Emerging genomic and proteomic data is creating new opportunities to identify novel biomarkers that will have pathway-specific therapeutic impact on cancer progression. Molecular cytogenetic and fluorescence in situ hybridization (FISH) methods have been primarily used in discovery genetic research laboratories until recently. New automated analytical platforms based on FISH technologies and tissue microarray methods are providing a rapid means to determine the impact of consistent genomic aberrations in clinical trials, and in studies designed to investigate differential chemotherapeutic response.