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Full Complexity Genomic Hybridization on 60-mer Oligonucleotide Microarrays for Array Comparative Genomic Hybridization (aCGH)

  • Alexei Protopopov
  • Bin Feng
  • Lynda Chin
Part of the Methods in Molecular Biology™ book series (MIMB, volume 439)

Abstract

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.

Keywords

Cancer genomics array-CGH (aCGH) oligo microarrays genomic profiling copy number changes 

Notes

Acknowledgments

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.

References

  1. 1.
    1. Pinkel D, Segraves R, Sudar D, Clark S, Poole I, Kowbel D et al (1998) High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet 20:207–211CrossRefPubMedGoogle Scholar
  2. 2.
    2. Brennan C, Zhang Y, Leo C, Feng B, Cauwels C, Aguirre AJ et al (2004) High-resolution global profiling of genomic alterations with long oligonucleotide microarray. Cancer Res 64:4744–4748CrossRefPubMedGoogle Scholar

Copyright information

© Humana Press, a part of Springer Science+Business Media, LLC 2008

Authors and Affiliations

  • Alexei Protopopov
    • 1
  • Bin Feng
    • 1
  • Lynda Chin
    • 1
  1. 1.Center for Applied Cancer Science, Belfer Institute for Innovative Cancer Science, Dana-Farber Cancer InstituteHarvard Medical SchoolBostonUSA

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