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

16 Citations (Scopus)

Abstract

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
Volume18
Issue number2
DOIs
Publication statusPublished - Jun 2009

Fingerprint

Paraffin
Formaldehyde
RNA
Breast Neoplasms
Messenger RNA
Gene Expression
Reverse Transcriptase Polymerase Chain Reaction
Transcriptome
Neoplasms
Complementary DNA
Fluorescence
Genes

Keywords

  • 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

Cite this

Reliability and reproducibility of a RNA preamplification method for low-density array analysis from formalin-fixed paraffin-embedded breast cancer samples. / Ciotti, Paola; Garuti, Anna; Ballestrero, Alberto; Cirmena, Gabriella; Chiaramondia, Maurizio; Baccini, Paola; Bellone, Emilia; Mandich, Paola.

In: Diagnostic Molecular Pathology, Vol. 18, No. 2, 06.2009, p. 112-118.

Research output: Contribution to journalArticle

Ciotti, Paola ; Garuti, Anna ; Ballestrero, Alberto ; Cirmena, Gabriella ; Chiaramondia, Maurizio ; Baccini, Paola ; Bellone, Emilia ; Mandich, Paola. / Reliability and reproducibility of a RNA preamplification method for low-density array analysis from formalin-fixed paraffin-embedded breast cancer samples. In: Diagnostic Molecular Pathology. 2009 ; Vol. 18, No. 2. pp. 112-118.
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