Exploratory visualization of array-based comparative genomic hybridization

Recent developments in DNA microarray technology have enabled a new and highly effective platform for performing comparative genomic hybridization (CGH) measurements. CGH measures anomalies in DNA copy number. Such copy number changes are now thought to play an important role in a number of diseases, particularly cancer and developmental disorders, and may also lead to important insights relevant to personalized treatments of such diseases. In contrast to gene expression measurements, the genomic positions of probe targets and their correlation to genomic aberrations lead to a natural ordering of the data. This ordering can be leveraged in data visualizations of CGH measurements. This paper describes a research prototype we have named VistaChrom, which provides a highly interactive, exploratory visualization scheme for analyzing array-based CGH data. For efficient navigation, VistaChrom is based on tiled, multi-level coordinated views organized by genome, chromosome, gene and microarray probe. Raw probe data, moving averages, and statistical measures can all be displayed individually or simultaneously to aid visual discovery of significant genomic aberrations. Visual analysis can be performed with single arrays or multi-array studies. The result is a novel and effective environment for visually analyzing CGH data. Example visualization results are shown for two different datasets derived from tumor cell lines. The application also provides a framework for further exploring advanced computational methods for aberration analysis.