GENOME ANALYSIS

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The Genome Analysis Core provides services and advice for DNA sequencing, genotyping, and gene expression analysis. The DNA sequencing services are instrumental in helping scientists determine causative mutations in the germline or somatic genes which lead to certain cancers or human diseases. DNA sequencing services are also used to interrogate the methylation status of genes. Loss of heterozygosity (LOH) and genetic linkage analyses are used for identifying regions of the genome likely to be involved in the occurrence and progression of malignancies. The Core has extensive experience performing micrbsatellite and single base extension SNP genotyping on the 3700 platform, and TaqMan allelic discrimination SNP typing on the 7900HT platform for these purposes. The sequencing capability is also used to determine whether there are exon-sized deletions in one allele of a cancer susceptibility gene once it has been determined that there are no point mutations. For these studies, the sequencer is used to analyze fluorescent fragments generated by the Multiplex Amplifiable Probe Hybridization (MAPH) or Multiplex Ligation-dependent Probe Amplification (MLPA), and Spectratyping techniques. A major focus of the Core's services is the use of quantitative real-time PCR (Q-PCR) on the 7900HT platform. Using an arsenal of TaqMan assays, the Core provides services for DNA copy number measurements and mRNA expression analyses, plus training courses for members of the Cancer Center to learn Q-PCR techniques. The Cancer Center Genome Analysis Core works to improve access of Cancer Center member to genetic and genomic technologies. The services from we offer, or propose to develop, are actively coordinated with the other UCSF genomics core facilities to avoid detrimental duplication of capacity. For example, Cancer Center members have access to extensive high throughput gene expression and genotyping technology (Affymetrix and Illumina) through core facilities at the Parnassus and Mission Bay campuses of UCSF.