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

OBERLI, Andrea, Vlad POPOVICI, Mauro DELORENZI, Anna BALTZER, Janine ANTONOV, Sybille MATTHEY, Stefan AEBI, Hans Joerg ALTERMATT a Rolf JAGGI. Expression profiling with RNA from formalin-fixed, paraffin-embedded material. BMC MEDICAL GENOMICS. LONDON: BIOMED CENTRAL LTD, 2008, roč. 1, 15 s. ISSN 1755-8794. Dostupné z: https://dx.doi.org/10.1186/1755-8794-1-9.

Základní údaje

• Originální název: Expression profiling with RNA from formalin-fixed, paraffin-embedded material
• Autoři: OBERLI, Andrea, Vlad POPOVICI, Mauro DELORENZI, Anna BALTZER, Janine ANTONOV, Sybille MATTHEY, Stefan AEBI, Hans Joerg ALTERMATT a Rolf JAGGI.
• Vydání: BMC MEDICAL GENOMICS, LONDON, BIOMED CENTRAL LTD, 2008, 1755-8794.

Další údaje

• Originální jazyk: angličtina
• Typ výsledku: Článek v odborném periodiku
• Utajení: není předmětem státního či obchodního tajemství
• Doi: http://dx.doi.org/10.1186/1755-8794-1-9
• UT WoS: 000272649700001

Anotace

Background: 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. Results: 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. Conclusion: 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.