Genome-wide analysis of DNA copy number alterations and loss of heterozygosity in intracranial germ cell tumors

Keita Terashima, Alexander Yu, Wing Yuk T. Chow, Wei chun J. Hsu, Peikai Chen, Stephen T. Wong, Yeung Sam Hung, Tomonari Suzuki, Ryo Nishikawa, Masao Matsutani, Hideo Nakamura, Ho Keung Ng, Jeffrey C. Allen, Kenneth D. Aldape, Jack M. Su, Adekunle M. Adesina, Hon chiu E. Leung, Tsz Kwong Man, Ching C. Lau

Research output: Contribution to journalArticle

28 Scopus citations

Abstract

Backgrounds: Intracranial germ cell tumors (GCTs) are rare and heterogeneous with very little is known about their pathogenesis and underlying genetic abnormalities. Procedures: In order to identify candidate genes and pathways which are involved in the pathogenesis of these tumors, we have profiled 62 intracranial GCTs for DNA copy number alterations (CNAs) and loss of heterozygosity (LOH) by using single nucleotide polymorphism (SNP) array and quantitative real time PCR (qPCR). Results: Initially 27 cases of tumor tissues with matched blood samples were fully analyzed by SNP microarray and qPCR. Statistical analysis using the genomic identification of significant targets in cancer (GISTIC) tool identified 10 regions of significant copy number gain and 11 regions of significant copy number loss. While overall pattern of genomic aberration was similar between germinoma and nongerminomatous germ cell tumors (NGGCTs), a few subtype-specific peak regions were identified. Analysis by SNP array and qPCR was replicated using an independent cohort of 35 cases. Conclusions: Frequent aberrations of CCND2 (12p13) and RB1 (13q14) suggest that Cyclin/CDK-RB-E2F pathway might play a critical role in the pathogenesis of intracranial GCTs. Frequent gain of PRDM14 (8q13) implies that transcriptional regulation of primordial germ cell specification might be an important factor in the development of this tumor. Pediatr Blood Cancer 2014;61:593-600.

Original languageEnglish (US)
Pages (from-to)593-600
Number of pages8
JournalPediatric Blood and Cancer
Volume61
Issue number4
DOIs
StatePublished - Apr 2014

Keywords

  • DNA copy number
  • Genomic profiling
  • Intracranial germ cell tumor
  • Loss of heterozygosity
  • SNP microarray

ASJC Scopus subject areas

  • Oncology
  • Pediatrics, Perinatology, and Child Health
  • Hematology

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