University of Southern California
USC Norris Comprehensive Cancer Center
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Genomics Core

The Genomics Core performs high throughput analyses of genetic (polymorphism/mutation) and epigenetic variations (DNA methylation) that underlie predisposition and progression to cancer. The Core uses the latest technology to evaluate primarily genetic variations for association studies using single nucleotide polymorphisms (SNPs). SNPs represent the most commonly occurring DNA sequence variations in the human genome and within several years these polymorphisms will be present at a density of 1 every 1-2 kb. A dense set of these markers can be used to identify genetic factors associated with complex disease traits. These analyses can be performed to investigate germline genetic changes giving rise to hereditary or familial cancer and to investigate somatic genetic changes that are hallmarks of clonal expansion in tumors.

In addition, the Core provides methods for evaluating the inheritance of information on the basis of epigenetics. DNA methylation is the only epigenetic mark preserved in genomic DNA isolated from tumors or biopsies. The large number of studies documenting associations between methylation patterns and gene expression suggest that the DNA methylation pattern of a cell may represent a rough blueprint for the expression profile of that cell. In addition, the use of genetically modified rats and mice as models for cancer and tumorigenesis is supported by the Genomics Core by genotyping mouse progeny in conjunction with the Transgenic/Knockout Core to follow genetic markers during mating. The new Core utilizes expertise in epidemiologic/population studies and DNA methylation present within the Cancer Center and provides a cost-effective means of assisting current Cancer Center projects and providing resources for future initiatives.

It is envisioned that future developments in gene chip array technology will be utilized to assess multiple SNPs simultaneously. Analysis of such DNA SNP arrays will be performed by the Microarray Core; however, DNA and template preparations for this purpose will still be performed by the Genomics Core.

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