Alterations in DNA copy number underlie certain developmental abnormalities and are frequent in solid tumors. Microarray-based comparative genomic hybridization (array CGH) provides a high throughput means to measure and map copy number aberrations on a genome-wide scale and to link them directly to genome sequence. For applications involving the analysis of tumors, the technology must provide reliable detection of single copy gains and losses in mixed cell populations such as tumor and normal cells, accurate quantification of high level copy number gains, and confident interpretation of aberrations affecting only a single array element. Further, one would like to minimize the amount of specimen material required for an analysis. These requirements can be met if there are good signal-to-noise ratios in the hybridization.