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Updated: Jun 8, 2026

Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
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Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material

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Gene expression array testing of FFPE archival breast tumor samples: an optimized protocol for WG-DASL sample

C C Ton1, N Vartanian, X Chai

  • 1Divisions of Human Biology, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N, Seattle, WA 98109, USA.

Breast Cancer Research and Treatment
|September 16, 2010
PubMed
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A new RNA extraction protocol enables gene expression profiling from archived formalin-fixed, paraffin-embedded (FFPE) tissues. This method successfully analyzes degraded RNA from decade-old breast cancer samples, aiding molecular cancer studies.

Area of Science:

  • Molecular Biology
  • Oncology
  • Biotechnology

Background:

  • Archived formalin-fixed, paraffin-embedded (FFPE) tissues are a valuable resource for cancer research.
  • RNA extracted from FFPE tissues is often degraded and chemically modified, limiting its use in molecular studies.
  • Existing RNA extraction methods are suboptimal for FFPE samples.

Purpose of the Study:

  • To develop and validate a modified RNA extraction protocol for FFPE tissues.
  • To assess the feasibility of gene expression profiling using RNA from FFPE samples.
  • To evaluate the quality and utility of extracted RNA for molecular subtyping of breast cancer.

Main Methods:

  • A modified RNA extraction protocol was applied to FFPE breast cancer tissues.
  • Gene expression profiling was performed using the WG-DASL platform.

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Last Updated: Jun 8, 2026

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  • Hierarchical clustering was used to analyze gene expression data and classify samples.

    • Main Results:

    • The modified protocol achieved a 100% success rate for RNA extraction from FFPE samples.
    • Gene expression data from FFPE samples showed high quality, with 100% replicate identification and high self-correlation (r=0.979).
    • Samples were accurately classified into Estrogen Receptor-positive (ER+) and ER- subtypes with high specificity (95% and 90%, respectively).

    Conclusions:

    • The developed protocol enables successful gene expression profiling from decade-old FFPE breast cancer samples.
    • This method overcomes limitations associated with RNA degradation in FFPE tissues.
    • Archived FFPE samples can be reliably used for molecular studies, including cancer subtyping.