%0 Journal Article
%T CDCOCA: A statistical method to define complexity dependence of co-occuring chromosomal aberrations
%A Nitin Kumar
%A Hubert Rehrauer
%A Haoyang Cai
%A Michael Baudis
%J BMC Medical Genomics
%D 2011
%I BioMed Central
%R 10.1186/1755-8794-4-21
%X We hypothesize that in cancer some linkage-independent CNA may display a non-random co-occurrence, and that these CNA could be of pathogenetic relevance for the respective cancer. We also hypothesize that the statistical relevance of co-occurring CNA may depend on the sample specific CNA complexity. We verify our hypotheses with a simulation based algorithm CDCOCA (complexity dependence of co-occurring chromosomal aberrations).Application of CDCOCA to example data sets identified co-occurring CNA from low complex background which otherwise went unnoticed. Identification of cancer associated genes in these co-occurring changes can provide insights of cooperative genes involved in oncogenesis.We have developed a method to detect associations of regional copy number abnormalities in cancer data. Along with finding statistically relevant CNA co-occurrences, our algorithm points towards a generally low specificity for co-occurrence of regional imbalances in CNA rich samples, which may have negative impact on pathway modeling approaches relying on frequent CNA events.Genetic alterations are an absolute requirement for malignant neoplasias in humans [1,2]. Both kind of genetic alterations and order of occurrence are important for cancer development and progression [3]. Additionally to sequential event models, large scale analysis of genomes from patient's tumors have shown that multiple genetic abnormalities can promote the development of one cancer entity [4]. Alterations in cancer genome can range from subtle sequence changes (e.g. point mutations) over structural alterations with functional impact on the coding sequence (e.g. generation of fusion genes by chromosomal translocations) to regional or whole-chromosome copy number abnormalities (see e.g. [5-7]).Through a gene dosage effect, genomic copy number alterations (CNA) may lead to insufficient expression of tumor suppressors or overexpression of proto-oncogenes, respectively. Recurrent CNA have been identified in ne
%U http://www.biomedcentral.com/1755-8794/4/21