Core--Genome analysis

$0P30FY2002CANIH

University Of California San Francisco, San Francisco CA

Investigators

Linked publications & trials

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Abstract

DESCRIPTION (provided by applicant): Since its inception, the Genome Analysis Core has been performing DNA sequencing, loss of heterozygosity (LOH), linkage, and single strand conformational polymorphism (SSCP) analyses. These services have proved important for detecting and verifying mutations in cancer related genes as a part of several Cancer Center members? projects. LOH and linkage also have been helpful for identifying regions of the genome likely to be involved in the occurrence and progression of several tumor types. In addition, the core has developed considerable expertise in quantitative real-time PCR (Q-PCR). The services provided include DNA copy number measurements and mRNA expression analysis plus training courses for members of the Cancer Center to learn these Q-PCR techniques. These Q-PCR methods were applied toward support of a number of projects, for example: (i) Quantitative microsatellite analysis of DNA from ovarian adenocarcinoma showed that gain of chromosome arm 8q and simultaneous loss of chromosome arm 16q was highly correlated with poor survival, (ii) Quantitative RT-PCR measurements demonstrated that expression of HPV E7 could distinguish between normal and dysplastic cervical cell specimens, (iii) Quantitative microsatellite analysis of DNA from oligodendrogliomas could detect combined loss of chromosome arms 1p and 19q, which indicate high chemosensitivity of such tumors. Another newly developed analysis uses single base extension with fluorescent dideoxynucleotides to provide high throughput SNP analysis. This assay has been applied to mouse specimens as well as human specimens to perform linkage analysis for particular genes as related to cancer resistance or susceptibility. A service to be provided in the near future uses denaturing high-pressure liquid chromatography (dHPLC) to provide an inexpensive alternative to DNA mini-sequencing and will surpass SSCP in mutation detection.

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