Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancerReport as inadecuate




Combined array-comparative genomic hybridization and single-nucleotide polymorphism-loss of heterozygosity analysis reveals complex genetic alterations in cervical cancer - Download this document for free, or read online. Document in PDF available to download.

BMC Genomics

, 8:53

First Online: 20 February 2007Received: 18 October 2006Accepted: 20 February 2007

Abstract

BackgroundCervical carcinoma develops as a result of multiple genetic alterations. Different studies investigated genomic alterations in cervical cancer mainly by means of metaphase comparative genomic hybridization mCGH and microsatellite marker analysis for the detection of loss of heterozygosity LOH. Currently, high throughput methods such as array comparative genomic hybridization array CGH, single nucleotide polymorphism array SNP array and gene expression arrays are available to study genome-wide alterations. Integration of these 3 platforms allows detection of genomic alterations at high resolution and investigation of an association between copy number changes and expression.

ResultsGenome-wide copy number and genotype analysis of 10 cervical cancer cell lines by array CGH and SNP array showed highly complex large-scale alterations. A comparison between array CGH and SNP array revealed that the overall concordance in detection of the same areas with copy number alterations CNA was above 90%. The use of SNP arrays demonstrated that about 75% of LOH events would not have been found by methods which screen for copy number changes, such as array CGH, since these were LOH events without CNA. Regions frequently targeted by CNA, as determined by array CGH, such as amplification of 5p and 20q, and loss of 8p were confirmed by fluorescent in situ hybridization FISH. Genome-wide, we did not find a correlation between copy-number and gene expression. At chromosome arm 5p however, 22% of the genes were significantly upregulated in cell lines with amplifications as compared to cell lines without amplifications, as measured by gene expression arrays. For 3 genes, SKP2, ANKH and TRIO, expression differences were confirmed by quantitative real-time PCR qRT-PCR.

ConclusionThis study showed that copy number data retrieved from either array CGH or SNP array are comparable and that the integration of genome-wide LOH, copy number and gene expression is useful for the identification of gene specific targets that could be relevant for the development and progression in cervical cancer.

Electronic supplementary materialThe online version of this article doi:10.1186-1471-2164-8-53 contains supplementary material, which is available to authorized users.

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Author: Judith N Kloth - Jan Oosting - Tom van Wezel - Karoly Szuhai - Jeroen Knijnenburg - Arko Gorter - Gemma G Kenter - Gert 

Source: https://link.springer.com/article/10.1186/1471-2164-8-53







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