Technical Advances
Degenerate Oligonucleotide Primed-Polymerase Chain Reaction-Based Array Comparative Genomic Hybridization for Extensive Amplicon Profiling of Breast Cancers: A New Approach for the Molecular Analysis of Paraffin-Embedded Cancer Tissue

https://doi.org/10.1016/S0002-9440(10)64118-1Get rights and content

We have developed a protocol for degenerate oligonucleotide-primed-polymerase chain reaction-based array comparative genomic hybridization (array CGH) that, when combined with a laser microdissection technique, allows the analysis of cancer cell populations isolated from routine, formalin-fixed, paraffin-embedded tissue samples. Comparison of copy number changes detected by degenerate oligonucleotide-primed-polymerase chain reaction-based array CGH to those detected by conventional array CGH or fluorescence in situ hybridization, demonstrated that amplifications can be reliably detected. Using a genomic microarray containing 57 oncogenes, we screened a total of 28 breast cancer samples and obtained a detailed amplicon profile that is the most comprehensive to date in human breast cancer. The array CGH method described here will allow the genetic analysis of paraffin-embedded human cancer materials for example in the context of clinical trials.

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Supported by The Cancer Research Campaign; the Uehara Memorial Foundation postdoctoral research fellowship (to Y. D.); and a Sackler Studentship, Overseas Research Studentship Award, and Cambridge Commonwealth Trust Prince of Wales Scholarship (to K. L. G.).

Y. D. and S.-F. C. contributed equally to this work.

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