RNA extraction from ten year old formalin-fixed paraffin-embedded breast cancer samples: a comparison of column purification and magnetic bead-based technologies.

Author(s): Ribeiro-Silva A, Zhang H, Jeffrey SS

Publication: BMC Mol Biol, 2007, Vol. 8, Page 118

PubMed ID: 18154675 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 storage duration and extraction method on RNA integrity and PCR success from FFPE breast tumor specimens.

   Summary of Findings:

   RNA with an RIN of >1.4 was obtained in 62-83% of RNA extractions from 10 y old specimens and 86-100% of specimens stored for 3-10 months. RNA with an RIN of >1.4 was most often obtained from 10 y old specimens when extracted with HighPure RNA paraffin kit or from 3-10 month old specimens using the absolutely RNA FFPE kit. Fragments of G6PD less than 151 bp long were amplified from all specimens with an RIN of >1.4, regardless of storage time, but a 242 bp fragment was not amplified in any of the specimens stored for 10 y and in only 43% of the specimens stored for 3-10 months.

   Biospecimens

   • Tissue - Breast

   Preservative Types

   • Formalin

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   RNA	Automated electrophoresis/Bioanalyzer
   RNA	Fluorometry
   RNA	RT-PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Storage	Storage duration	3-10 months 10 years
   Analyte Extraction and Purification	Analyte isolation method	RecoverAll kit for FFPE specimens HighPure RNA paraffin kit Absolutely RNA FFPE kit Agencourt FormaPure kit
   RT-PCR Specific	Length of gene fragment	67 bp 151 bp 242 bp
   RT-PCR Specific	Targeted nucleic acid	G6PD

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