Genomic alterations are one of several key factors involved in carcinogenesis. Over the years, much focus has been dedicated to the study of genomic copy number changes using uorescent in situ hybridization (FISH) techniques such as comparative genomic hybridization (CGH) and spectral karyotyping. Mapping copy number gains and losses has led to potentially valuable diagnostic and prognostic markers for cancer and prenatal defects. In recent years, researchers have applied the concept of CGH to high-density deoxyribonucleic acid (DNA) microarrays (Figure 15.1) (array CGH), enabling unprecedented characterization of genomic aberrations on a genome-wide level [1].