Recently, Bignell et al.³⁵⁾ showed that the SNP array could be used to detect copy number variations in cancer cell lines. Their method differs from spotted-array-based CGH and fundamentally similar to Affymetrix expression array experiments. This system could reliably reveal high-level amplifications and homozygous deletions extending over the regions of <1Mb to several megabases. Although this platform has limited resolution for detection of chromosome imbalances, the SNP-based technology can provide information pertaining to both copy number and status of each parental allele, playing a powerful tool to discriminate the provenance of the chromosome region involved in copy number aberration in both cancer as uniparental disomy disorders. Lucito et al.³⁶⁾ developed a methodology for representational oligonucleotide microarray analysis (ROMA) with array assembled from 85000 oligonucleotides (70mers) through the entire genome. Using this system, they achieved an average resolution of 30 kb throughout the genome and readily detect amplifications and homozygous and hemizygous deletions in cancer genomes. Further, using this method between normal human genomes, they frequently detect large (100 kb to 1 Mb) deletions or duplications, indicating that array-CGH can solve a puzzle even in anthropological subjects.

More recently, Mitelman et al. analyzed published reports of 44750 cytogentically abnormal neplasms and concluded that solid tumors can result from much the same translocational gene rearrangements and gene fusions that initiate leukemia and lymphomas.²⁾ They also suggest that cytogenetic aberrations resulting in deregulated or rearranged gene may be more important as an initial step in epithelial tumorigenesis than generally believed. Just timely, Ishikanian et al.²³⁾ constructed a tiling resolution DNA microarray completely covered the entire human genome, and reported that its resolving power can provide the definition of breakpoints involved in unbalanced chromosome translocation to within single BAC clone. Those results raise the possibility that high-density submegabase array can reveal causative translocation-breakpoints of neoplastic transformation, masked under complex karyotypes in epithelial solid tumors. Microarray-CGH paves the way for identification of genes involved in translocation breakpoints that have not yet been detected by existing technologies. Further, in near future, array-based CGH technology, that is enabled us to high-throughput analysis of copy number aberrations in a single test of DNA, will certainly be utilized in practical clinics as a tool for diagnosis of cancer as well as genetic diseases.