STTR Phase I: Development of a high-performance clinical genomics analysis platform to support precision medicine

这个小型企业技术转移（STTR）项目的更广泛的影响/商业潜力是研究开发一种新的临床基因组软件分析平台的可行性，该平台可能有助于减少或消除与基因检测相关的一些最重大的挑战。在美国，基因组学在包括癌症、心脏病、中风、糖尿病和阿尔茨海默病在内的10种主要死亡原因中的9种中起着重要作用。因此，基因检测的发展非常迅速，同时也面临着规模、性能、成本和质量方面的一些相关挑战。基因组医学和基因检测是精准医学的关键基础，可能有助于改善诊断、治疗，甚至预防复杂疾病和失调。这项可行性研究的目标是开发一种先进的分析软件平台，以解决分析瓶颈，并最终提高治疗时间。团队将根据原型关键技术和方法来确定可行性，以解决当前状态的限制，并指出改进的未来状态方法。该研究将与实际的临床基因组学用户密切合作，为目标市场和最终用户提供明确而引人注目的好处，并为快速增长的细分市场提供高价值的解决方案。这个STTR第一阶段的项目提出了一个新的基因组软件分析平台的设计和原型。它将包括访问大型生物信息学应用程序工作平台，并在可扩展的基于公共云的、符合hipaa的计算基础设施上运行性能优化的临床分析工作流程。该平台将按照软件即服务模式开发，旨在优化下一代测序（NGS）分析的性能和成本。该项目将需要开发先进的专有计算算法来并行执行分析任务，并创建高度优化的基因组学分析工作流程。与当前状态的方法相比，这些工作流程将大大节省时间并降低成本。项目工作还将侧重于开发复杂的资源配置逻辑，以利用在公共云基础设施上运行的规模和成本优化。此外，该项目将包括开发一个用于研发和临床使用的双重用途平台的可行性，以更快地进行测试，并采用更新和先进的工具和程序。这项技术将以更快的速度、更高的质量和更低的成本提供结果，从而有助于改善病人的护理。此外，用户将能够构建和验证满足HIPAA， CLIA-CAP和其他临床需求的自定义分析工作流。

The broader impact/commercial potential of this Small Business Technology Transfer (STTR) project is to investigate the feasibility of developing a novel clinical genomics software analysis platform that may help reduce or eliminate some of the most significant challenges associated with genetic testing. In the US, genomics plays a role in 9 of the 10 leading causes of death including cancer, heart disease, stroke, diabetes, and Alzheimer's disease. As such, genetic testing is growing very rapidly, as are some of the associated challenges of scale, performance, cost and quality. Genomic medicine and genetic testing are key underpinnings of precision medicine, which may help lead to improved diagnosis, treatment, and even prevention of complex diseases and disorders. This feasibility study targets the development of an advanced analysis software platform to address analysis bottlenecks and ultimately improve time-to-treatment. The team will determine feasibility based on prototyping key technologies and methods to address current state limitations and point towards an improved future-state approach. The study will be done in close collaboration with actual clinical genomics users to deliver clear and compelling benefits to the target market and end-users and to provide a high-value solution to the rapidly growing market segment.This STTR Phase I project proposes to design and prototype a novel genomics software analysis platform. It will include access to a large work bench of bioinformatics applications and performance optimized clinical analysis workflows running on scalable public cloud-based, HIPAA-compliant computing infrastructure. The platform will be developed following the software-as-a-service model, designed to optimize performance and costs for next generation sequencing (NGS) analysis. The project will entail development of advanced proprietary computational algorithms to parallelize execution of analysis tasks, and the creation of highly optimized genomics analysis workflows. These workflows will result in dramatic time-savings as well as reduced costs compared to current state approaches. Project efforts also will focus on the development of sophisticated resource provisioning logic to exploit scale and cost optimization running on public cloud infrastructure. In addition, the project will include the feasibility of developing a dual-purpose platform for R&D and clinical usage for faster testing and adoption of newer and advanced tools and procedures. The technology will help to improve patient care by delivering results substantially faster, with higher quality and at lower cost. Additionally, users will be able to construct and validate custom analysis workflows that meet HIPAA, CLIA-CAP, and other clinical requirements.