Visualization of genomic aberrations using Affymetrix SNP arrays

MOTIVATION: DNA copy number aberrations are frequently found in different types of cancer. Recent developments of microarray-based approaches have broadened the knowledge on number and structure of such aberrations. High-density single nucleotide polymorphism (SNP) microarrays provide an extremely high resolution with up to 500,000 SNPs per genome. Owing to the enormous amount of data the detection of common aberrations in large datasets is a great challenge. We describe a novel open source software tool--IdeogramBrowser--which was specifically designed for use with the Affymetrix SNP arrays. It provides an interactive karyotypic visualization of multiple aberration profiles and direct links to GeneCards. Visualization of consensus regions together with gene representation allows the explorative assessment of the data. AVAILABILITY: IdeogramBrowser and its source code are freely available under a creative commons license and can be obtained from http://www.informatik.uni-ulm.de/ni/staff/HKestler/ideo/. IdeogramBrowser is a platform independent Java application.