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. © Springer Science+Business Media, New York 2013.
CITATION STYLE
George, J., Gorringe, K. L., Smyth, G. K., & Bowtell, D. D. L. (2013). Identifying associations between genomic alterations in tumors. Methods in Molecular Biology, 1049, 9–19. https://doi.org/10.1007/978-1-62703-547-7_2
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