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Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarrays

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Abstract

Oligonucleotide microarrays are widely used to investigate gene expression in a large-scale approach. A major limitation is the dependency on frozen material to obtain high-quality ribonucleic acid because most clinical specimens are formalin-fixed and paraffin-embedded (FFPE). The ability to analyze these samples using microarrays would enlarge the investigable sample stocks manifold. We conducted a comparison of snap-frozen and FFPE tissues investigating two malignomas. Gene expression profiles were obtained from both materials of the tumors. Independently processed triplicates of snap-frozen and FFPE specimen, respectively, were two-round-amplified and hybridized on Affymetrix GeneChips® (Palo Alto, CA, USA). Differentially expressed genes were identified in both FFPE and frozen material. All replicates had a correlation coefficient (R) of greater than 0.95 after normalization. Only direct comparison of FFPE to frozen replicates resulted in a mean R of 0.86, rendering a “mixed” investigation unfeasible. More than 50% (419 genes) of the more than fivefold differentially expressed genes (800 in FFPE, 685 in frozen material) were detected concomitantly regardless of the material used, which is similar to other comparisons of different gene expression analysis platforms. Thus, global gene expression analyses using solely FFPE material seem to be feasible with nearly comparable results to frozen tissue studies.

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Acknowledgements

This work was supported by the Deutsche Krebshilfe (70-3173-Tr3) and Affymetrix, who provided their GeneChips, and by Dr. Wieland Keilholz. The authors thank Ralf Lieberz for technical assistance, Dr. Birgit Anderegg (formerly of Arcturus) for support on the Paradise Reaction System, and Dr. Klaus Willenbrock for critical reading of the manuscript. The experiments were conducted and the tissues were used and processed in accordance with national ethical principles and comply with the current laws in Germany.

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Authors and Affiliations

  1. Senckenbergisches Institut für Pathologie, Klinikum der Johann Wolfgang Goethe-Universität Frankfurt, Theodor-Stern-Kai 7, 60590, Frankfurt am Main, Germany

    Matthias Frank, Claudia Döring, Susan Eckerle & Martin-Leo Hansmann

  2. Institut für Informatik, Fachbereich Informatik und Mathematik, Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt am Main, Germany

    Dirk Metzler

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  1. Matthias Frank
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  2. Claudia Döring
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  4. Susan Eckerle
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  5. Martin-Leo Hansmann
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Correspondence to Matthias Frank.

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Frank, M., Döring, C., Metzler, D. et al. Global gene expression profiling of formalin-fixed paraffin-embedded tumor samples: a comparison to snap-frozen material using oligonucleotide microarrays. Virchows Arch 450, 699–711 (2007). https://doi.org/10.1007/s00428-007-0412-9

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