renal cell cancer susceptibility: a meta-analysis

et al. 2016

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ABSTRACT. Epigenetic inactivation of Ras-associated domain family 1A (RASSF1A) by hyper-methylation of its promoter region has been identified in various cancers. However, the role of RASSF1A in renal cancer has neither been thoroughly investigated nor reviewed. In this study, we reviewed and performed a meta-analysis of 13 published studies reporting correlations between methylation frequency of the RASSF1A promoter region and renal cancer risk. The odds ratios (ORs) of eligible studies and their corresponding 95% confidence intervals (95%CIs) were used to correlate RASSF1A promoter methylation with renal cell cancer risk and clinical or pathological variables, respectively. RASSF1A promoter methylation was significantly associated with the risk of renal cell cancer (OR = 19.35, 95%CI = 9.57-39.13). RASSF1A promoter methylation was significantly associated with pathological tumor grade (OR = 3.32, 95%CI = 1.55-7.12), and a possible positive correlation between RASSF1A promoter methylation status and tumor stage was noted (OR = 1.89, 95%CI = 1.00-3.56, P = 0.051). Overall, this meta-analysis demonstrated that RASSF1A promoter methylation is significantly associated with increased risk of renal cell cancer. RASSF1A promoter methylation frequency was positively correlated with pathological tumor grade, but not the clinical stage. This study showed that RASSF1A promoter methylation could be utilized to predict renal cell cancer prognosis.

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Section: Discussionmentioning

confidence: 99%

Association between RASSF1A promoter methylation and renal cell cancer susceptibility: a meta-analysis

et al. 2016

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“…The DNA methylation status of CCNG2, DDIT4, DEDD, FHIT, PRDM13, PTPRG, SAMD14, SMPD3, TP53BP2 and the collagen type II α1 (COL2A1:reference gene 37 ) were determined by quantitative methylation-specific polymerase chain reaction (MSP) using primers specific for methylated sequences on a bisulfite-modified genomic DNA template (EZ DNA methylation Gold Kit, Zymo Research). Each reaction was performed in duplicate and the results were obtained from two or three independent assays.…”

Section: Disclosure Of Potential Conflicts Of Interestmentioning

confidence: 99%

Boswellic acid induces epigenetic alterations by modulating DNA methylation in colorectal cancer cells

Yan

Takahashi

Byun

et al. 2012

Cancer Biology & Therapy

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“…SMART-MSP is an methylation-specific PCR (MSP)-based methodology that uses real-time amplification for quantification and high resolution melting analysis (HRM) to quality control the results (14). This allowed us to exclude false positive results due to incomplete conversion.…”

Section: A Panel Of 89 Normal Individuals (Red Cross Blood Donors)mentioning

confidence: 99%

Detection of MGMT Promoter Methylation in Normal Individuals Is Strongly Associated with the T Allele of the rs16906252 MGMT Promoter Single Nucleotide Polymorphism

Candiloro

Dobrovic

2009

Cancer Prevention Research

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Methylation of the CpG island in the MGMT promoter region is a frequent event in several cancer types including colorectal cancer, lung cancer, lymphoma, and glioblastoma. A correlation between methylation and the T allele of the rs16906252 single nucleotide polymorphism (SNP) in colorectal carcinomas has previously been reported. As aberrant MGMT methylation can be an early event in tumor development, we tested the hypothesis that normal individuals possessing the T allele may be predisposed to somatic methylation at the MGMT promoter. Peripheral blood monononuclear cell DNA from 89 normal, healthy individuals was genotyped at rs1690625 and assessed for the methylation status of the MGMT promoter region using independent quantitative methodologies capable of detecting lowlevel methylation: MethyLight and Sensitive Melting Analysis after Real-time MethylationSpecific PCR (SMART-MSP). There was a strong association between presence of the T allele and detectable methylation (P = 0.00005) in the peripheral blood DNA. Furthermore, when a MSP assay flanking the SNP was used to amplify methylated sequences in heterozygotes, only the T allele was methylated. Thus, detectable somatic methylation of the MGMT promoter in normal individuals is strongly associated with the T allele of the rs16906252 MGMT promoter SNP.Inactivation of tumor suppressor genes and DNA stability genes by promoter methylation is a common occurrence in human cancer. In some cases, epigenetic inactivation of one of these genes is likely to be the initiating event in cancer development (reviewed in ref. 1). Evidence for this is particularly strong for certain hereditary cancer genes where constitutional methylation of the gene predisposes to cancer development (2-4).It is also likely that constitutional methylation of other genes not normally involved in heritable cancer can predispose to cancer. One of the most plausible candidates for a gene whose inactivation may initiate carcinogenesis is MGMT, which codes for a protein that removes alkyl adducts from the O6 position of guanine (5). Loss of MGMT function will give rise to a mutator phenotype, as alkylation damage from a variety of environmental sources is a common occurrence and as alkylated guanine is likely to mispair with thymine during DNA replication. MGMT methylation is commonly found in various cancers including colorectal cancers, gliomas, head and neck cancers, and lymphomas (6). MGMT promoter methylation has been used as a predictive marker in cancers; it indicates those individuals who are likely to respond to chemotherapy with alkylating agents (7,8).MGMT methylation may be an early or even predisposing event in colorectal cancer. Esteller et al. (9) reported that MGMT methylation was present in adenomas. Shen et al. (10) reported that MGMT methylation was found in apparently normal colonic tissue up to 10 cm from an MGMT-methylated colorectal cancer indicating that MGMT methylation can even be observed prior to any detectable change in morphology.Ogino et al. (11) investi...

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Sensitive Melting Analysis after Real Time- Methylation Specific PCR (SMART-MSP): high-throughput and probe-free quantitative DNA methylation detection

Cited by 162 publications

References 42 publications

Association between RASSF1A promoter methylation and renal cell cancer susceptibility: a meta-analysis

Association between RASSF1A promoter methylation and renal cell cancer susceptibility: a meta-analysis

Boswellic acid induces epigenetic alterations by modulating DNA methylation in colorectal cancer cells

Detection of MGMT Promoter Methylation in Normal Individuals Is Strongly Associated with the T Allele of the rs16906252 MGMT Promoter Single Nucleotide Polymorphism

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