Development of Oncomine Professional as a Platform for Biopharmaceutical Research

Period of Performance: 05/28/2008 - 01/31/2009


Phase 2 SBIR

Recipient Firm

Compendia Bioscience, Inc.
Ann Arbor, MI 48104
Principal Investigator


DESCRIPTION (provided by applicant): DNA microarray studies, largely sponsored by the NIH and other granting agencies, have generated a wealth of data uncovering the complex gene expression patterns of cancer. Currently however, there is no unifying organizational or bioinformatics resource to integrate the myriad independent observations into a single, global, computable environment. Such a resource would not only provide wide access to data from individual studies, but would also provide an opportunity to apply advanced analysis techniques to the aggregated data. In the absence of such a resource, the majority of cancer molecular profiling data remains severely under-utilized by both the academic cancer research community, and by the pharmaceutical and biotechnology companies who could utilize this data to aid in their efforts to develop new biomarkers and therapies. We propose to develop a commercial-scale solution for cancer molecular profiling research to address this problem. The solution builds upon the prototype of Oncomine developed at the University of Michigan, which utilizes a data pipeline, a data warehouse, an analysis engine, and a web interface to deliver human cancer genomic data in an intuitive platform to scientists and clinicians. The specific aims in Phase I of this proposal are to: 1. Modify the Academic Data Pipeline to Support Commercial Operations. 2. Re-host and re-structure the Oncomine Database. 3. Develop a commercial technical operating model for the Oncomine Web Application. In Phase II of this proposal we will: 1. Develop a controlled cancer genomics data pipeline to support the rapid and proactive collection, standardization and analysis of heterogeneous cancer genomics data from repositories, academic laboratories and pharmaceutical companies. 2. Develop a scalable and secure cancer genomics data warehouse to support the storage and retrieval of public and proprietary data. 3. Develop an optimized user interface to support cancer drug discovery and development. The result of this work will be a fully integrated, end-to-end platform for providing publicly funded research results to the commercial sector, with a goal of utilizing that data to develop new diagnostic and therapeutic approaches for treating cancer. The Oncomine prototype is already broadly accepted in academia, and has been verified as a research tool with high utility by over 10,000+ non-profit users. Since 2006 Compendia has worked to establish the commercial merit of Oncomine; as a result, tens of thousands of valuable high-throughput experiments are now being utilized by several of the world's top pharmaceutical companies. However, additional funding is required to transition Oncomine from an academic tool to a commercial platform, and to realize the full commercial potential of this approach to advance research and save lives.Cancer is a leading cause of mortality, and is responsible for one in every four deaths in the United States. In recent years global gene expression technologies have generated important new information about the molecular mechanisms underlying cancer by revealing specific aberrations in genes, proteins, and signaling pathways. This proposal seeks funding to provide a platform for aggregating, analyzing, and presenting this genomic data to drug development companies, with a goal of optimizing the clinical usefulness of cancer genomic data for drug discovery and development.