Table of Contents
ISRN Oncology
Volume 2012, Article ID 710692, 10 pages
http://dx.doi.org/10.5402/2012/710692
Research Article

Comparison of Whole Genome Amplification Methods for Analysis of DNA Extracted from Microdissected Early Breast Lesions in Formalin-Fixed Paraffin-Embedded Tissue

1Division of Applied Molecular Oncology, Ontario Cancer Institute, Princess Margaret Hospital, Toronto, ON, Canada M5G 2M9
2Campbell Family Institute for Breast Cancer Research, Toronto, ON, Canada M5G 2M9
3Laboratory Medicine Program, University Health Network, Toronto, ON, Canada M5G 2C4
4Department of Laboratory Medicine, St. Michael’s Hospital, Toronto, ON, Canada M5B 1W8
5Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada M5S 1A8
6Department of Surgical Oncology, Princess Margaret Hospital, Toronto, ON, Canada M5G 2C4
7Campbell Family Institute for Cancer Research, Princess Margaret Hospital, Techna Institute, University Health Network, Toronto, ON, Canada M5G 2C1
8Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada M5G 1A1
9Department of Computer Science, University of Toronto, Toronto, ON, Canada M5S 3G4

Received 30 September 2011; Accepted 9 November 2011

Academic Editors: G. M. Carbone and M. O. Hoque

Copyright © 2012 Nona Arneson et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

To understand cancer progression, it is desirable to study the earliest stages of its development, which are often microscopic lesions. Array comparative genomic hybridization (aCGH) is a valuable high-throughput molecular approach for discovering DNA copy number changes; however, it requires a relatively large amount of DNA, which is difficult to obtain from microdissected lesions. Whole genome amplification (WGA) methods were developed to increase DNA quantity; however their reproducibility, fidelity, and suitability for formalin-fixed paraffin-embedded (FFPE) samples are questioned. Using aCGH analysis, we compared two widely used approaches for WGA: single cell comparative genomic hybridization protocol (SCOMP) and degenerate oligonucleotide primed PCR (DOP-PCR). Cancer cell line and microdissected FFPE breast cancer DNA samples were amplified by the two WGA methods and subjected to aCGH. The genomic profiles of amplified DNA were compared with those of non-amplified controls by four analytic methods and validated by quantitative PCR (Q-PCR). We found that SCOMP-amplified samples had close similarity to non-amplified controls with concordance rates close to those of reference tests, while DOP-amplified samples had a statistically significant amount of changes. SCOMP is able to amplify small amounts of DNA extracted from FFPE samples and provides quality of aCGH data similar to non-amplified samples.