Evaluation of a high-throughput, microfluidics platform for performing TaqMan™ qPCR using formalin-fixed paraffin-embedded tumors

Background: Compared with the standard qPCR, nanoliter-scale qPCR can use smaller quantities of RNA and increase throughput. The TaqMan OpenArray((R)) NT Cycler System was assessed for use with degraded RNA from formalin-fixed paraffin-embedded (FFPE) tumors. Results: Expression of candidate prognostic genes was quantified using the OpenArray platform and matching fresh frozen and FFPE patient renal cell carcinomas. Reverse transcription, with gene-specific reverse transcription and preamplification, optimized the percentage of detectable transcripts. When using high quality RNA from fresh frozen tumors, the OpenArray platform identified 30 prognostic genes. However, when using RNA from FFPE tumors, only 13 prognostic genes were identified, but this increased to 33 with addition of preamplification. Conclusion: The OpenArray platform can be optimized to quantify gene expressions from FFPE tumors.