High-Resolution Analysis of Gene Copy Number Alterations in Human Prostate Cancer Using CGH on cDNA Microarrays: Impact of Copy Number on Gene Expression

Neoplasia: An International Journal for Oncology Research

Outi Monni¹  Minna Allinen²  Abdel Elkahloun²  Yidong Chen²  Sampsa Hautaniemi³  Anne Kallioniemi⁴  Ritva Karhu⁴  Maija Wolf⁵  Olli-P Kallioniemi⁵  Pia Huusko⁶  Spyro Mousses⁶ 

[1]Biomedicum Biochip Center, University of Helsinki, Helsinki FIN-00014, Finland

[2]Cancer Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA

[3]Institute of Signal Processing, Tampere University of Technology, Tampere FIN-33101, Finland

[4]Laboratory of Cancer Genetics, Tampere University Hospital and Institute of Medical Technology, University of Tampere, Tampere FIN-33520, Finland

[5]Medical Biotechnology, VTT Technical Research Centre of Finland and University of Turku, Turku FIN-20520, Finland

[6]Translational Genomics Research Institute, Gaithersburg, MD 20878-1762, USA

关键词: Copy number alteration;    prostate cancer;    gene expression;    cDNA microarray;    CGH microarray;   

DOI  :  10.1593/neo.03439

来源: DOAJ

【 摘 要 】

Identification of target genes for genetic rearrangements in prostate cancer and the impact of copy number changes on gene expression are currently not well understood. Here, we applied high-resolution comparative genomic hybridization (CGH) on cDNA microarrays for analysis of prostate cancer cell lines. CGH microarrays identified most of the alterations detected by classical chromosomal CGH, as well as a number of previously unreported alterations. Specific recurrent regions of gain (28) and loss (18) were found, their boundaries defined with sub-megabasepair accuracy. The most common changes included copy number decreases at 13% and gains at iq and 5p. Refined mapping identified several sites, such as at 13q (33-44, 49-51, 74-76 Mbp from the p-telomere), which matched with minimal regions of loss seen in extensive loss of heterozygosity mapping studies of large numbers of tumors. Previously unreported recurrent changes were found at 2p, 2q, 3p, 17q (losses), at 3q, 5p, 6p (gains). Integration of genomic and transcriptomic data revealed the role of individual candidate target genes for genomic alterations as well as a highly significant (P < .0001) overall association between copy number levels and the percentage of differentially expressed genes. Across the genome, the overall impact of copy number on gene expression levels was, to a large extent, attributable to low-level gains and losses of copy number, corresponding to common deletions and gains of often large chromosomal regions.

【 授权许可】

Unknown