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Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors.

Sandy Devries1, Sarah Nyante, Jim Korkola

  • 1Cancer Center, Box 0808, University of California San Francisco, San Francisco, CA 94143-0808, USA.

The Journal of Molecular Diagnostics : JMD
|February 1, 2005
PubMed
Summary

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Random-primed amplification is a superior method for whole genome amplification from archival tumor samples for array-based comparative genomic hybridization (CGH). This robust technique ensures high-quality DNA extraction for genomic marker identification.

Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Identifying prognostic and predictive genomic markers necessitates long-term patient follow-up.
  • High-quality DNA extraction from formalin-fixed, paraffin-embedded (FFPE) tissues is crucial for these studies.
  • Robust whole genome amplification (WGA) methods are vital for small tissue samples, especially for high-resolution genomic analyses.

Purpose of the Study:

  • To evaluate and compare different DNA amplification protocols for array-based comparative genomic hybridization (CGH).
  • To determine the optimal WGA method for analyzing DNA extracted from archival FFPE tumor samples.

Main Methods:

  • Tested random-primed amplification (RPA) and degenerate oligonucleotide-primed amplification (DOP-PCR) protocols.

Related Experiment Videos

  • Utilized varying amounts of normal and breast tumor DNA from fresh and FFPE sources.
  • Employed quantitative polymerase chain reaction (qPCR) for accurate DNA input quantification.

    • Main Results:

    • RPA demonstrated superior performance compared to DOP-PCR for array-based CGH.
    • Optimal DNA amplification quality and reproducibility were achieved with 50 ng of input DNA.
    • High-quality results were obtainable with as little as 5 ng of input DNA in some cases.

    Conclusions:

    • Random-primed amplification is a robust and reproducible method for WGA of DNA from FFPE sections.
    • This approach is suitable for array-based CGH analysis of archival tumor samples.
    • Accurate DNA quantification is critical for achieving reproducible and high-quality genomic analysis.