Analysis of ependymomas using comparative genomic hybridisation

Background and objectives Ependymomas are the third most common CNS tumours in childhood, and account for 9–12% of CNS neoplasms in all age groups. However, the prognosis for cases not completely excised is poor and the underlying biology of their development and progression is poorly understood. The few studies published to date have suggested that specific chromosomal abnormalities may be associated with the development of a significant proportion of these tumours. We set out to screen a large series of intracranial and spinal ependymomas for genetic imbalances, and to correlate these with histology and clinical behaviour. Methods Comparative genomic hybridisation (CGH) was used to detect chromosome imbalances on 86 ependymomas from 77 patients, of which 22 were children under 16, treated at one of three UK centres (Newcastle, Nottingham, Southampton). Cases were first analysed without reference to histology or clinical features, and were then divided up according to anatomical location, histology and age at presentation. Results Chromosomal imbalances were detected in tumours from 63/77 patients (82%). The majority involved entire chromosomes or chromosome arms, many showing patterns of gains suggestive of intermediate ploidy. Of previously reported abnormalities in ependymoma, the most frequent findings were gain of 1 q, seen in 13 cases (17%), and loss of 22 in 20 (26%). Whereas 1 q gain was seen mainly in posterior fossa tumours and was restricted to those with classic and anaplastic histology, loss of 22 was rarely observed in tumours from this location and their histology was predominantly classic or myxopapillary. In contrast to previous studies, loss of 6q was found in only 6 cases (8%) and in only one child. Out of 7 tumours biopsied at presentation and relapse, 4 revealed imbalances and 3 of these demonstrated progression of abnormalities at relapse. Conclusions Chromosomal imbalance is common in ependymoma and patterns of abnormality are emerging that are associated with histology or location. Further studies are needed to establish the prognostic significance of these abnormalities.