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

Lin J, Kennedy SH, Svarovsky T, Rogers J, Joseph W. Kemnitz, Anlong Xu, Krina T. Zondervan
Analytical biochemistry · 2009 · doi:10.1016/j.ab.2009.08.016 · PMID:19698695 · PMC2764035
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A novel deparaffinization method using mineral oil for formalin-fixed, paraffin-embedded samples yielded high-quality genomic DNA with a 97% PCR success rate suitable for genetic studies.

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This technical note describes a method for extracting high-quality genomic DNA from formalin-fixed and paraffin-embedded (FFPE) tissue samples by utilizing mineral oil for deparaffinization. The researchers utilized archived samples provided by the Wisconsin National Primate Research Center and collaborated with the Southwest National Primate Research Center to select appropriate microsatellite markers for validation. The study demonstrates that this modified extraction protocol yields sufficient DNA integrity for downstream applications such as polymerase chain reaction analysis using beta-actin primers. The paper does not explicitly discuss endometriosis or adenomyosis; it was included in the corpus via a keyword match in the upstream search index.

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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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Ack

We thank the Wisconsin National Primate Research Center, University of Wisconsin–Madison, USA, for providing their archived FFPE samples and the Southwest National Primate Research Center in San Antonio, USA, for their help in selecting the microsatellite markers.

Fn Group

Abbreviations used : FFPE, formalin fixed and paraffin embedded; PCR, polymerase chain reaction. Supplementary data associated with this article can be found, in the online version, at doi:10.1016/j.ab.2009.08.016 .

Supplementary

PCR primers for beta-actin.

Associated Data

PCR primers for beta-actin.

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