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    Efficient DNA extraction from 25-year-old paraffin-embedded tissues: Study of 365 samples

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    Aims: Archival fixed paraffin-embedded tissue (PET) is a valuable source for population-based molecular genetic studies but the extraction of high quality DNA is still a problematic issue. The present study tested the grade of DNA fragmentation and the DNA adequacy for genetic investigations in a large series of tissue specimens that were formalin- or Bouin-fixed and paraffin-embedded between 1979 and 1983. Specific aims were to: (1) estimate the amount of archival tissue samples from which DNA is recoverable by conventional methods and the influence of variables (origin, fixative, section size) on DNA recovery; and (2) evaluate the feasibility of genetic investigations in large scale population studies. Methods: DNA was extracted in 2005 from 365 PET samples from Italy and Spain and subjected to PCR analysis targeting fragments of 152, 268 and 676 bp of the ß-globin gene. Results: Amplification of a 152 bp fragment was obtained in 252/365 (69%) PET samples, a 268 bp fragment in 62/365 (17%), a 676 bp fragment in 19/365 (5%) and no amplification for any fragment was obtained in 113/365 (31%). A second processing of newly cut sections performed in a 25% simple random sample gave comparable results, with substantial concordance between the first and second tests (kappa value 0.62 [95% CI 0.59-0.64]). Conclusions: The results of this study show that DNA can be efficiently extracted from PETs archived for more than 20 years, and that large scale population studies based on PCR amplification of short target sequences are feasible. © 2007 Royal College of Pathologists of Australasia

    Association between hypermethylated tumor and paired surgical margins in head and neck squamous cell carcinomas

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    PURPOSE: Surgical margin status is reported to be a relevant prognostic factor in head and neck squamous cell carcinoma (HNSCC), associated with a high risk of local recurrence. This study examines whether gene-promoter hypermethylation could be detected in HNSCC surgical margins with no histologic evidence of malignancy, and if so, whether it reflects epigenetic events of primary tumors. EXPERIMENTAL DESIGN: Promoter methylation status of MGMT, p16, and DAP-K genes was evaluated by methylation-specific PCR in 20 primary HNSCC tumors. Histopathologically negative surgical margins of hypermethylated tumors were collected, and their methylation status compared with the primary tumor status. RESULTS: Promoter hypermethylation in at least one of the three tested genes was detected in 65% (13 of 20) of tumors. MGMT was hypermethylated in 50% (10 of 20), DAP-K in 45% (9 of 20), and p16 in 20% (4 of 20) of tumors. Methylation status was analyzed in 35 margins from 11 of 13 patients showing promoter hypermethylation in the tumor tissue. Identical methylation events were seen for at least one gene in primary tumor and surgical margins in 9 of 11 cases (82%). Association was found for gene-specific hypermethylation status in tumors and paired surgical margins, and gene-specific concordance was 63% for MGMT (kappa = 0.24), 90% for DAP-K (kappa = 0.74), and 90% for p16 (kappa = 0.79). CONCLUSIONS: Our results support the hypothesis that detection of gene promoter hypermethylation in HNSCC tumor cells-free surgical margins may be a helpful biomarker to identify molecularly altered fields in areas adjacent to the tumor
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