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Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues

Here we report a systematic comparison of formalin-fixed paraffin-embedded tissue kits for RNA and DNA extraction. Overall, TrimGen's WaxFree and phenol-chloroform methods recovered the largest DNA yields, while Ambion's RecoverAll kit recovered the largest quantity of amplifiable RNA.

Jan 15, 2010

Authors: J. Okello, J. Zurek, A. Devault, M. Kuch, A. Okwi, N. Sewankambo, G. Bimenya, D. Poinar, H. Poinar

Analytical Biochemistry, Vol. 400, Issue 1, pp. 110-117. May 2010. DOI:10.1016/j.ab.2010.01.014


Archival formalin-fixed paraffin-embedded (FFPE) human tissue collections are typically in poor states of storage across the developing world. With advances in biomolecular techniques, these extraordinary and virtually untapped resources have become an essential part of retrospective epidemiological studies. To successfully use such tissues in genomic studies, scientists require high nucleic acid yields and purity. In spite of the increasing number of FFPE tissue kits available, few studies have analyzed their applicability in recovering high-quality nucleic acids from archived human autopsy samples. Here we provide a study involving 10 major extraction methods used to isolate total nucleic acid from FFPE tissues ranging in age from 3 to 13 years. Although all 10 methods recovered quantifiable amounts of DNA, only 6 recovered quantifiable RNA, varying considerably and generally yielding lower DNA concentrations. Overall, we show quantitatively that TrimGen’s WaxFree method and our in-house phenol–chloroform extraction method recovered the highest yields of amplifiable DNA, with considerable polymerase chain reaction (PCR) inhibition, whereas Ambion’s RecoverAll method recovered the most amplifiable RNA.

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