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Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses

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Abstract

Tissues used for clinical diagnostics are mostly formalin-fixed and paraffin-embedded (FFPE) which provides many advantages. However, the quality of the obtained nucleic acids (NA) is reduced and this turns out to be a challenge for further molecular analyses. Although the spectrum of analyses of NA extracted from FFPE tissue has increased, the standard operating procedures for NA isolation from old tissue blocks still need to be improved. Here, we compared the efficiency of different NA extraction methods, using FFPE tissues of variable age and origin, with respect to downstream analyses. Our study showed that the phenol–chloroform isoamyl alcohol (PCI) and the commercial Qiagen protocol yielded samples with highest purity. The PCI protocol delivered the longest amplicons even from samples from the 1970s. We developed a short (1 h) tissue lysis procedure that turned out to be highly time- and cost-effective when DNA quality was tested using single and multiplex PCR. Compared to a 1-day lysis-protocol, the amplicons were only 100 bp shorter. In addition, single-copy genes used in daily routine were successfully amplified from long-term stored FFPE samples following 1-h tissue-lysis. The RNA integrity numbers (RIN) determined on RNA isolated from FFPE tissues indicated degraded RNA; however, all RINs were above the generally agreed threshold of 1.4. We showed that, depending on the purpose of the analysis, NA retrieved from FFPE tissues older than 40 years may be successfully used for molecular analysis.

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Acknowledgments

The authors thank Nina Weber and Katrin Lindner for great technical assistance. This work was supported by a grant from the European Community’s Seventh Framework Programme (FP7, EURATOM) contract no. 232628 (STORE—Sustaining access to Tissues and data frOm Radiobiological Experiments).

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Institute of Pathology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany

    Natalie Ludyga, Barbara Grünwald, Sonja Englert, Heinz Höfler & Michaela Aubele

  2. Institute of Radiation Biology, Helmholtz Zentrum München, German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764, Neuherberg, Germany

    Omid Azimzadeh & Soile Tapio

  3. Institute of Pathology, Technische Universität München, Trogerstrasse 18, 81675, Munich, Germany

    Heinz Höfler

Authors
  1. Natalie Ludyga
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  2. Barbara Grünwald
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  3. Omid Azimzadeh
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  4. Sonja Englert
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  5. Heinz Höfler
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  6. Soile Tapio
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  7. Michaela Aubele
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Corresponding author

Correspondence to Michaela Aubele.

Additional information

Natalie Ludyga and Barbara Grünwald contributed equally to this work.

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Ludyga, N., Grünwald, B., Azimzadeh, O. et al. Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses. Virchows Arch 460, 131–140 (2012). https://doi.org/10.1007/s00428-011-1184-9

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  • DOI: https://doi.org/10.1007/s00428-011-1184-9

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