High resolution CGH of breast cancer. D.N. Roberts¹, C.A. Carmack¹, A. De Witte¹, S. Milligan¹, E. Lin¹, J. Gao¹, S. Giles¹, S. Shchegrova¹, E. LeProust¹, P. Webb¹, D. Amorese¹, J. Gregg². 1) Integrated Biology Solutions, Agilent Technologies, Santa Clara, CA; 2) UC Davis Medical Center, Sacramento, CA.
   Array based Comparative Genomic Hybridization (CGH) provides a means for the determination of DNA copy number aberrations. We have designed a CGH array consisting of ~244,000 in situ synthesized 60-mer oligonucleotides spanning the entire human genome, resulting in an average genomic distance between probes of ~12 Kbp. Using these arrays, we performed an analysis of copy number changes in breast carcinomas and in breast carcinoma cell lines. In several cases displaying amplifications around ERBB2, we utilized a second, high definition CGH array with >20,000 probes dedicated to chromosome 17, with particular emphasis on the region encompassing ERBB2 (17q21.2-q21.3). Using these data in combination, we define multiple common aberrations in our sample set. Further, we analyze patient chromosomal/gene copy number with respect to the levels of ERBB2 protein, clinical classification, and outcome.