Comparative genomic hybridization in hypotriploid/hyperdiploid tumors

Hypotriploidy/hyperdiploidy ("intermediate ploidy") often occurs in testicular germ cell tumors of adolescents and adults. Disomic and trisomic chromosomes represent significant parts of the tumor genome and a few chromosomes fall outside the two- to three-copy number range. We performed comparative genomic hybridization (CGH) with DNA isolated from a cell line from a case of testicular germ cell tumor of adolescents and adults and found most of the ratio values to be dislocated from the baseline 1.0 and placed adjacent of the diagnostic thresholds of 0.8 and 1.2. We attributed that to the fact that, in current software packages for analysis of CGH, the fluorescence ratio baseline is assumed to correspond to the copy number of most loci of the genome. We then evaluated, instead of the commonly used fluorescent ratio value from the whole metaphase, the use of the fluorescence ratios of single chromosomes. The results permitted a clear distinction between the chromosomes with two and three copies and, in particular, of the regions deleted or amplified outside the two- to three-copy range. We concluded that the evaluation of unbalances of DNA copy number in intermediate ploidy cases is best carried out using multiple normalization.