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Abstract Background Recently it has been suggested that acquisition of methylation of the BRCA1 promoter detectable in peripheral blood (PB) DNA, could give raise to development of breast cancer. In this study, we aimed to investigate a relationship between methylation of three breast cancer related genes in PB DNA, and tumor specific (somatic) methylation of these genes in the same individual. Findings We have examined methylation status of the BRCA1, APC and RASSF1A promoter regions in a panel of 75 breast tumor and PB DNA samples from the same individual. In our study group, 4.0% of the patients displayed methylation of BRCA1 and APC in both tumor and the corresponding PB DNA. At the same time despite of marked methylation in tumor DNA, no methylation of BRCA1 and APC was seen in PB DNA of 4.3% and 2.7% of the patients respectively. The RASSF1A promoter did not show methylation in PB DNA. Conclusions Our results show that for at least a subset of cancer patients methylation of certain cancer related genes in PB DNA does not seem to be directly linked to somatic methylation of the same genes in tumor DNA, and therefore may only be specific to PB DNA.

Abstract Background The High Resolution Melting (HRM) technology has recently been introduced as a rapid and robust analysis tool for the detection of DNA methylation. The methylation status of multiple tumor suppressor genes may serve as biomarkers for early cancer diagnostics, for prediction of prognosis and for prediction of response to treatment. Therefore, it is important that methodologies for detection of DNA methylation continue to evolve. Sensitive Melting Analysis after Real Time - Methylation Specific PCR (SMART-MSP) and Methylation Sensitive - High Resolution Melting (MS-HRM) are two methods for single locus DNA methylation detection based on HRM. Methods Here, we have assessed the quality of DNA extracted from up to 30 years old Formalin Fixed Paraffin Embedded (FFPE) tissue for DNA methylation analysis using SMART-MSP and MS-HRM. The quality assessment was performed on DNA extracted from 54 Non-Small Cell Lung Cancer (NSCLC) samples derived from FFPE tissue, collected over 30 years and grouped into five years intervals. For each sample, the methylation levels of the CDKN2A (p16) and RARB promoters were estimated using SMART-MSP and MS-HRM assays designed to assess the methylation status of the same CpG positions. This allowed for a direct comparison of the methylation levels estimated by the two methods for each sample. Results CDKN2A promoter methylation levels were successfully determined by SMART-MSP and MS-HRM in all 54 samples. Identical methylation estimates were obtained by the two methods in 46 of the samples. The methylation levels of the RARB promoter were successfully determined by SMART-MSP in all samples. When using MS-HRM to assess RARB methylation five samples failed to amplify and 15 samples showed a melting profile characteristic for heterogeneous methylation. Twenty-seven of the remaining 34 samples, for which the methylation level could be estimated, gave the same result as observed when using SMART-MSP. Conclusion MS-HRM and SMART-MSP can be successfully used for single locus methylation studies using DNA derived from up to 30 years old FFPE tissue. Furthermore, it can be expected that MS-HRM and SMART-MSP will provide similar methylation estimates when assays are designed to analyze the same CpG positions.