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

Andrea Oberli^*¹ , Vlad Popovici^*² , Mauro Delorenzi²^,3 , Anna Baltzer¹ , Janine Antonov¹ , Sybille Matthey¹ , Stefan Aebi¹ , Hans Jörg Altermatt⁴ and Rolf Jaggi¹

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

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

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

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

author email corresponding author email* Contributed equally

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


Published:	19 April 2008

Additional files

Additional file 1:

Comparison of normalized expression for each gene in FF and FFPE material. Expression was determined by QPCR from RNA derived of FF and FFPE material (own protocol). Normalized expression levels (see Methods for details) are shown for each gene and the 14 tumors as polygonal plots.

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Additional file 2:

Polygonal representation of ER, HER2, Proliferation and Total scores. Gene expression was measured from RNA derived of FF and FFPE material (own protocol) and ER, HER2, proliferation and Total scores were computed for each RNA of the 14 tumors and results are shown as polygonal plots. Parallel lines indicate good correlations and crossing lines are indicative for discrepancies between scores computed from FF and FFPE-derived RNA

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