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

Renata A. Coudry, Sibele I. Meireles, Radka Stoyanova, Harry S. Cooper, Alan Carpino, Xianqun Wang, Paul F. Engstrom, Margie L. Clapper

Research output: Contribution to journalArticlepeer-review

84 Scopus citations


The establishment of a reliable method for using RNA from formalin-fixed, paraffin-embedded (FFPE) tissue would provide an opportunity to obtain novel gene expression data from the vast amounts of archived tissue. A custom-designed 22,000 oligonucleotide array was used in the present study to compare the gene expression profile of colonic epithelial cells isolated by laser capture microdissection from FFPE-archived samples with that of the same cell population from matched frozen samples, the preferred source of RNA. Total RNA was extracted from FFPE tissues, amplified, and labeled using the Paradise Reagent System. The quality of the input RNA was assessed by the Bioanalyzer profile, reverse transcriptase-polymerase chain reaction, and agarose gel electrophoresis. The results demonstrate that it is possible to obtain reliable microarray data from FFPE samples using RNA acquired by laser capture microdissection. The concordance between matched FFPE and frozen samples was evaluated and expressed as a Pearson's correlation coefficient, with values ranging from 0.80 to 0.97. The presence of ribosomal RNA peaks in FFPE-derived RNA was reflected by a high correlation with paired frozen samples. A set of practical recommendations for evaluating the RNA integrity and quality in FFPE samples is reported.

Original languageEnglish (US)
Pages (from-to)70-79
Number of pages10
JournalJournal of Molecular Diagnostics
Issue number1
StatePublished - Feb 2007
Externally publishedYes

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine


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