Analysis of Segmental DNA Changes in Cancer using GSP-Array7700. Y. Murayama¹, S. Ozawa², S. Asakawa¹, Y. Saikawa², H. Hasegawa², H. Jinno², K. Aiura², A. Takayanagi¹, M. Maekawa³, M. Kitajima², N. Shimizu¹. 1) Dept. Mol. Biol., 144-8 Ogura Saiwai-ku, Kawasaki, Kanagawa, Japan; 2) Keio University School of Medicine, Department of Surgery, Tokyo, Japan; 3) GSP Lab. Inc., Japan.
   BAC microarray-based comparative genome hybridization (CGH) provides a highly efficient method to detect deletion or amplification of specific DNA segments in the genomes at individual chromosome basis. We constructed human BAC library (Keio BAC library) in 1994 and since then we have utilized it for the genomic DNA sequencing of human genome. To develop a high resolution BAC microarray, we read the end-sequences of 10,000 BAC clones, mapped them on the human chromosomes using the updated genome sequence data (Build35), and selected 7,718 BAC clones. Then, these BAC-DNAs were spotted on a glass microscope slide in triplicate (GSP-Array7700) so that the resolution of the GSP-Array7700 is about a BAC probe/400kb throughout the human genome. We employed the GSP-Array7700 to detect segmental DNA copy number changes in cancer cells and tissues including epidermoid carcinoma A431 cells, TE-series esophagus cancers cells, and esophagus cancer tissues from patients. We in fact detected copy number changes of various DNA segments, some of which corresponded to oncogenes such as EGFR and CCND1 and suppressor genes such as FAT3. Further analysis of these data would provide new information on the cancer related marker genes.