Duplication of 7q34 in Pediatric Low‐Grade Astrocytomas Detected by High‐Density Single‐Nucleotide Polymorphism‐Based Genotype Arrays Results in a Novel BRAF Fusion Gene

In the present study, DNA from 28 pediatric low‐grade astrocytomas was analyzed using Illumina HumanHap550K single‐nucleotide polymorphism oligonucleotide arrays. A novel duplication in chromosome band 7q34 was identified in 17 of 22 juvenile pilocytic astrocytomas and three of six fibrillary astrocytomas. The 7q34 duplication spans 2.6 Mb of genomic sequence and contains approximately 20 genes, including two candidate tumor genes, HIPK2 and BRAF. There were no abnormalities in HIPK2, and analysis of two mutation hot‐spots in BRAF revealed a V600E mutation in only one tumor without the duplication. Fluorescence in situ hybridization confirmed the 7q34 copy number change and was suggestive of a tandem duplication. Reverse transcription polymerase chain reaction‐based sequencing revealed a fusion product between KIAA1549 and BRAF. The predicted fusion product includes the BRAF kinase domain and lacks the auto‐inhibitory N‐terminus. Western blot analysis revealed phosphorylated mitogen‐activated protein kinase (MAPK) protein in tumors with the duplication, consistent with BRAF‐induced activation of the pathway. Further studies are required to determine the role of this fusion gene in downstream MAPK signaling and its role in development of pediatric low‐grade astrocytomas.

[1]  M. Watson,et al.  High-resolution, dual-platform aCGH analysis reveals frequent HIPK2 amplification and increased expression in pilocytic astrocytomas , 2008, Oncogene.

[2]  G. Reifenberger,et al.  BRAF gene duplication constitutes a mechanism of MAPK pathway activation in low-grade astrocytomas. , 2008, The Journal of clinical investigation.

[3]  L.,et al.  Pathologist Interobserver Variability of Histologic Features in Childhood Brain Tumors: Results from the CCG-945 Study , 2008, Pediatric and developmental pathology : the official journal of the Society for Pediatric Pathology and the Paediatric Pathology Society.

[4]  D. Peeper,et al.  BRAFE600 in benign and malignant human tumours , 2008, Oncogene.

[5]  M. Meisler,et al.  Evidence for a direct role of the disease modifier SCNM1 in splicing. , 2007, Human molecular genetics.

[6]  P. Gimotty,et al.  Application of a BRAF pyrosequencing assay for mutation detection and copy number analysis in malignant melanoma. , 2007, The Journal of molecular diagnostics : JMD.

[7]  P. Wesseling,et al.  RAS/RAF pathway activation in gliomas: the result of copy number gains rather than activating mutations , 2007, Acta Neuropathologica.

[8]  T. Shaikh,et al.  High-density single nucleotide polymorphism array analysis in patients with germline deletions of 22q11.2 and malignant rhabdoid tumor , 2007, Human Genetics.

[9]  A. Fusco,et al.  High-mobility group A1 inhibits p53 by cytoplasmic relocalization of its proapoptotic activator HIPK2. , 2007, The Journal of clinical investigation.

[10]  S. Gabriel,et al.  High-throughput oncogene mutation profiling in human cancer , 2007, Nature Genetics.

[11]  K. Gunderson,et al.  High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping. , 2006, Genome research.

[12]  P. Paquier,et al.  Functional outcome after low‐grade astrocytoma treatment in childhood , 2006, Cancer.

[13]  R. Mulhern,et al.  Intellectual and functional outcome of children 3 years old or younger who have CNS malignancies. , 2005, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[14]  R. Reis,et al.  Mutation analysis of B-RAF gene in human gliomas , 2005, Acta Neuropathologica.

[15]  M. Nikiforova,et al.  Oncogenic AKAP9-BRAF fusion is a novel mechanism of MAPK pathway activation in thyroid cancer. , 2005, The Journal of clinical investigation.

[16]  F. Gilles,et al.  Outcome of children with centrally reviewed low‐grade gliomas treated with chemotherapy with or without radiotherapy on Children's Cancer Group high‐grade glioma study CCG‐945 , 2003, Cancer.

[17]  D. Figarella-Branger,et al.  Pilocytic Astrocytomas in Children: Prognostic Factors—A Retrospective Study of 80 Cases , 2003, Neurosurgery.

[18]  James M Boyett,et al.  The influence of central review on outcome associations in childhood malignant gliomas: results from the CCG-945 experience. , 2003, Neuro-oncology.

[19]  E. Shaw,et al.  Prospective clinical trials of intracranial low-grade glioma in adults and children. , 2003, Neuro-oncology.

[20]  A. Nicholson,et al.  Mutations of the BRAF gene in human cancer , 2002, Nature.

[21]  I. Pollack,et al.  Expression of p53 and prognosis in children with malignant gliomas. , 2002, The New England journal of medicine.

[22]  D. Louis,et al.  Glioma classification: a molecular reappraisal. , 2001, The American journal of pathology.

[23]  W. Paulus,et al.  Epidemiology of central nervous system tumors in childhood and adolescence based on the new WHO classification , 2001, Child’s Nervous System.

[24]  R. McLendon,et al.  Chromosomal characteristics of childhood brain tumors. , 1997, Cancer genetics and cytogenetics.

[25]  J. Langston,et al.  Low-grade astrocytoma: a decade of experience at St. Jude Children's Research Hospital. , 1997, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[26]  E. Schröck,et al.  Recurrent gain of chromosome arm 7q in low‐grade astrocytic tumors studied by comparative genomic hybridization , 1996, Genes, chromosomes & cancer.

[27]  J. Biegel,et al.  p53 gene mutations in pediatric brain tumors. , 1995, Medical and pediatric oncology.

[28]  D. Schofield,et al.  Nonrandom chromosomal gains in pilocytic astrocytomas of childhood. , 1995, Human pathology.

[29]  R. McLendon,et al.  Alterations of the TP53 gene in human gliomas. , 1994, Cancer research.

[30]  D. Cochrane,et al.  Cytogenetic analysis of 109 pediatric central nervous system tumors. , 1993, Cancer genetics and cytogenetics.

[31]  F. Gilles,et al.  Cytogenetic analysis of 39 pediatric central nervous system tumors. , 1992, Cancer genetics and cytogenetics.

[32]  T. Mikkelsen,et al.  Clonal expansion of p53 mutant cells is associated with brain tumour progression , 1992, Nature.

[33]  C. James,et al.  Mitotic recombination of chromosome 17 in astrocytomas. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[34]  S Rozen,et al.  Primer3 on the WWW for general users and for biologist programmers. , 2000, Methods in molecular biology.

[35]  L. Rorke,et al.  Chromosome abnormalities in pediatric brain tumors. , 1988, Cancer research.