High-quality genomic DNA extraction from formalin-fixed and paraffin-embedded samples deparaffinized using mineral oil |
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| Authors: | Jianghai Lin Stephen H Kennedy Therese Svarovsky Jeffrey Rogers Joseph W Kemnitz Anlong Xu Krina T Zondervan |
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| Institution: | aNuffield Department of Obstetrics and Gynaecology, University of Oxford, Oxford, UK;bSchool of Life Science, Sun Yat-sen University, Guangzhou, China;cWisconsin National Primate Research Center, University of Wisconsin–Madison, Madison, WI, USA;dHuman Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA;eWellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK |
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| Abstract: | 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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