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

Author(s): Ciotti P, Garuti A, Ballestrero A, Cirmena G, Chiaramondia M, Baccini P, Bellone E, Mandich P

Publication: Diagn Mol Pathol, 2009, Vol. 18, Page 112-8

PubMed ID: 19430292 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine the effects of FFPE or frozen OCT embedded normal and cancerous breast tissue and RNA preamplification on RNA yield, quality and expression profile analysis of 96 genes relevant to breast cancer.

   Summary of Findings:

   RNA from FFPE specimens was highly degraded with no detectable ribosomal RNA bands, and most fragments were shorter than 300 bp. OCT embedded specimens yielded more RNA than FFPE specimens from the same tissue specimen; however, no significant quantitative differences in expression profile between FFPE and OCT embedded normal breast tissue were found. Preamplification increased the quantity of RNA and increased the percentage of amplifiable targets from 89% in OCT embedded and 82% in FFPE specimens to 100% for both specimen types. In conclusion, FFPE specimens can be used along with preamplification for quantitative expression analysis in breast specimens.

   Biospecimens

   • Tissue - Breast

   Preservative Types

   • Formalin
   • OCT

   Diagnoses:

   • Normal
   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   RNA	Real-time qRT-PCR
   RNA	Automated electrophoresis/Bioanalyzer

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	OCT Formalin (buffered)
   Real-time qRT-PCR Specific	Technology platform	Preamplification No preamplification

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