Genomics and Bioinformatics Shared Resource The Genomics and Bioinformatics Shared Resource (GBSR) was created in 2013 by the merging of the Microarray and DNA Sequencing Shared Resources in recognition of the dramatic changes in high-throughput DNA sequencing technologies in the past five years. Kelly A Frazer, PhD was appointed as Director of the new GBSR. Dr. Frazer is an established and highly productive investigator, who has broad expertise in the field of genomics. Additionally, Trey Ideker, PhD, a highly accomplished scientist in the field of Network Analysis, was appointed as co-Director. Under the new leadership, the reconfigured Shared Resource now includes a Bioinformatics Unit, whose services are deemed integral to the performance and analyses and interpretation of the various genomic assays. The current GBSR is a confederation of three units, the Biogem facility under the leadership of Kristen Jepsen, PhD, the VA Microarray and NGS facility under Nicholas Webster, PhD, and a Bioinformatics unit under Olivier Harismendy, PhD. The major objectives of the Genomics and Bioinformatics Shared Resource are to provide Cancer Center investigators with high quality standard, cutting-edge, and custom genomics services and data analyses, as well as consultation on experimental design and training/education about genomic methods and bioinformatics. The specific goals of the GBSR are as follows: 1. To provide expert consultation to MCC membership on experimental designs and analysis approaches of large-scale microarray and NGS datasets. 2. To generate high-throughput sequence data on Next Generation platforms in a cost-effective manner and offer this as a service for the MCC membership. 3. To develop pipelines for performing intermediate analysis of high-throughput sequence data including, DNA variant calling, mRNA isoform calling, miRNA analysis and DNA methylation analysis. 4. To establish the Infrastructure for advanced data analysis including, tumor profiling for DNA somatic mutations, differential expression analysis, as well as network and systems analysis.

Public Health Relevance

The availability of the Genomics and Bioinformatics Shared Resource enables our researchers to identify signal transduction pathways involved in carcinogenesis, new targets for therapeutic intervention, and biomarkers for cancer detection, prognosis, and treatment decision-making.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Center Core Grants (P30)
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Subcommittee G - Education (NCI)
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Shafik, Hasnaa
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University of California San Diego
La Jolla
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