The mission of the Bioinformatics Core (BIC) is to provide bioinformatics support for diverse approaches to cancer research in the COHCCC. The BIC collaborates with COHCCC governance committees to promulgate standards, optimize systems and minimize redundancy through continued integration of data, databases, applications and processes for enabling cost effective, collaborative, translational research. Since the last competitive renewal, the BIC has been working with experts in the field to establish a scalable high performance cyber-infrastructure equipped with close to 500 TB tiered storage repository with high bandwidth network connection, integrated cloud computing with internal TBs shared memory servers with more than 4000 hyper-threaded CPU and GPGPU processors, and external cloud computing to maximize both our infrastructure investment and provide infrastructure-on-demand. In addition, the BIC provides integrated laboratory information management systems (LIMS), which harbor research information portals shared among multiple core facilities (e.g., Functional Genomics and Genomic Sequencing, Drug Discovery and Structural Biology, Analytical Cytometry, Small Animal Imaging, and the developing Proteomics and Translational Research cores). The BIC also provides researchers with high-throughput biological data analysis, including integration with high-quality publicly available multi-disease, multi-cohort gene expression datasets. With highly-trained staff working in multidisciplinary teams, the BIC facilitates experimental design, QC/QA, data analysis, integration, annotation, dissemination, visualization and training for researchers. A new subscription-based chargeback policy was implemented in 2009 to offer tiered services to COHCCC members to be included in their grant proposals for adequate chargeback. The usage has nearly doubled from 45 subscribers in 2008 to 78 in 2010, and chargeback revenue has tripled from $46,487 in 2008 to $141,078 in 2010. Between 2007 and 2011, the BIC was used by a total of 88 principal investigators, 67 of whom are COHCCC members, and BIC staff collectively co-authored 52 peer-reviewed publications. The BIC's ongoing goal is to foster comprehensive bioinformatics support for researchers to enable collaborations among, basic, translational, clinical and population sciences researchers.

Public Health Relevance

The overall goal of the Bioinformatics Core facility is to provide COHCCC investigators with high-throughput biological data analysis tools, data management and cyber-infrastructure, and training to foster collaborations and develop modern computational techniques. This goal enables the Cancer Center's mission of developing innovative new disease-fighting strategies in the battle against cancer.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Center Core Grants (P30)
Project #
5P30CA033572-31
Application #
8764847
Study Section
Subcommittee G - Education (NCI)
Project Start
Project End
Budget Start
2013-12-01
Budget End
2014-11-30
Support Year
31
Fiscal Year
2014
Total Cost
$169,609
Indirect Cost
$68,652
Name
City of Hope/Beckman Research Institute
Department
Type
DUNS #
027176833
City
Duarte
State
CA
Country
United States
Zip Code
91010
Tirughana, Revathiswari; Metz, Marianne Z; Li, Zhongqi et al. (2018) GMP Production and Scale-Up of Adherent Neural Stem Cells with a Quantum Cell Expansion System. Mol Ther Methods Clin Dev 10:48-56
Raz, Dan J; Wu, Geena X; Consunji, Martin et al. (2018) The Effect of Primary Care Physician Knowledge of Lung Cancer Screening Guidelines on Perceptions and Utilization of Low-Dose Computed Tomography. Clin Lung Cancer 19:51-57
Solomon, Ilana; Rybak, Christina; Van Tongeren, Lily et al. (2018) Experience Gained from the Development and Execution of a Multidisciplinary Multi-syndrome Hereditary Colon Cancer Family Conference. J Cancer Educ :
Wang, Dongrui; Aguilar, Brenda; Starr, Renate et al. (2018) Glioblastoma-targeted CD4+ CAR T cells mediate superior antitumor activity. JCI Insight 3:
Cheng, Chun-Ting; Qi, Yue; Wang, Yi-Chang et al. (2018) Arginine starvation kills tumor cells through aspartate exhaustion and mitochondrial dysfunction. Commun Biol 1:178
Cho, H; Ayers, K; DePills, L et al. (2018) Modelling acute myeloid leukaemia in a continuum of differentiation states. Lett Biomath 5:S69-S98
Querfeld, Christiane; Leung, Samantha; Myskowski, Patricia L et al. (2018) Primary T Cells from Cutaneous T-cell Lymphoma Skin Explants Display an Exhausted Immune Checkpoint Profile. Cancer Immunol Res 6:900-909
Liu, Xuxiang; Cao, Minghui; Palomares, Melanie et al. (2018) Metastatic breast cancer cells overexpress and secrete miR-218 to regulate type I collagen deposition by osteoblasts. Breast Cancer Res 20:127
Das, Sadhan; Reddy, Marpadga A; Senapati, Parijat et al. (2018) Diabetes Mellitus-Induced Long Noncoding RNA Dnm3os Regulates Macrophage Functions and Inflammation via Nuclear Mechanisms. Arterioscler Thromb Vasc Biol 38:1806-1820
Al Malki, Monzr M; Nathwani, Nitya; Yang, Dongyun et al. (2018) Melphalan-Based Reduced-Intensity Conditioning is Associated with Favorable Disease Control and Acceptable Toxicities in Patients Older Than 70 with Hematologic Malignancies Undergoing Allogeneic Hematopoietic Stem Cell Transplantation. Biol Blood Marrow Transplant 24:1828-1835

Showing the most recent 10 out of 1396 publications