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

Oberli, Andrea; Popovici, Vlad; Delorenzi, Mauro; Baltzer, Anna; Antonov, Janine; Matthey, Sybille; Aebi, Stefan; Altermatt, Hans Jörg; Jaggi, Rolf (2008). Expression profiling with RNA from formalin-fixed, paraffin-embeeded material. BMC Genomics, 1(1), p. 9. London: BioMed Central 10.1186/1755-8794-1-9

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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.

Item Type:

Journal Article (Original Article)


04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR) > Forschungsbereich Pathologie > Forschungsgruppe Molekularbiologie
04 Faculty of Medicine > Pre-clinic Human Medicine > BioMedical Research (DBMR)
04 Faculty of Medicine > Department of Haematology, Oncology, Infectious Diseases, Laboratory Medicine and Hospital Pharmacy (DOLS) > Clinic of Medical Oncology

UniBE Contributor:

Oberli, Andrea Elisabeth, Baltzer, Anna, Antonov, Janine, Matthey, Sybille, Aebi, Stefan, Jaggi, Rolf




BioMed Central




Factscience Import

Date Deposited:

04 Oct 2013 15:03

Last Modified:

02 Mar 2023 23:22

Publisher DOI:


Web of Science ID:




URI: (FactScience: 106224)

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