Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays

Am J Pathol. 2004 Nov;165(5):1799-807. doi: 10.1016/S0002-9440(10)63435-9.

Abstract

We recently developed a sensitive and flexible gene expression profiling system that is not dependent on an intact poly-A tail and showed that it could be used to analyze degraded RNA samples. We hypothesized that the DASL (cDNA-mediated annealing, selection, extension and ligation) assay might be suitable for the analysis of formalin-fixed, paraffin-embedded tissues, an important source of archival tissue material. We now show that, using the DASL assay system, highly reproducible tissue- and cancer-specific gene expression profiles can be obtained with as little as 50 ng of total RNA isolated from formalin-fixed tissues that had been stored from 1 to over 10 years. Further, tissue- and cancer-specific markers derived from previous genome-wide expression profiling studies of fresh-frozen samples were validated in the formalin-fixed samples. The DASL assay system should prove useful for high-throughput expression profiling of archived clinical samples.

Publication types

  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Algorithms
  • Breast / pathology
  • Breast Neoplasms / pathology
  • Cell Line, Tumor
  • Cluster Analysis
  • Colon / pathology
  • Colonic Neoplasms / pathology
  • DNA Primers / chemistry
  • DNA, Complementary / metabolism
  • Formaldehyde / pharmacology
  • Gene Expression Profiling / methods*
  • Gene Expression Regulation*
  • Humans
  • Oligonucleotide Array Sequence Analysis
  • RNA / metabolism
  • RNA, Transfer / metabolism
  • Reverse Transcriptase Polymerase Chain Reaction
  • Time Factors

Substances

  • DNA Primers
  • DNA, Complementary
  • Formaldehyde
  • RNA
  • RNA, Transfer