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Detection of Prostate Cancer BioMarkers by Expression Microarray Analysis of TransPlex® WTA2 Amplified FFPE Tissue RNA
Ken Heuerman and Brian Ward
Sigma Life Science
Sponsored by Sigma-Aldrich
Published in September 2010 2010 (p.6) DOI:  10.2144/000113526 Sponsored,vendor-submitted protocol
The Transplex® Complete Whole Transcriptome Amplification (WTA2) Kit has been enhanced to effectively amplify damaged RNA and low input amounts of RNA.Total RNA samples isolated from matched FFPE(formalin-fixedparaffin-embedded) and frozen prostate tissues (malignant and normal) were amplified with the Transplex® Complete WTA2 Kit and analyzed on Agilent Whole Genome expression microarrays. A call rate of >65% was observed for combined FFPE and frozen expression differentials (Malignant/Normal), with >90% commonality between the FFPE and frozen datasets. Amplification reproducibility of experimental replicates was demonstrated by principal component analysis.Pair-wise comparison of FFPE malignant and normal expression(p<0.0001) resulted in detection of 66 known prostate cancer biomarkers. Similar microarray pair-wise analysis of the original matched FFPE RNAs amplified with the Nugen WT-Ovation™FFPE Kit at significantly lower level of confidence(p<0.05) revealed only a single array feature, disallowing a comprehensive comparison with Transplex WTA2.These results confirm the utility of the Transplex WTA2Kit for amplification of damaged DNA.
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