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Related Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
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Published on: February 21, 2015

High-resolution copy number profiling by array CGH using DNA isolated from formalin-fixed, paraffin-embedded tissues.

Hendrik F van Essen1, Bauke Ylstra

  • 1University of Antwerp, Antwerpen, Belgium.

Methods in Molecular Biology (Clifton, N.J.)
|January 10, 2012
PubMed
Summary

This study details protocols for extracting high-quality DNA from formalin-fixed, paraffin-embedded (FFPE) tissues. These methods enable reliable use of archival FFPE samples for array comparative genome hybridization (CGH) in cancer research.

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Area of Science:

  • Genomic research
  • Molecular pathology
  • Biotechnology

Background:

  • Formalin-fixed, paraffin-embedded (FFPE) tissues are routinely archived in pathology departments worldwide.
  • These FFPE archives represent an invaluable resource for large-scale genomics studies due to available clinical follow-up and survival data.
  • FFPE tissues are attractive for genomic studies, including test/learning and validation experiments, as demonstrated by previous array CGH studies.

Purpose of the Study:

  • To describe robust protocols for obtaining high-quality DNA from FFPE tissues.
  • To facilitate the application of array comparative genome hybridization (CGH) on FFPE samples.
  • To optimize DNA extraction and preparation from archival FFPE solid malignancies.

Main Methods:

  • Detailed protocols cover FFPE block sectioning and pathological review.
  • Specific procedures for DNA isolation, quality assessment, and amplification are elaborated.
  • Methods are tailored for array CGH analysis of FFPE solid tumors, up to DNA labeling.

Main Results:

  • The described protocols yield high-quality DNA suitable for array CGH.
  • These methods enable the effective utilization of FFPE tissue archives for genomic analysis.
  • The protocols address critical steps from tissue processing to DNA labeling.

Conclusions:

  • The developed protocols provide a standardized approach for DNA acquisition from FFPE tissues for array CGH.
  • These methods enhance the utility of FFPE archives for cancer genomics research.
  • The protocols are essential for researchers utilizing FFPE samples in array CGH studies.