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

J 2008

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

OBERLI, Andrea; Vlad POPOVICI; Mauro DELORENZI; Anna BALTZER; Janine ANTONOV et. al.

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

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

Změněno: 4. 3. 2013 15:29, doc. Ing. Vlad Popovici, PhD

Anotace

V originále

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.

Citovat

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.

@article{1090314,
   author = {Oberli, Andrea and Popovici, Vlad and Delorenzi, Mauro and Baltzer, Anna and Antonov, Janine and Matthey, Sybille and Aebi, Stefan and Altermatt, Hans Joerg and Jaggi, Rolf},
   article_location = {LONDON},
   doi = {http://dx.doi.org/10.1186/1755-8794-1-9},
   language = {eng},
   issn = {1755-8794},
   journal = {BMC MEDICAL GENOMICS},
   title = {Expression profiling with RNA from formalin-fixed, paraffin-embedded material},
   volume = {1},
   year = {2008}
}

TY  - JOUR
ID  - 1090314
AU  - Oberli, Andrea - Popovici, Vlad - Delorenzi, Mauro - Baltzer, Anna - Antonov, Janine - Matthey, Sybille - Aebi, Stefan - Altermatt, Hans Joerg - Jaggi, Rolf
PY  - 2008
TI  - Expression profiling with RNA from formalin-fixed, paraffin-embedded material
JF  - BMC MEDICAL GENOMICS
VL  - 1
PB  - BIOMED CENTRAL LTD
SN  - 17558794
N2  - 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.
ER  -

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. \textit{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.

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