BACKGROUND: Compared with the standard qPCR, nanoliter-scale qPCR can use smaller quantities of RNA and increase throughput. The TaqMan™ OpenArray® 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.
BACKGROUND: Compared with the standard qPCR, nanoliter-scale qPCR can use smaller quantities of RNA and increase throughput. The TaqMan™ OpenArray® 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 patientrenal 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.
Authors: Soonmyung Paik; Steven Shak; Gong Tang; Chungyeul Kim; Joffre Baker; Maureen Cronin; Frederick L Baehner; Michael G Walker; Drew Watson; Taesung Park; William Hiller; Edwin R Fisher; D Lawrence Wickerham; John Bryant; Norman Wolmark Journal: N Engl J Med Date: 2004-12-10 Impact factor: 91.245
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Authors: Maureen Cronin; Mylan Pho; Debjani Dutta; James C Stephans; Steven Shak; Michael C Kiefer; Jose M Esteban; Joffre B Baker Journal: Am J Pathol Date: 2004-01 Impact factor: 4.307
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Authors: Hyung L Kim; Susan Halabi; Ping Li; Greg Mayhew; Jeff Simko; Andrew B Nixon; Eric J Small; Brian Rini; Michael J Morris; Mary-Ellen Taplin; Daniel George Journal: EBioMedicine Date: 2015-09-08 Impact factor: 8.143