The study of aberrant chromosome structure has significantly increased our understanding of the cause and progression of human cancers. Many cancers are common to both dogs and humans, in part reflecting the high degree of similarity in their genetic material and in their environmental exposure to carcinogens. The extent and identity of chromosome aberrations associated with canine cancers, however, remains largely unknown. This is primarily due to the difficulty in identifying dog chromosomes by conventional means alone. Comparative genomic hybridization (CGH) is a technique that allows a comprehensive analysis of chromosome aberrations present within tumors. We have developed this technique for application to dog cancers and are obtaining valuable information. However, chromosome-based CGH is labor intensive, has a limited resolution and requires detailed knowledge of dog chromosomes. In this study we aim to identify a set of large insert clones that are evenly spaced, at small intervals, along all dog chromosomes. These clones will be a very valuable resource for chromosome studies of dog cancers. The clones will be used to generate an ordered microarray to replace chromosome-based analyses. This will significantly and rapidly advance the study of canine cancer, leading to improved diagnosis and prognosis and thus health and welfare.