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High-resolution analysis of allelic imbalance in neuroblastoma cell lines by single nucleotide polymorphism arrays

Lookup NU author(s): Dr Jane Carr-Wilkinson, Dr Nicholas Bown, Marian Case, Emeritus Professor Andy Hall, Professor John Lunec, Professor Deborah Tweddle

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Abstract

Genomic copy number changes are detectable in many malignancies, including neuroblastoma, using techniques such as comparative genomic hybridization (CGH), microsatellite analysis, conventional karyotyping, and fluorescence in situ hybridization (FISH). We report the use of 10K single nucleotide polymorphism (SNP) microarrays to detect copy number changes and allelic imbalance in six neuroblastoma cell lines (IMR32, SHEP, NBL-S, SJNB-1, LS, and SKNBE2c). SNP data were generated using the GeneChip DNA Analysis and GeneChip chromosome copy number software (Affymetrix). SNP arrays confirmed the presence of all previously reported cytogenetic abnormalities in the cell lines, including chromosome 1p deletion, MYCN amplification, gain of 17q and 11q, and 14q deletions. In addition, the SNP arrays revealed several chromosome gains and losses not detected by CGH or karyotyping; these included gain of 8q21.1∼24.3 and gain of chromosome 12 in IMR-32 cells; loss at 4p15.3∼16.1 and loss at 16p12.3∼13.2, 11q loss with loss of heterozygosity (LOH) at 11q14.3∼23.3 in SJNB-1 cells; and loss at 8p21.2∼23.3 and 9p21.3∼22.1 with corresponding LOH in SHEP cells. The SNP arrays refined the mapping of the 2p amplicons in LS, BE2c, and IMR-32 cell lines, the 12q amplicon in LS cells, and also identified an 11q13 amplicon in LS cells. There was good concordance among SNP arrays, CGH, and karyotyping. SNP array analysis is a powerful tool for the detection of allelic imbalance in neuroblastoma and also allows identification of LOH without changes in copy number (uniparental disomy). © 2007 Elsevier Inc. All rights reserved.


Publication metadata

Author(s): Carr, J., Bown, N.P., Case, M.C., Hall, A.G., Lunec, J., Tweddle, D.A.

Publication type: Article

Publication status: Published

Journal: Cancer Genetics and Cytogenetics

Year: 2007

Volume: 172

Issue: 2

Pages: 127-138

Print publication date: 15/01/2007

ISSN (print): 0165-4608

ISSN (electronic): 1873-4456

URL: http://dx.doi.org/10.1016/j.cancergencyto.2006.08.012

DOI: 10.1016/j.cancergencyto.2006.08.012

PubMed id: 17213021


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