The NCI and NCBI SKY/CGH Interactive Online Database. T. Knutsen1, M. Augustus1, V. Gobu2, H. Padilla-Nash1, E. Schröck1, C. Shenmen2, J. Plotkin2, S. Greenhut1, J. Kriebel1, K. Sirotkin2, T. Ried1. 1) Genetics Branch, National Cancer Institute, NIH, Bethesda, MD; 2) National Center for Biotechnology Information, NIH, Bethesda, MD.
Spectral Karyotyping (SKY) and Comparative Genomic Hybridization (CGH) are complimentary fluorescent molecular cytogenetic techniques. SKY permits the simultaneous visualization of all human or mouse chromosomes in a different color, facilitating the identification of chromosomal aberrations. CGH utilizes the hybridization of differentially labeled tumor and reference DNA to generate a map of DNA copy number changes in tumor genomes. The NCI/NCBI SKY/CGH interactive online database permits the input of clinical and research SKY and CGH data, both human and mouse, directly from the cytogenetic community and the resulting information is available for public viewing in a searchable format. In the SKY database, the submitter enters the karyotype and then describes each abnormal chromosome by typing in the beginning and ending bands of each different segment, starting from the top. The computer then builds a full ideogram, with each chromosome displayed in its unique SKY classification color, with band overlay. Each breakpoint is automatically linked by a button marked FISH to the Map View database, which provides the genes at that site and available FISH clones for that breakpoint. This allows for a seamless integration of cytogenetic aberrations with the sequence of the human genome. Detailed clinical and research information is entered for each case. The CGH database displays gains, losses, and amplification of chromosomes and chromosome segments. CGH data is entered manually, or automatically from CGH software programs. In the manual format, the submitter enters the start band and stop band for each chromosome gain or loss, and the computer program displays the final ideogram with vertical bars to the left or right indicating loss or gain, respectively. This database offers the biomedical community the opportunity to participate directly in the development of data critical to the search for new oncogenes and tumor suppressor genes, and other genetic changes which lie at the root of all cancers.