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Limited tissue fixation times and whole genomic amplification do not impact array CGH profiles

¹ Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
² Division of Applied Molecular Oncology, Ontario Cancer Institute, University Health Network, Toronto, ON, Canada
³ Department of Pathology, University Health Network, Toronto, ON, Canada and Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada

Correspondence to:
Dr S J Done
Ontario Cancer Institute, 610 University Ave. Room 10-721, Toronto, ON M5G 2M9, Canada; susan.done{at}uhn.on.ca Background: Array comparative genomic hybridisation (CGH) is a powerful method for the genetic analysis of lesional and normal tissues to identify genomic imbalances associated with malignancies. However, the use of this technique with DNA extracted from archival formalin fixed, paraffin embedded (FFPE) tissue specimens, the most widely available resource for retrospective studies, is subject to quantitative and qualitative limitations. In this report, the suitability and integrity of the DNA extracted from FFPE MCF7 breast cancer cells fixed for different periods of time for array CGH applications were examined.

Results: Using our established cDNA microarray protocol in conjunction with whole genome amplification methods, the genetic profiles of freshly harvested MCF7 cells and their matched FFPE counterparts were analysed. Congruent profiles between FFPE MCF7 cells and their fresh counterpart and between amplified and non-amplified FFPE MCF7 cells were observed. Our results demonstrate that formalin fixation of <20 hours has no significant adverse effect on the integrity of DNA for array CGH studies.

Conclusions: Our findings attest to the fidelity of our array CGH methods to effectively examine material recovered from FFPE tissue specimens for microarray applications. This in turn has great potential to identify novel diagnostic and prognostic markers for human disease.

Abbreviations: CGH, comparative genomic hybridisation; DOP, degenerate oligonucleotide primed; FFPE, formalin fixed, paraffin embedded; Q-PCR, quantitative real time PCR; SCOMP, single cell comparative genomic hybridisation; WGA, whole genome amplification

Keywords: microarray; CGH; formalin fixed paraffin embedded (FFPE); whole genome amplification

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