Open Access Research article

A large scale survey reveals that chromosomal copy-number alterations significantly affect gene modules involved in cancer initiation and progression

Eva Alloza1, Fátima Al-Shahrour12, Juan C Cigudosa34 and Joaquín Dopazo135*

Author Affiliations

1 Department of Bioinformatics and Genomics, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain

2 Broad Institute, 7 Cambridge Center, Cambridge, MA 02142, USA

3 CIBER de Enfermedades Raras (CIBERER), ISCIII, CIPF, Valencia, Spain

4 Molecular Cytogenetics Group. Centro Nacional de Investigaciones Oncologicas (CNIO), Madrid, Spain

5 Functional Genomics Node (INB), CIPF, Valencia, Spain

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BMC Medical Genomics 2011, 4:37  doi:10.1186/1755-8794-4-37

Published: 6 May 2011



Recent observations point towards the existence of a large number of neighborhoods composed of functionally-related gene modules that lie together in the genome. This local component in the distribution of the functionality across chromosomes is probably affecting the own chromosomal architecture by limiting the possibilities in which genes can be arranged and distributed across the genome. As a direct consequence of this fact it is therefore presumable that diseases such as cancer, harboring DNA copy number alterations (CNAs), will have a symptomatology strongly dependent on modules of functionally-related genes rather than on a unique "important" gene.


We carried out a systematic analysis of more than 140,000 observations of CNAs in cancers and searched by enrichments in gene functional modules associated to high frequencies of loss or gains.


The analysis of CNAs in cancers clearly demonstrates the existence of a significant pattern of loss of gene modules functionally related to cancer initiation and progression along with the amplification of modules of genes related to unspecific defense against xenobiotics (probably chemotherapeutical agents). With the extension of this analysis to an Array-CGH dataset (glioblastomas) from The Cancer Genome Atlas we demonstrate the validity of this approach to investigate the functional impact of CNAs.


The presented results indicate promising clinical and therapeutic implications. Our findings also directly point out to the necessity of adopting a function-centric, rather a gene-centric, view in the understanding of phenotypes or diseases harboring CNAs.