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Related Experiment Videos

High resolution oligonucleotide CGH using DNA from archived prostate tissue.

Pamela L Paris1, Shivaranjani Sridharan, Alicia Scheffer

  • 1Department of Urology, Comprehensive Cancer Center, University of California at San Francisco, San Francisco, California 94143, USA.

The Prostate
|July 27, 2007
PubMed
Summary
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High-resolution oligonucleotide arrays effectively detect genomic aberrations in archived prostate tissue. This technology aids biomarker discovery and clinical applications using formalin-fixed paraffin-embedded samples.

Area of Science:

  • Genomics
  • Cancer Research
  • Biomarker Discovery

Background:

  • Advances in understanding carcinogenesis and technology drive biomarker discovery.
  • Biomarkers are crucial for diagnosis, prognosis, treatment selection, and drug development.
  • There is a need for high-resolution tools using archived tissue for biomarker discovery and clinical translation.

Purpose of the Study:

  • To compare oligonucleotide array comparative genomic hybridization (oCGH) with BAC-based aCGH.
  • To evaluate the utility of these methods using formalin-fixed paraffin-embedded (FFPE) prostate tissue.

Main Methods:

  • Oligonucleotide array comparative genomic hybridization (oCGH) was employed.
  • BAC-based aCGH was used as a comparison method.
  • Unamplified total genomic DNA from FFPE prostate tissue was analyzed.

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Main Results:

  • Copy number aberrations detected by both array types showed high correlation when probes were in similar genomic locations.
  • The oligonucleotide array platform offered more precise genomic mapping due to its higher probe density.
  • oCGH demonstrated effectiveness with FFPE samples.

Conclusions:

  • High-resolution oligonucleotide arrays are suitable for CGH measurements using archived tissue.
  • This technology facilitates biomarker discovery and the development of clinical assays.
  • oCGH provides a valuable tool for genomic analysis in FFPE samples.