As mentioned above, CGH has already showed a significant impact in the field of cancer cytogenetics as a powerful tool for detection of chromosome copy number aberrations even in epithelial solid tumors, in which conventional cytogenetics is hard to elucidate tumor specific genome alterations. However, the resolution of CGH to metaphase chromosomes can provide only limited resolution at 5-10 Mb level for detection of copy number losses and gains, and at 2Mb for amplifications. To circumvent this limitation, an innovative strategy, called matrix-CGH¹⁷⁾ or array-based CGH¹⁸⁾ has been devised. CGH using cDNA microarray was also reported to be useful for detection and mapping of gene amplification and homozygous deletions.¹⁹⁾ In array CGH, chromosomal targets are replaced by arrays consisting of well-defined genomic clones such as BAC, PAC or cosmid clones, which are spotted onto a microscopic slide-glass using robotic devices. Since the clones spotted on slide-glass contain sequences information directly connecting with the genome database, we can easily obtain particular biological aspects of genes mapped within regions involved in copy number aberrations detected by array-CGH, facilitating identification of genes responsible for cancer as well as unknown genetic diseases including learning disability.^20,21,22) (Fig.1)

Snijders et al.²³⁾ reported construction of a genome wide DNA microarray that consisted of ~2400 BACs distributed through the genome. Recently, a tiling resolution array consisting of 32,433 overlapping BAC clones covering the entire genome has been constructed.²⁴⁾ We have also constructed different types of BAC-based CGH-arrays. The first array consists of ~4500 BACs for genome-wide analysis (named MCG Whole Genome Array-4500) and this array provides resolution of ~0.7Mb. The second consists of ~800 BACs harboring known 800 cancer-related genes for diagnosis of copy number aberrations in cancer (MCG Cancer Array-800, see URL: http://www.cghtmd.jp/) ²⁵⁾, and the third contains 212 contig BACs spanning the ~20 Mb region at 1p36 (MCG 1p36 Contig Array). In construction of our custom-made arrays, each DpnI/RsaI/HaeIII-restricted BAC/PAC DNA is amplified by two rounds of ligation-mediated PCR, and printed in duplicate by inkjet-type spotter on slide glasses. In our system, CGH-array hybridizations are carried out as described by Snijders et al.²³⁾ and Massion et al.²⁶⁾ with modifications.²⁵⁾ DpnII-restricted test and reference (male) genomic DNAs were labeled with Cy3 and Cy5, respectively. The arrays were scanned with a scanner, and acquired images were analyzed with an imaging software. Fluorescence ratios are normalized so that the mean of the middle third of log2ratios across the array was zero as described²⁷⁾ with modifications.²⁵⁾ Average ratios that deviated significantly (>2 SD) from 0 were considered abnormal.