Development of Oncomine Professional as a Platform for Biopharmaceutical Research

描述（申请人提供）：DNA微阵列研究，主要由美国国立卫生研究院和其他授权机构赞助，已经产生了丰富的数据，揭示了复杂的基因表达模式的癌症。然而，目前还没有统一的组织或生物信息学资源来将无数的独立观察整合到一个单一的、全球的、可计算的环境中。这样的资源不仅可以广泛获取个别研究的数据，而且还提供了对汇总数据应用先进分析技术的机会。在缺乏这种资源的情况下，大多数癌症分子谱数据仍然严重未被学术癌症研究界以及制药和生物技术公司利用，这些公司可以利用这些数据来帮助他们开发新的生物标志物和疗法。我们建议开发一种商业规模的癌症分子谱研究解决方案来解决这个问题。该解决方案基于密歇根大学开发的Oncomine原型，该原型利用数据管道、数据仓库、分析引擎和Web界面，以直观的平台向科学家和临床医生提供人类癌症基因组数据。本提案第一阶段的具体目标是：1.修改学术数据管道以支持商业运营。2.重新托管和重组Oncomine数据库。3.为Oncomine Web应用程序开发商业技术操作模型。在第二阶段，我们将：1。开发一个受控的癌症基因组数据管道，以支持从存储库，学术实验室和制药公司快速，主动地收集，标准化和分析异质癌症基因组数据。2.开发一个可扩展和安全的癌症基因组学数据仓库，以支持公共和专有数据的存储和检索。3.开发优化的用户界面，以支持癌症药物的发现和开发。这项工作的结果将是一个完全集成的端到端平台，为商业部门提供公共资助的研究成果，目标是利用这些数据开发治疗癌症的新诊断和治疗方法。Oncomine原型已经被学术界广泛接受，并已被超过10，000名非营利用户验证为具有高实用性的研究工具。自2006年以来，Compendia一直致力于建立Oncomine的商业价值;因此，数以万计的有价值的高通量实验现在正在被几家世界顶级制药公司使用。然而，需要额外的资金将Oncomine从学术工具转变为商业平台，并实现这种方法的全部商业潜力，以推进研究和拯救生命。癌症是死亡的主要原因，在美国，每四例死亡中就有一例是由癌症引起的。近年来，全球基因表达技术通过揭示基因、蛋白质和信号通路中的特定畸变，产生了关于癌症潜在分子机制的重要新信息。该提案旨在为药物开发公司提供一个聚合、分析和展示这些基因组数据的平台，目的是优化癌症基因组数据在药物发现和开发中的临床有用性。

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.