Copy Number Variation in Neuroblastoma

Neuroblastoma is a tumour of the sympathetic nervous system, with a clinical phenotype resulting from complex patterns of genetic abnormalities, accounting for the most common extracranial neoplasia in childhood. Here we report 44 copy number variations, validated by qPCR, in paired tumour and blood samples of seven patients with neuroblastoma. Thirty four genes were included in altered regions while 11 altered regions did not apparently contain known genes. Five changes were present both in tumour and blood DNA samples in four patients, suggesting presence of germline and/or somatic changes maintained throughout tumorigenesis. Furthermore, some similar or identical changes were observed in different patients. The X chromosome showed the largest number of alterations. DNA from peripheral blood and tumour samples was isolated following using Qiagen DNA Blood Mini Kit. Microarray assays were performed in an Affymetrix platform with Cytogenetics Whole-Genome 2.7 M Array® (Affymetrix, Inc., Santa Clara, CA) for detecting copy number variation across coverage of the whole genome with the highest density of markers for superior resolution. Assays were performed following the procedure of Cytogenetics Copy Number Assay User Guide (Affymetrix®) and analysed with the Affymetrix® Chromosome Analysis Suite (ChAS) software. Gains and losses in tumour and blood samples from each patient were estimated with 95% confidence intervals.