Genome‐controlled reverse transcriptase‐polymerase chain reaction for targeted gene‐expression analysis

Stenman, Jakob; Räsänen, Jari; Tenkanen, Tuomas; Haglund, Caj; Salo, Jarmo A.; Orpana, Arto; Paju, Annukka

doi:10.1080/00365510600987736

Scandinavian Journal of Clinical and Laboratory Investigation

2006

DOI: 10.1080/00365510600987736

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Genome‐controlled reverse transcriptase‐polymerase chain reaction for targeted gene‐expression analysis

Jakob Stenman

Jari Räsänen²,

Tuomas Tenkanen³

et al.

Abstract: We demonstrate that this new technique enables accurate analysis of mRNA expression in cultured cells and endoscopic tissue biopsies. Sensitive analysis FFPE tissue is also possible thanks to the short PCR amplicons.

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2010

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Quantitative Expression Profiling in Formalin-Fixed Paraffin-Embedded Samples by Affymetrix Microarrays

Abdueva¹,

Wing²,

Schaub³

et al. 2010

The Journal of Molecular Diagnostics

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To date , few studies have systematically characterized microarray gene expression signal performance with degraded RNA from fixed (FFPE) in comparison with intact RNA from unfixed fresh-frozen (FF) specimens. RNA was extracted and isolated from paired tumor and normal samples from both FFPE and FF kidney, lung , and colon tissue specimens and microarray signal dynamics on both the raw probe and probeset level were evaluated. A contrast metric was developed to directly compare microarray signal derived from RNA extracted from matched FFPE and FF specimens. Gene-level summaries were then compared to determine the degree of overlap in expression profiles. RNA extracted from FFPE material was more degraded and fragmented than FF, resulting in a reduced dynamic range of expression signal. In addition, probe performance was not affected uniformly and declined sharply toward 5 end of genes. The most significant differences in FFPE versus FF signal were consistent across three tissue types and enriched with ribosomal genes. Our results show that archived FFPE samples can be used to profile for expression signatures and assess differential expression similar to unfixed tissue sources. This study provides guidelines for application of these methods in the discovery, validation, and clinical application of microarray expression profiling with FFPE material. (J Mol

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Quantitative Expression Profiling in Formalin-Fixed Paraffin-Embedded Samples by Affymetrix Microarrays

Abdueva¹,

Wing²,

Schaub³

et al. 2010

The Journal of Molecular Diagnostics

View full text Add to dashboard Cite

show abstract

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Genome‐controlled reverse transcriptase‐polymerase chain reaction for targeted gene‐expression analysis

Abstract: We demonstrate that this new technique enables accurate analysis of mRNA expression in cultured cells and endoscopic tissue biopsies. Sensitive analysis FFPE tissue is also possible thanks to the short PCR amplicons.

Cited by 1 publication

References 16 publications

Quantitative Expression Profiling in Formalin-Fixed Paraffin-Embedded Samples by Affymetrix Microarrays

Quantitative Expression Profiling in Formalin-Fixed Paraffin-Embedded Samples by Affymetrix Microarrays

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