The Biometry Core provides advanced molecular diagnostics and informatics/biostatistics support to Program Project members. The major molecular diagnostic effort of the Core will be the provision of DNA microarrays containing customized sets of elements as requested by the Project investigators. The arrays will be used for analysis of DNA copy number (array CGH) and gene expression. The Core will consult with Project investigators on the proper design of arrays, collect and maintain the DNA reagents for the arrays, collect and maintain the DNA reagents for the arrays (BACs for DNA copy number, cDNAs and oligonucleotides for gene expression), and prepare for the DNA solutions for printing. The printing will be performed be the UCSF Cancer Center Microarray facility. The Core will then distribute the arrays to requesters, provide instruction on hybridization, fluorescence imaging and analysis, and on data interpretation. The budget for the Core provides the ability to prepare 1,500 DNA samples for printing each year. (Arrays for large scale analysis of gene expression or whole genome scans for DNA copy number variation will be available directly to the Projects from the UCSF Cancer Center Microarray facility.) The Biometry Core will also select probes for specific loci for use in fluorescence in situ hybridization (FISH) analyses or for the custom array measurements described above. The informatics functions of the Core include adaptation of a template UCSF Cancer Center patient tracking and tissue Database (in Oracle) to the specific needs of the Ovarian Program Project, transfer of the legacy data from the existing Filemaker database, development of data models for array CGH, expression arrays, and tissue arrays, and implementation of Web-based user interfaces and links so that investigators at multiple sites have access to patient and tissue information, and the correlated experimental data. The biostatistics functions of the Core include applying statistical, computational and data visualization methods in order to rigorously identify significant correlations between patient outcome, disease phenotype, and DNA copy number variations, and to test hypothesis about the involvement of expression changes in specific genes in tumor progression and response to therapy. These methods will be available to Project investigators over the Web, and will be tightly integrated with the database system.
Showing the most recent 10 out of 117 publications
