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Expression Analysis on Archival Material: Comparison of 5 Commercially Available RNA Isolation Kits for FFPE Material

Boeckx, Carolien MSc*; Wouters, An PhD*; Pauwels, Bea PhD*; Deschoolmeester, Vanessa PhD*; Specenier, Pol MD, PhD*,†; Lukaszuk, Krzysztof MD, PhD; Vermorken, Jan B. MD, PhD*,†; Pauwels, Patrick MD, PhD*,§; Peeters, Marc MD, PhD*,†; Lardon, Filip PhD*; Baay, Marc F.D. PhD*

doi: 10.1097/PDM.0b013e3182230937
Original Articles
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Background: Formalin-fixed paraffin-embedded (FFPE) tissue is the most common tissue specimen widely available. Moreover, long clinical follow-up is on hand. Therefore, FFPE material is a precious source of material for identifying predictive and/or prognostic biomarkers in cancer research on the basis of gene expression. However, the main drawback of FFPE tissue is the significant reduction in quantity and quality of the extracted RNA. The aim of this study is the comparison of different commercially available kits for the RNA isolation in FFPE tissue material.

Methods: Five commercially available RNA isolation kits were tested and the concentration, purity, integrity, and raw cycle threshold values were determined.

Results: The mean total RNA concentrations were as follows: Qiagen 25957±19417 ng, Ambion 8249±2898 ng, SA Biosciences 8070±3700 ng, and Macherey-Nagel 622±394 ng. The mean A260/A280 ratios were as follows: Qiagen: 1.81, SA Biosciences: 0.66, Ambion: 1.03, and Macherey-Nagel: 1.04. The mean A260/A230 ratios were as follows: Qiagen: 1.88, SA Biosciences: 1.61, Ambion: 1.54, and Macherey-Nagel: 1.88. The RNA extractions from Epicentre could not be measured by the Nanodrop and, therefore, were excluded from further analysis. The mean RNA integrity number (range, 2.09 to 2.47) and the mean raw cycle threshold values (range, 33.43 to 35.37) were more or less the same for all the tested RNA isolation kits.

Conclusions: Altogether, on the basis of the number of adequate isolations, the kit from Qiagen seems to be the most appropriate kit to be used in our further studies that require RNA isolation from FFPE material.

*Center for Oncological Research (CORE) Antwerp, Laboratory of Cancer Research and Clinical Oncology, University of Antwerp, Wilrijk

Department of Medical Oncology, University Hospital Antwerp (UA/UZA)

§Department of Pathology, University Hospital Antwerp (UA/UZA), Edegem, Belgium

Department of Gynaecologic Endocrinology, Medical University of Gdansk, Poland

C.B. was supported by a scholarship from the University of Antwerp and this study was supported by grants from the Special Research Fund (BOF) of the University of Antwerp to B.P and M.B. The other authors declare no conflict of interest.

Reprints: Carolien Boeckx, MSc, University of Antwerp, Laboratory of Cancer Research and Clinical Oncology, Universiteitsplein 1 (T3.11), B2610 Wilrijk, Belgium (e-mail: carolien.boeckx@ua.ac.be).

© 2011 Lippincott Williams & Wilkins, Inc.