Sensitive determination of BRAF copy number in clinical samples by pyrosequencing

Diagnostic Molecular Pathology

Volumn 20, Issue 3, 2011, Pages 148-157

  Waha, Andreas ^a   Setty, Prashanth ^a   Gessi, Marco ^a   Waha, Anke ^a   Hammes, Jennifer ^a   El Maarri, Osman ^b   Pietsch, Torsten ^a  

^a UNIVERSITY HOSPITAL BONN   (Germany)

^b UNIVERSITY OF BONN   (Germany)

Author keywords

BRAF; copy number; pilocytic astrocytoma; pyrosequencing; translocation

Indexed keywords

B RAF KINASE; DNA FRAGMENT;

ADOLESCENT; ARTICLE; BIOASSAY; CALIBRATION; CHILD; CLINICAL ARTICLE; CONTROLLED STUDY; DNA DETERMINATION; EXON; FEMALE; FUSION GENE; GENE AMPLIFICATION; GENE DOSAGE; GENE EXPRESSION; HUMAN; HUMAN TISSUE; MALE; PILOCYTIC ASTROCYTOMA; PRIORITY JOURNAL; PSEUDOGENE; PYROSEQUENCING; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SCHOOL CHILD;

ADOLESCENT; ASTROCYTOMA; BRAIN NEOPLASMS; CHILD; CHROMOSOMES, HUMAN, PAIR 7; CHROMOSOMES, HUMAN, X; FEMALE; GENE DOSAGE; GENE FUSION; HUMANS; MALE; PROTO-ONCOGENE PROTEINS B-RAF; PSEUDOGENES; SEQUENCE ANALYSIS, DNA;

EID: 80052272777     PISSN: 10529551     EISSN: 15334066     Source Type: Journal    
DOI: 10.1097/PDM.0b013e3182143817     Document Type: Article

References (22)

1. Rickert CH, Paulus W. Epidemiology of central nervous system tumors in childhood and adolescence based on the new WHO classification. Childs Nerv Syst. 2001;17:503-511. (Pubitemid 32842704)
2. Louis DN, Ohgaki H, Wiestler OD, et al. The 2007 WHO classification of tumours of the central nervous system. Acta Neuropathol. 2007;114:97-109. (Pubitemid 47103521)
3. Tomlinson FH, Scheithauer BW, Hayostek CJ, et al. The significance of atypia and histologic malignancy in pilocytic astrocytoma of the cerebellum: A clinicopathologic and flow cytometric study. J Child Neurol. 1994;9:301-310. (Pubitemid 24255251)
4. Dirven CM, Mooij JJ, Molenaar WM. Cerebellar pilocytic astrocytoma: A treatment protocol based upon analysis of 73 cases and a review of the literature. Childs Nerv Syst. 1997;13:17-23. (Pubitemid 27104553)
5. van't Veer LJ, Bernards R. Enabling personalized cancer medicine through analysis of gene-expression patterns. Nature. 2008;452: 564-570. (Pubitemid 351483370)
6. Jacob K, Albrecht S, Sollier C, et al. Duplication of 7q34 is specific to juvenile pilocytic astrocytomas and a hallmark of cerebellar and optic pathway tumours. Br J Cancer. 2009;101:722-733.
7. White FV, Anthony DC, Yunis EJ, et al. Nonrandom chromosomal gains in pilocytic astrocytomas of childhood. Hum Pathol. 1995; 26:979-986.
8. Rickert CH, Paulus W. Comparative genomic hybridization in central and peripheral nervous system tumors of childhood and adolescence. J Neuropathol Exp Neurol. 2004;63:399-417. (Pubitemid 38669662)
9. Wemmert S, Romeike BF, Ketter R, et al. Intratumoral genetic heterogeneity in pilocytic astrocytomas revealed by CGH-analysis of microdissected tumor cells and FISH on tumor tissue sections. Int J Oncol. 2006;28:353-360.
10. Pfister S, Janzarik WG, Remke M, et al. BRAF gene duplication constitutes a mechanism of MAPK pathway activation in low-grade astrocytomas. J Clin Invest. 2008;118:1739-1749. (Pubitemid 351632377)
11. Bar EE, Lin A, Tihan T, et al. Frequent gains at chromosome 7q34 involving BRAF in pilocytic astrocytoma. J Neuropathol Exp Neurol. 2008;67:878-887.
12. Deshmukh H, Yeh TH, Yu J, et al. High-resolution, dual-platform aCGH analysis reveals frequent HIPK2 amplification and increased expression in pilocytic astrocytomas. Oncogene. 2008;27: 4745-4751.
13. Jones DT, Kocialkowski S, Liu L, et al. Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas. Cancer Res. 2008;68:8673-8677.
14. Sievert AJ, Jackson EM, Gai X, et al. Duplication of 7q34 in pediatric low-grade astrocytomas detected by high-density singlenucleotide polymorphism-based genotype arrays results in a novel BRAF fusion gene. Brain Pathol. 2009;19:449-458.
15. Yu J, Deshmukh H, Gutmann RJ, et al. Alterations of BRAF and HIPK2 loci predominate in sporadic pilocytic astrocytoma. Neurology. 2009;73:1526-1531.
16. Forshew T, Tatevossian RG, Lawson AR, et al. Activation of the ERK/MAPK pathway: A signature genetic defect in posterior fossa pilocytic astrocytomas. J Pathol. 2009;218:172-181.
17. Eychene A, Barnier JV, Apiou F, et al. Chromosomal assignment of two human B-raf(Rmil) proto-oncogene loci: B-raf-1 encoding the p94Braf/Rmil and B-raf-2, a processed pseudogene. Oncogene. 1992; 7:1657-1660.
18. Korshunov A, Meyer J, Capper D, et al. Combined molecular analysis of BRAF and IDH1 distinguishes pilocytic astrocytoma from diffuse astrocytoma. Acta Neuropathol. 2009;118:401-405.
19. Dougherty MJ, Santi M, Brose MS, et al. Activating mutations in BRAF characterize a spectrum of pediatric low-grade gliomas. Neuro Oncol. 2010;12:621-630.
20. Pielberg G, Day AE, Plastow GS, et al. A sensitive method for detecting variation in copy numbers of duplicated genes. Genome Res. 2003;13:2171-2177. (Pubitemid 37161774)
21. Spittle C, Ward MR, Nathanson KL, et al. Application of a BRAF pyrosequencing assay for mutation detection and copy number analysis in malignant melanoma. J Mol Diagn. 2007;9: 464-471. (Pubitemid 47434113)
22. Soderback E, Zackrisson AL, Lindblom B, et al. Determination of CYP2D6 gene copy number by pyrosequencing. Clin Chem. 2005; 51:522-531. (Pubitemid 40300227)