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Expression profiling with RNA from formalin-fixed, paraffin-embedded material

Andrea Oberli1, Vlad Popovici2, Mauro Delorenzi23, Anna Baltzer1, Janine Antonov1, Sybille Matthey1, Stefan Aebi1, Hans Jörg Altermatt4 and Rolf Jaggi1*

Author affiliations

1 Department of Clinical Research, University of Bern, Murtenstrasse 35 CH-3010 Bern, Switzerland

2 Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland

3 National Center of Competence in Research (NCCR) Molecular Oncology, Swiss Institute for Experimental Cancer Research (ISREC), Epalinges, Switzerland

4 Pathology Länggasse, Forstweg 56, CH-3012 Bern, Switzerland

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Citation and License

BMC Medical Genomics 2008, 1:9  doi:10.1186/1755-8794-1-9

Published: 19 April 2008



Molecular characterization of breast and other cancers by gene expression profiling has corroborated existing classifications and revealed novel subtypes. Most profiling studies are based on fresh frozen (FF) tumor material which is available only for a limited number of samples while thousands of tumor samples exist as formalin-fixed, paraffin-embedded (FFPE) blocks. Unfortunately, RNA derived of FFPE material is fragmented and chemically modified impairing expression measurements by standard procedures. Robust protocols for isolation of RNA from FFPE material suitable for stable and reproducible measurement of gene expression (e.g. by quantitative reverse transcriptase PCR, QPCR) remain a major challenge.


We present a simple procedure for RNA isolation from FFPE material of diagnostic samples. The RNA is suitable for expression measurement by QPCR when used in combination with an optimized cDNA synthesis protocol and TaqMan assays specific for short amplicons. The FFPE derived RNA was compared to intact RNA isolated from the same tumors. Preliminary scores were computed from genes related to the ER response, HER2 signaling and proliferation. Correlation coefficients between intact and partially fragmented RNA from FFPE material were 0.83 to 0.97.


We developed a simple and robust method for isolating RNA from FFPE material. The RNA can be used for gene expression profiling. Expression measurements from several genes can be combined to robust scores representing the hormonal or the proliferation status of the tumor.