Development of comparative genomic hybridization for the detection of genetic imbalances, with particular reference to paediatric solid tumours

Comparative genomic hybridization (CGH) is a new technique which allows the detection of unbalanced chromosomal aberrations but avoids the need for tissue culture. DNA is extracted from the tumour, labelled with a fluorochrome and cohybridized with normal reference DNA, labelled with a different colour, on to normal metaphase spreads. Gains or losses of chromosomal material by the tumour are deduced from deviations of the fluorescence intensity ratio of the two colours, measured along the length of each chromosome. The aim of this project was to develop the technique of CGH at the Wessex Regional Genetics Laboratory, and apply it principally to the study of paediatric solid tumours, with a view to identifying abnormalities prognostic significance.The technique was established for use with fresh and frozen tumour material and validated using conventional chromosome analysis, fluorescence in situ hybridization (FISH) and microsatellite analysis. The study of diagnostic specimens of paediatric solid tumours of different types, including neuroblastoma, Wilms tumour and rhabdomyosarcoma in small numbers, confirmed the potential of the technique as a screen for known prognostic indicators. A series of 39 CNS primitive neuroectodermal tumours (PNETs) was studied by CGH and compared with histological findings. A number of associations between specific chromosomal abnormalities and histological variant were identified, and the finding of monosomy 22 as an indicator or poor prognosis was also demonstrated in a small subgroup of PNETs. The use of CGH was extended to the study of selected case of haematological malignancy and cases with constitutional chromosomal abnormalities, where conventional cytogenetic analysis had failed to characerterise the abnormalities fully.In conclusion, CGH was found to be an effective and reliable screen for chromosome imbalance, with implications for the identification of prognostic indicators in malignancies, and a valuable tool for the diagnostic laboratory in selected cases.