Full Complexity Genomic Hybridization on 60-mer Oligonucleotide Microarrays for Array Comparative Genomic Hybridization (aCGH)
Recurrent structural alterations, such as amplification, deletion, or translocation, are hallmark features of the cancer genome. Mapping of these DNA copy number aberrations, using approaches such as comparative genomic hybridization (CGH), has enabled the discovery of bona fide tumor suppressor genes and oncogenes. With the emergence of high-density oligo-based microarray platforms, array-based CGH has become a powerful technology that can facilitate the accurate mapping and rapid identification of novel cancer genes. Here, we describe the optimized technical protocol for comparative genomic hybridization with full-complexity genomic DNA on 60-mer oligonucleotide microarrays.
KeywordsCancer genomics array-CGH (aCGH) oligo microarrays genomic profiling copy number changes
Acknowledgments We acknowledge significant contributions of Craig Cauwels, Melissa Donovan, and Ilana Perna in the development and optimization of these technical protocols and Dr. Cameron Brennan for customization of the analysis tools. This work has been performed in the Arthur and Rochelle Belfer Cancer Genomics Center, made possible by a gift from the Belfer Foundation. Additional support from the NIH (RO1CA99041, PO1CA095616, P50CA093683) and the Goldhirsh Foundation are acknowledged.