title: Genomic characterization of ependymomas reveals 6q loss as the most common aberration.
abstract: Ependymomas are rare tumors of the central nervous system (CNS). They are classified based on tumor histology and grade, but the prognostic value of the WHO grading system remains controversial. Treatment is mainly surgical and by radiation. An improved knowledge of ependymoma biology is important to elucidate the pathogenesis, to improve classification schemes, and to identify novel potential treatment targets. Only 113 ependymoma karyotypes with chromosome aberrations are registered in the Mitelman database. We present the first study of ependymoma genomes combining karyotyping and high resolution comparative genomic hybridization (HR-CGH). Nineteen tumor samples were collected from three pediatric and 15 adult patients treated at Oslo University Hospital between 2005 and 2012. Histological diagnoses included subependymoma and myxopapillary ependymoma (WHO grade I), ependymoma (WHO grade II) and anaplastic ependymoma (WHO grade III). Four tumors were intraspinal and 15 were intracranial. Seventeen samples were successfully karyotyped, HR-CGH analysis was undertaken on 17 samples, and 15 of 19 tumors were analyzed using both methods. Twelve tumors had karyotypic abnormalities, mostly gains or losses of whole chromosomes. Structural rearrangements were found in four tumors, in two of which 2p23 was identified as a breakpoint region. Twelve tumors displayed genomic imbalances by HR-CGH analysis with loss of material at 6q as the most common. 6q loss, which was detected by one or both methods in seven of 12 (58%) abnormal tumors, and 5p gain (observed in five tumors; 42%) were the most common genomic aberrations in this series.
authors.affiliation: Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital - The Norwegian Radium Hospital, Nydalen, 0424 Oslo, Norway.
authors.forename: Thale Kristin
authors.initials: TK
authors.lastname: Olsen
authors.affiliation: Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital - The Norwegian Radium Hospital, Nydalen, 0424 Oslo, Norway.
authors.forename: Ludmila
authors.initials: L
authors.lastname: Gorunova
authors.affiliation: Department of Neurosurgery, Oslo University Hospital - Rikshospitalet, Nydalen, 0424 Oslo, Norway.
authors.forename: Torstein R
authors.initials: TR
authors.lastname: Meling
authors.affiliation: Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital - The Norwegian Radium Hospital, Nydalen, 0424 Oslo, Norway.
authors.forename: Francesca
authors.initials: F
authors.lastname: Micci
authors.affiliation: Department of Pathology, Oslo University Hospital - Rikshospitalet, Nydalen, 0424 Oslo, Norway.
authors.forename: David
authors.initials: D
authors.lastname: Scheie
authors.affiliation: Department of Neurosurgery, Oslo University Hospital - Rikshospitalet, Nydalen, 0424 Oslo, Norway.
authors.forename: Bernt
authors.initials: B
authors.lastname: Due-Tønnessen
authors.affiliation: Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital - The Norwegian Radium Hospital, Nydalen, 0424 Oslo, Norway.
authors.forename: Sverre
authors.initials: S
authors.lastname: Heim
authors.affiliation: Section for Cancer Cytogenetics, Institute for Cancer Genetics and Informatics, Oslo University Hospital - The Norwegian Radium Hospital, Nydalen, 0424 Oslo, Norway.
authors.forename: Petter
authors.initials: P
authors.lastname: Brandal
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D001932:Brain Neoplasms / Q000235:genetics* / Q000473:pathology; D002648:Child; D002675:Child, Preschool; D002869:Chromosome Aberrations; D002872:Chromosome Deletion; D002895:Chromosomes, Human, Pair 5; D002896:Chromosomes, Human, Pair 6; D055028:Comparative Genomic Hybridization; D004806:Ependymoma / Q000235:genetics* / Q000473:pathology; D015894:Genome, Human; D006801:Humans; D007223:Infant; D007621:Karyotyping; D008297:Male; D008875:Middle Aged; D009664:Norway; D013125:Spinal Neoplasms / Q000235:genetics* / Q000473:pathology; D055815:Young Adult