title: Identifying associations between genomic alterations in tumors.
abstract: Single-nucleotide polymorphism (SNP) mapping arrays are a reliable method for identifying somatic copy number alterations in cancer samples. Though this is immensely useful to identify potential driver genes, it is not sufficient to identify genes acting in a concerted manner. In cancer cells, co-amplified genes have been shown to provide synergistic effects, and genomic alterations targeting a pathway have been shown to occur in a mutually exclusive manner. We therefore developed a bioinformatic method for detecting such gene pairs using an integrated analysis of genomic copy number and gene expression data. This approach allowed us to identify a gene pair that is co-amplified and co-expressed in high-grade serous ovarian cancer. This finding provided information about the interaction of specific genetic events that contribute to the development and progression of this disease.
authors.affiliation: Cancer Genetics and Genomics Laboratory, Peter MacCallum Cancer Centre, East Melbourne, VIC, Australia.
authors.forename: Joshy
authors.initials: J
authors.lastname: George
authors.forename: Kylie L
authors.initials: KL
authors.lastname: Gorringe
authors.forename: Gordon K
authors.initials: GK
authors.lastname: Smyth
authors.forename: David D L
authors.initials: DD
authors.lastname: Bowtell
mesh_terms: D019295:Computational Biology / Q000379:methods*; D005260:Female; D018628:Gene Dosage; D015972:Gene Expression Regulation, Neoplastic; D023281:Genomics; D006801:Humans; D019656:Loss of Heterozygosity / Q000235:genetics; D053858:Metabolic Networks and Pathways; D010051:Ovarian Neoplasms / Q000235:genetics* / Q000473:pathology; D020641:Polymorphism, Single Nucleotide / Q000235:genetics