High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil

Nuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, UK.
Analytical Biochemistry (Impact Factor: 2.22). 08/2009; 395(2):265-7. DOI: 10.1016/j.ab.2009.08.016
Source: PubMed


Extracting DNA from formalin-fixed and paraffin-embedded (FFPE) tissue remains a challenge, despite numerous attempts to develop a more effective method. Polymerase chain reaction (PCR) success rates with DNA extracted using current methods remain low. We extracted DNA from 140 long-term archived FFPE samples using a simple but effective deparaffinization method, removing the wax with mineral oil, and a commercially available DNA extraction kit. DNA quality was subsequently tested in a genotyping experiment with 14 microsatellite markers. High-quality DNA was obtained with a mean PCR success rate of 97% (range: 88-100%) across markers. The results suggested that DNA extracted using this novel method is likely to be suitable for genetic studies involving DNA fragments <200 bp.

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    • "Efficient deparaffinization also aids in the removal of residues that may affect amplification. Lin et al reported the use of mineral oil to remove wax from FFPE samples 1. Automated systems use heat and magnetization 3. "
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    ABSTRACT: Aim: Discussing a protocol involving xylene-ethanol deparaffinization on slides followed by a kit-based extraction that allows for the extraction of high quality DNA from FFPE tissues. Methods: DNA was extracted from the FFPE tissues of 16 randomly selected blocks. Methods involving deparaffinization on slides or tubes, enzyme digestion overnight or for 72 hours and isolation using phenol chloroform method or a silica-based commercial kit were compared in terms of yields, concentrations and the amplifiability. Results: The highest yield of DNA was produced from the samples that were deparaffinized on slides, digested for 72 hours and isolated with a commercial kit. Samples isolated with the phenol-chloroform method produced DNA of lower purity than the samples that were purified with kit. The samples isolated with the commercial kit resulted in better PCR amplification. Conclusion: Silica-based commercial kits and deparaffinized on slides should be considered for DNA extraction from FFPE.
    International journal of medical sciences 03/2014; 11(5):494-9. DOI:10.7150/ijms.8842 · 2.00 Impact Factor
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    • "E. Rabelo-Gonç alves et al. / Pathology – Research and Practice 210 (2014) 142– 146 143 In recent years, several protocols have been developed to optimize DNA recovery from FFPE tissues [1] [2] [4] [5] [13] [16] [17] [23]. In general, the first step of these protocols is removing paraffin from tissue slices using organic solvents such as xylene. "
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    ABSTRACT: Since Helicobacter spp. DNA was identified in liver tissue resected from patients with hepatocelullar carcinoma (HCC), researchers have suggested a role of this bacterium in hepatic carcinogenesis. Archives of formalin-fixed, paraffin-embedded (FFPE) tissues represent an extraordinary source for clinical studies providing many advantages. However, DNA extraction from FFPE tissues is laborious, time-consuming and still remains a challenge. The aim of this study was to evaluate five protocols for DNA extraction from FFPE liver obtained from patients with HCC in order to detect Helicobacter pylori DNA. These methods were: (1) QIAamp FFPE Tissue Kit, (2) QIAamp DNA Mini Kit, (3) Wizard SV Genomic DNA Purification System, (4) RealiaPrep FFPE gDNA Miniprep System and (5) phenol–chloroform. H. pylori detection was performed using 16S rRNA gene amplification by PCR. The highest total amount of DNA was obtained using the phenol–chloroform method. Analyses of 16S rRNA gene amplification did not show statistically significant differences among the methods (p = 0.466), although the highest percentage of positive cases (70%) was found in samples extracted with phenol/chloroform. We suggest that of the five methods evaluated, phenol/chloroform is the most suitable for detection of H. pylori in FFPE liver from patients with HCC.
    Pathology - Research and Practice 11/2013; 210(3). DOI:10.1016/j.prp.2013.11.003 · 1.40 Impact Factor
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    • "For this purpose the samples were pre-treated with mineral oil at 95 °C for 5 min for three times [14] to eliminate the paraffin embedding tissues. This pre-treatment is necessary to avoid PCR inhibition and permits the amplification of target DNA sequences as long as 611 nts. "
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    BMC Veterinary Research 06/2012; 8:81. DOI:10.1186/1746-6148-8-81 · 1.78 Impact Factor
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