) The Genetics/Genomics Core is organized to provide both consultation and state-of-the-art technologies and data interpretation in genomics and bioinformatics. Core scientists interact with CCC researchers at the design phase of projects and assist in incorporating genomics approaches by a) generation of preliminary data, b) writing methodologies, c) high throughput implementation of technology, and d) data mining in public and proprietary databases. The Core supports research investigating genetic elements responsible for cancer susceptibility and genetic factors involved in neoplastic initiation and progression. Existing Core technologies include: 1) high-throughput DNA sequencing and genotyping (ABI 3700); 2) real-time quantitative PCR for mRNA and/or DNA (ABI 7700); 3) high-volume microsatellite-repeat genotyping (ABI 377s) and SNP analysis (ABI TaqMan7700); 4) rapid, inexpensive 96-well-based polymorphism/mutation hunting with HPLC heteroduplexing (WAVE); 5) 24-fluor color SKY painting of chromosomes; 6) FISH gene mapping to chromosomes; 7) Comparative Genome Hybridization (CGH); and 8) high throughput robotic assistance in picking and arraying clones, growing large library collections, and general liquid handling; 9) single cell micromanipulation and molecular/cytogenetics; and 10) gene expression profiling using in-house microprinted glass microarrays of the entire (up-to-date UNIGENE) human and rat EST collections. The facility is Certified by federal (CLIA-88), state (DoH), and professional societies (ASHG and CAP) for data integrity. Bioinformatics is a critical component of any genomics and proteomics facility and the Core operates, in partnership with PE-Informatics, software for a) sample acquisition and tracking, correlation with clinical information, work assignment, clone/plate management and raw data reporting (SQL*LIMS & SQL*GT); b) data mining tools (extensive software); and c) systems microarray and sequence analysis (GeneKeeper) and sophisticated publish/subscribe/share capability throughout the CCC (BioMerge). The Core has onsite, a 40-gigabite database of sequence data accessible with these software tools, a UNIX based SGI supercomputer and multiple SUN workstations linked to researchers via a GigaPoP fiber backbone. Bioinformatics personnel include an OS system manager, Oracle databasers, application specialists, and technology-specific project managers.
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