The interactive online SKY/M-FISH & CGH Database and the Entrez Cancer Chromosomes search database: Linkage of chromosomal aberrations with the genome sequence

• Published in: Genes chromosomes & cancer 2005-09, Vol.44 (1), p.52-64
• Main Authors: Knutsen, Turid, Gobu, Vasuki, Knaus, Rodger, Padilla-Nash, Hesed, Augustus, Meena, Strausberg, Robert L., Kirsch, Ilan R., Sirotkin, Karl, Ried, Thomas
• Format: Article
• Language: English
• Subjects: Base Sequence; Chromosome Aberrations; Chromosome Mapping; Databases, Nucleic Acid; Genome, Human; Humans; In Situ Hybridization, Fluorescence; Karyotyping; Neoplasms - genetics; Nucleic Acid Hybridization - methods; Online Systems
• ISSN: 1045-2257; 1098-2264
• DOI: 10.1002/gcc.20224

To catalog data on chromosomal aberrations in cancer derived from emerging molecular cytogenetic techniques and to integrate these data with genome maps, we have established two resources, the NCI and NCBI SKY/M‐FISH & CGH Database and the Cancer Chromosomes database. The goal of the former is to allow investigators to submit and analyze clinical and research cytogenetic data. It contains a karyotype parser tool, which automatically converts the ISCN short‐form karyotype into an internal representation displayed in detailed form and as a colored ideogram with band overlay, and also has a tool to compare CGH profiles from multiple cases. The Cancer Chromosomes database integrates the SKY/M‐FISH & CGH Database with the Mitelman Database of Chromosome Aberrations in Cancer and the Recurrent Chromosome Aberrations in Cancer database. These three datasets can now be searched seamlessly by use of the Entrez search and retrieval system for chromosome aberrations, clinical data, and reference citations. Common diagnoses, anatomic sites, chromosome breakpoints, junctions, numerical and structural abnormalities, and bands gained and lost among selected cases can be compared by use of the “similarity” report. Because the model used for CGH data is a subset of the karyotype data, it is now possible to examine the similarities between CGH results and karyotypes directly. All chromosomal bands are directly linked to the Entrez Map Viewer database, providing integration of cytogenetic data with the sequence assembly. These resources, developed as a part of the Cancer Chromosome Aberration Project (CCAP) initiative, aid the search for new cancer‐associated genes and foster insights into the causes and consequences of genetic alterations in cancer. Published 2005 Wiley‐Liss, Inc.