Comparative genomic hybridization (CGH) provides a genome-wide scan that detects chromosomal regions which have copy number abnormalities (CNAs). For example, one can detect the loss of a region containing a tumour-suppressor gene or the amplification of one harbouring an oncogene. Typically, two genomes are compared by labelling total genomic DNA with different flourescent dyes and then co-hybridizing these complex probes to metaphase spreads. This enables mapping as well as semi-quantitative measurement of CNAs. Array CGH exploits contigued BACs (for example, BAC clones) as targets for increased resolution (∼100 kb) and increased quantitative capacity. In oligonucleotide-array CGH, a probe of reduced complexity and no repetitive elements is produced by making a PCR-based representation of each genomic DNA sample. In a ‘proof-of-principle’ approach, a multiplex PCR was performed for ten loci using primer pairs that contained gene-specific and adapter sequences. The target elements, printed on plastic slides, consisted of 50-mer oligonucleotides that mapped to the region flanked by primer sequences. This method requires less than 25 ng of starting genomic DNA template. The normalized copy number measurements shown below are similar to those obtained using the well-established FISH methodology, by which the amplifications of ZNF217 and AIBC1 in MCF7 and CCND1 in 600MPE were clearly detected, as was a loss of TP53 in 600MPE. This consistancy supports the feasibility of this approach.