Reliability and reproducibility of a RNA preamplification method for low-density array analysis from formalin-fixed paraffin-embedded breast cancer samples

Paola Ciotti, Anna Garuti, Alberto Ballestrero, Gabriella Cirmena, Maurizio Chiaramondia, Paola Baccini, Emilia Bellone, Paola Mandich

Research output: Contribution to journalArticle


Molecular signatures of tumors with prognostic and predictive value are now available. However, several technical problems prevent the performing of gene expression profiles in routine diagnostics. The highly sensitive fluorescence-based real-time quantitative reverse transcriptase-polymerase chain reaction procedure is able to analyze mRNA levels from formalin-fixed paraffin-embedded (FFPE) tissues, the most commonly available source of tumor samples with well-documented information. However, the time-dependent fragmentation and small amount of RNA extracted from FFPE requires a preliminary mRNA amplification step to amplify small amounts of mRNA without significantly distorting relative mRNA levels. The purpose of this study was to determine the performance of a commercial cDNA preamplification kit (TaqMan PreAmp Master Mix Kit) on RNA samples obtained from FFPE tissues, prepared, and archived for routine diagnosis. We tested the reliability and reproducibility of this procedure for performing low-density gene expression assay from FFPE tissue samples. The whole procedure reported herein is a powerful and reproducible approach for routine clinical purposes that can be performed even using poorer RNA quality samples and that allows the analysis of gene expression for 96 genes in stored samples.

Original languageEnglish
Pages (from-to)112-118
Number of pages7
JournalDiagnostic Molecular Pathology
Issue number2
Publication statusPublished - Jun 2009



  • Formalin-fixed paraffin-embedded tissue
  • Low-density gene expression assay
  • Real-time quantitative reverse transcriptase-polymerase chain reaction
  • RNA

ASJC Scopus subject areas

  • Cell Biology
  • Molecular Biology
  • Medicine(all)
  • Pathology and Forensic Medicine

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