The Genomics Core Laboratory offers high throughput analyses of genetic (polymorphisms) and epigenetic (methylation) variations in genomic DMA. It came into existence in 1999 primarily to serve the cancer epidemiology community of the Cancer Center who wanted to expand into the analysis """"""""genetic"""""""" variations within their large epidemiology studies and at present serves 16 federally funded members of the Cancer Center. Predisposition to cancer in most cases can be viewed as complex and it is thought that mutations that lead to such a phenotype occur in multiple genes. In addition, many more loci contribute to, or modify expression of the disease phenotype in quantitative ways. The Genomics Core Laboratory provides Cancer Center members with high throughput DMA extraction/isolation from blood and tissue sources, analyses of established SNPs and deletion polymorphisms, analyses of microsatellite polymorphisms, analyses of DMA methylation, and DMA variant detection/identification. A major new expansion of service include the capability to detect SNPs by three genotyping platforms: ABI TaqMan for single SNP analysis, ABI SNPlex for multiplex analysis up to 48 SNPs, and Illumina BeadArray reader and GoldenGate assay methodology for multiplex analysis of up to 1536 SNPs. The Illumina system was purchased ($1.25 million) by the provost of USC as an institutional commitment for this type of work. A further expansion of services is DNA methylation analysis performed utilizing MethyLight (developed at USC) and bisulfite DNA sequencing. Major discoveries from this work include the discoveries of significant gene/environment (gene-diet) interactions in a variety of cancer sites as well as the ability to comprehensively hapmap selected loci.
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