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.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
2P30CA023100-28
Application #
8934944
Study Section
Subcommittee G - Education (NCI)
Program Officer
Shafik, Hasnaa
Project Start
2014-07-21
Project End
2019-04-30
Budget Start
2014-07-21
Budget End
2015-04-30
Support Year
28
Fiscal Year
2014
Total Cost
$447,838
Indirect Cost
$156,033
Name
University of California San Diego
Department
Type
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Sen, Supriya; Langiewicz, Magda; Jumaa, Hassan et al. (2015) Deletion of serine/arginine-rich splicing factor 3 in hepatocytes predisposes to hepatocellular carcinoma in mice. Hepatology 61:171-83
Hoffmann, Hanne M; Tamrazian, Anika; Xie, Huimin et al. (2014) Heterozygous deletion of ventral anterior homeobox (vax1) causes subfertility in mice. Endocrinology 155:4043-53
Hartman, Lisa L R; Crawford, John R; Makale, Milan T et al. (2014) Pediatric phase II trials of poly-ICLC in the management of newly diagnosed and recurrent brain tumors. J Pediatr Hematol Oncol 36:451-7
Williams, Richard T; Barnhill, Lisa M; Kuo, Huan-Hsien et al. (2014) Chimeras of p14ARF and p16: functional hybrids with the ability to arrest growth. PLoS One 9:e88219
Huang, Carlos P; Fofana, Mariama; Chan, Jefferson et al. (2014) Copper transporter 2 regulates intracellular copper and sensitivity to cisplatin. Metallomics 6:654-61
Paolini, Paul; Pick, Daniel; Lapira, Jennifer et al. (2014) Developmental and extracellular matrix-remodeling processes in rosiglitazone-exposed neonatal rat cardiomyocytes. Pharmacogenomics 15:759-74
Goellner, Eva M; Smith, Catherine E; Campbell, Christopher S et al. (2014) PCNA and Msh2-Msh6 activate an Mlh1-Pms1 endonuclease pathway required for Exo1-independent mismatch repair. Mol Cell 55:291-304
Glidewell-Kenney, Christine A; Trang, Crystal; Shao, Paul P et al. (2014) Neurokinin B induces c-fos transcription via protein kinase C and activation of serum response factor and Elk-1 in immortalized GnRH neurons. Endocrinology 155:3909-19
Jiang, P; Mukthavaram, R; Chao, Y et al. (2014) In vitro and in vivo anticancer effects of mevalonate pathway modulation on human cancer cells. Br J Cancer 111:1562-71
Jacques, Bonnie E; Montgomery 4th, William H; Uribe, Phillip M et al. (2014) The role of Wnt/*-catenin signaling in proliferation and regeneration of the developing basilar papilla and lateral line. Dev Neurobiol 74:438-56

Showing the most recent 10 out of 359 publications