We continueWe have successfully maintained and expanded our Discover web-based tools, with emphasis on CellMiner. Our CellMiner NCI-60 Analysis Tools section is providing a significant resource for pharmacogenomic integration, research, and discovery. It is currently the host for five tools, all of which are designed to reduce the time required by the scientist to integrate molecular and pharmacological data. Within the last year, four substaintial upgrades have been made, i) Gene DNA copy number signatures, ii) Genetic variant summation signatures, iii)Graphical output for DNA: Exome sequencing, and iv) Genetic variant versus drug visualization. Two new databases for the NCI-60 have been introduced, for DNA copy number from array comparative genomic hybridization hybridization, and exome sequencing of all genes. The CellMiner data and tools are creating major opportunities for progress in rational drug discovery, application, and individualization of therapy for cancer patients. As molecular alterations of many types can contribute to the outcome of therapy, the Genomic and Bioinformatics Group (GBG) manages and integrate molecular and pharmacological data in such a way that enhances understanding, and facilitates the generation of testable hypotheses in the context of pharmacology. The GBG thus provides access to high throughput data, in addition to providing software resources that facilitate the understanding, mining and exploitation of these data. Using our expertise in molecular biology, molecular pharmacology, biostatistics, bioinformatics, and computer science, we continue to generated public databases, and software to query and mine those data. The drug database is continuously expanded by the DTP, including new drugs entering clinical trials. The NCI-60 is by far the most comprehensively profiled panel of mammalian cells anywhere. Currently our Discover and CellMiner sites have thousands of individual users from 73 countries per month. It has in the past and currently continues to lead to translational discoveries.

Agency
National Institute of Health (NIH)
Institute
National Cancer Institute (NCI)
Type
Scientific Cores Intramural Research (ZIC)
Project #
1ZICBC011475-03
Application #
9154337
Study Section
Project Start
Project End
Budget Start
Budget End
Support Year
3
Fiscal Year
2015
Total Cost
Indirect Cost
Name
Basic Sciences
Department
Type
DUNS #
City
State
Country
Zip Code
Luna, Augustin; Rajapakse, Vinodh N; Sousa, Fabricio G et al. (2016) rcellminer: exploring molecular profiles and drug response of the NCI-60 cell lines in R. Bioinformatics 32:1272-4
Reinhold, William C; Sunshine, Margot; Varma, Sudhir et al. (2015) Using CellMiner 1.6 for Systems Pharmacology and Genomic Analysis of the NCI-60. Clin Cancer Res 21:3841-52
Reinhold, William C; Varma, Sudhir; Rajapakse, Vinodh N et al. (2015) Using drug response data to identify molecular effectors, and molecular ""omic"" data to identify candidate drugs in cancer. Hum Genet 134:3-11
Varma, Sudhir; Pommier, Yves; Sunshine, Margot et al. (2014) High resolution copy number variation data in the NCI-60 cancer cell lines from whole genome microarrays accessible through CellMiner. PLoS One 9:e92047
Reinhold, William C; Varma, Sudhir; Sousa, Fabricio et al. (2014) NCI-60 whole exome sequencing and pharmacological CellMiner analyses. PLoS One 9:e101670
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Reinhold, William C; Sunshine, Margot; Liu, Hongfang et al. (2012) CellMiner: a web-based suite of genomic and pharmacologic tools to explore transcript and drug patterns in the NCI-60 cell line set. Cancer Res 72:3499-511