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

Marina Bibikova1, Dimitri Talantov, Eugene Chudin

  • 1Genetic Analysis, Illumina, Inc., 9885 Towne Center Drive, San Diego, CA 92121, USA.

The American Journal of Pathology
|October 29, 2004
PubMed
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The cDNA-mediated annealing, selection, extension and ligation (DASL) assay effectively analyzes gene expression in degraded RNA from archival formalin-fixed tissues. This method provides reproducible, cancer-specific profiles, enabling validation of markers from fresh-frozen samples.

Area of Science:

  • Molecular Biology
  • Genomics
  • Biotechnology

Background:

  • Gene expression profiling is crucial for understanding tissue and cancer biology.
  • Formalin-fixed, paraffin-embedded (FFPE) tissues are a valuable resource for archival research but pose challenges for RNA analysis due to degradation.
  • Existing methods often require intact RNA, limiting their application to FFPE samples.

Purpose of the Study:

  • To evaluate the suitability of the cDNA-mediated annealing, selection, extension and ligation (DASL) assay for gene expression profiling of FFPE tissues.
  • To determine the reproducibility and specificity of gene expression profiles obtained from archival FFPE samples using the DASL assay.
  • To validate previously identified tissue- and cancer-specific markers in FFPE samples.

Main Methods:

Related Experiment Videos

  • Development of a gene expression profiling system independent of intact poly-A tails.
  • Application of the DASL assay to RNA isolated from formalin-fixed tissues stored for 1 to over 10 years.
  • Analysis of gene expression profiles and validation of specific markers.

Main Results:

  • The DASL assay generated highly reproducible tissue- and cancer-specific gene expression profiles from as little as 50 ng of total RNA from FFPE tissues.
  • The assay demonstrated effectiveness even with RNA from samples stored for over a decade.
  • Tissue- and cancer-specific markers identified in fresh-frozen samples were successfully validated in the FFPE samples using the DASL assay.

Conclusions:

  • The DASL assay is a sensitive and flexible method for gene expression profiling of degraded RNA from archival FFPE tissues.
  • This approach enables high-throughput expression profiling of valuable clinical samples, overcoming limitations of RNA degradation.
  • The DASL assay facilitates the validation of molecular markers in a clinical archival setting.