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Array Comparative Genomic Hybridization (Array CGH) for Detection of Genomic Copy Number Variants
Published on: February 21, 2015
Limited tissue fixation times and whole genomic amplification do not impact array CGH profiles
A A Ghazani1, N C R Arneson, K Warren
1Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.
Journal of Clinical Pathology
|March 1, 2006
Summary
Array comparative genomic hybridization (CGH) using DNA from formalin-fixed, paraffin-embedded (FFPE) tissues is reliable for cancer research. Formalin fixation under 20 hours preserves DNA integrity for accurate genomic analysis.
Area of Science:
- Genomics
- Molecular Biology
- Cancer Research
Background:
- Array comparative genomic hybridization (CGH) analyzes genomic imbalances in tissues.
- Formalin-fixed, paraffin-embedded (FFPE) tissues are valuable for retrospective studies but pose challenges for DNA analysis.
- Investigating DNA integrity from FFPE tissues for array CGH is crucial.
Purpose of the Study:
- To assess the suitability of DNA from FFPE MCF7 breast cancer cells for array CGH.
- To determine the effect of fixation duration on DNA integrity for array CGH applications.
Main Methods:
- Utilized cDNA microarray protocol with whole genome amplification.
- Analyzed genetic profiles of fresh and FFPE MCF7 cells.
- Compared amplified and non-amplified FFPE DNA.
Main Results:
- Observed congruent genetic profiles between fresh and FFPE MCF7 cells.
- Found consistent profiles between amplified and non-amplified FFPE DNA.
- Demonstrated that formalin fixation <20 hours does not significantly impact DNA integrity for array CGH.
Conclusions:
- Developed a reliable array CGH method for FFPE tissue specimens.
- FFPE tissues are suitable for microarray applications with appropriate methods.
- This approach has potential for identifying novel diagnostic and prognostic markers.
