Development of Oncomine Professional as a Platform for Biopharmaceutical Research

描述(申请人提供)：主要由美国国立卫生研究院和其他授权机构赞助的DNA微阵列研究产生了大量数据，揭示了癌症的复杂基因表达模式。然而，目前还没有统一的组织或生物信息学资源来将无数独立的观察结果整合到一个单一的、全球的、可计算的环境中。这种资源不仅将提供对个别研究数据的广泛访问，而且还将提供将先进分析技术应用于汇总数据的机会。在缺乏这种资源的情况下，大多数癌症分子图谱数据仍然严重未得到学术癌症研究界以及制药和生物技术公司的充分利用，这些公司可以利用这些数据来帮助他们开发新的生物标记物和疗法。我们建议为癌症分子图谱研究开发一种商业规模的解决方案来解决这个问题。该解决方案建立在密歇根大学开发的Oncomine原型的基础上，该原型利用数据管道、数据仓库、分析引擎和网络界面，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.开发Oncomine Web应用的商业技术运营模型。在这项提议的第二阶段，我们将：1.开发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和主动地收集、标准化和分析异质癌症基因组数据。2.开发可扩展的、安全的癌症基因组数据仓库，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，支持抗癌药物的发现和开发。这项工作的结果将是一个完全整合的端到端平台，用于向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原型已经在学术界得到了广泛的接受，并被10,000多名非营利性用户验证为具有高实用性的研究工具。自2006年以来，Compendia一直致力于确立Oncomine的商业价值；因此，数万项有价值的高通量实验现在正被几家世界顶级制药公司利用。然而，需要额外的资金才能将Oncomine从一个学术工具转变为一个商业平台，并实现这种方法在推进研究和挽救生命方面的全部商业潜力。癌症是主要的死亡原因，在美国每四例死亡中就有一例是癌症造成的。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异常，产生了关于癌症潜在分子机制的重要新信息。这项提案寻求资金，以提供一个平台，用于汇总、分析和向药物开发公司展示这些基因组数据，目标是优化癌症基因组数据对药物发现和开发的临床有用性。

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.