Successful application of microarray technology to microdissected formalin-fixed, paraffin-embedded tissue.

Author(s): Coudry RA, Meireles SI, Stoyanova R, Cooper HS, Carpino A, Wang X, Engstrom PF, Clapper ML

Publication: J Mol Diagn, 2007, Vol. 9, Page 70-9

PubMed ID: 17251338 PubMed Review Paper? No

Purpose of Paper

Conclusion of Paper

Studies

1. Study Purpose

   The purpose of this study was to determine if the quality of extracted RNA is influenced by (1) the preservation method, (2) the method of cell capture, or (3) a 2 hour room temperature delay in preservation.

   Summary of Findings:

   As determined by examination of bioanalyzer generated electropherogram patterns, RNA quality was compromised in FFPE specimens in comparison to OCT frozen case-matched controls. A 2 hour delay in frozen preservation, but not formalin fixation, yielded evidence of RNA degradation; while both methods of cell population capture (LCM, tissue scraping) generated RNA of identical quality.

   Biospecimens

   • Tissue - Colorectal

   Preservative Types

   • Formalin
   • OCT

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   RNA	Automated electrophoresis/Bioanalyzer

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) OCT
   Storage	Time at room temperature	2 h 0 h
   Biospecimen Aliquots and Components	Cell capture method	Laser-capture microdissection Slide scraping

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2. Study Purpose

   The purpose of this study was to determine if the yield, quality, or microarray performance of extracted RNA amplified via in vitro transcription was affected by biospecimen preservation method.

   Summary of Findings:

   While the yield of amplified RNA was equivalent among OCT frozen and FFPE specimens, the length of RNA fragments generated was slightly shorter for FFPE compared to OCT frozen specimens, 400 bp versus 500 bp, respectively. Successful RT-PCR amplification of differentially sized products was not significantly affected by preservation method. FFPE and case-matched OCT frozen specimens generated microarray expression data that was well correlated (r=0.80-0.96), as well as an equivalent percentage of expressed genes.

   Biospecimens

   • Tissue - Colorectal

   Preservative Types

   • Formalin
   • OCT

   Diagnoses:

   • Neoplastic - Carcinoma

   Platform:

   Analyte	Technology Platform
   RNA	DNA microarray
   RNA	Electrophoresis
   RNA	RT-PCR

   Pre-analytical Factors:

   Classification	Pre-analytical Factor	Value(s)
   Biospecimen Preservation	Type of fixation/preservation	Formalin (buffered) OCT

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