Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues
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Date
2010
Journal Title
Journal ISSN
Volume Title
Publisher
Analytical biochemistry
Abstract
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.
Description
Keywords
Archival FFPE tissues, DNA/RNA extraction, Histopathology, Inhibition, Nucleic acid, Quantitative PCR
Citation
Okello, J. B., Zurek, J., Devault, A. M., Kuch, M., Okwi, A. L., Sewankambo, N. K., ... & Poinar, H. N. (2010). Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues. Analytical biochemistry, 400(1), 110-117. doi:10.1016/j.ab.2010.01.014