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[Cancer Research 64, 4744-4748, July 15, 2004]
© 2004 American Association for Cancer Research

Regular Articles

High-Resolution Global Profiling of Genomic Alterations with Long Oligonucleotide Microarray

Cameron Brennan1, Yunyu Zhang1, Christopher Leo1, Bin Feng1, Craig Cauwels1, Andrew J. Aguirre1, Minjung Kim1, Alexei Protopopov1 and Lynda Chin1,2

1 Department of Medical Oncology, Dana Farber Cancer Institute, and 2 Department of Dermatology, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts

Cancer represents the phenotypic end point of multiple genetic lesions that endow cells with a full range of biological properties required for tumorigenesis. Among the hallmark features of the cancer genome are recurrent regional gains and losses that, upon detailed characterization, have provided highly productive discovery paths for new oncogenes and tumor suppressor genes. In this study, we describe the use of an oligonucleotide-based microarray platform and development of requisite assay conditions and bioinformatic mining tools that permits high-resolution genome-wide array-comparative genome hybridization profiling of human and mouse tumors. Using a commercially available 60-mer oligonucleotide microarray, we demonstrate that this platform provides sufficient sensitivity to detect single-copy difference in gene dosage of full complexity genomic DNA while offering high resolution. The commercial availability of the microarrays and associated reagents, along with the technical protocols and analytical tools described in this report, should provide investigators with the immediate capacity to perform DNA analysis of normal and diseased genomes in a global and detailed manner.




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