Cloud-Based Analysis of TCR Repertoire Sequencing Data

描述(由申请人提供)：我们建议建立一个基于云的平台和网站，用于处理、存储、分析、比较和可视化T细胞受体(TCR)谱系深度测序产生的数据。分析克隆性T细胞亚群的丰度和扩展(由TCR序列确定)填补了在疾病进展期间或在免疫治疗反应中监测免疫系统的未得到满足的诊断需求。虽然有几个小组已经使用下一代测序(NGS)来描述TCR谱系，但由于缺乏生物信息学工具和资源，这种方法和其他NGS方法的广泛采用受到了阻碍(Kahn，2011；Pollack，2011)。对于一般的NGS应用确实存在分析工具，但对于TCR曲目测序等专门应用仍然存在技术差距。GigaGen将TCR曲目测序作为一项服务进行，提供分析工具将使我们相对于其他提供商具有竞争优势，同时总体上拓宽免疫签名分析方法的市场。我们已经开发了一条处理原始测序仪输出的计算管道，但我们看到客户显然需要工具来解释和分析TCR曲目数据。在这一第一阶段拨款中，我们将：(1)扩展我们现有的渠道，以实现NGS数据处理和传输的完全自动化；(2)为用户建立一个网站，以访问和管理他们的数据；以及(3)开发允许用户使用云计算分析复杂数据的算法、工具和工作流。可行性测试将由缺乏计算专业知识或资源的免疫学研究人员通过标准网络浏览器对其数据执行以下操作：(1)跟踪用户指定的跨多个数据集的TCR序列的丰富性和扩展；(2)使用在云中运行的基于重新采样的统计测试比较TCR谱系数据集；以及(3)创建和配置信息量大、出版质量高的数据可视化。我们在第一阶段开发的基础设施将使TCR谱系测序在第二阶段实现广泛的商业化。我们还计划将我们开发的基础设施作为建立公共网站和免疫测序数据存储库的基础，并与教育机构或政府实体共同主办。 公共卫生相关性：新的DNA测序方法有可能彻底改变我们在疾病进展和治疗期间监测患者免疫系统的方式。我们正在构建基于网络的数据处理和分析工具，使临床医生和研究人员能够使用DNA测序数据来更好地了解免疫系统。

DESCRIPTION (provided by applicant): We propose to build a cloud-based platform and website for the processing, storage, analysis, comparison, and visualization of data generated by deep sequencing of the T cell receptor (TCR) repertoire. Profiling the abundance and expansion of clonally T cell subpopulations (as determined by TCR sequence) fills an unmet diagnostic need for monitoring the immune system during disease progression or in response to immunotherapy. Although several groups have used next-generation sequencing (NGS) to profile the TCR repertoire, widespread adoption of this and other NGS methods is hampered by a lack of bioinformatics tools and resources (Kahn, 2011; Pollack, 2011). Analysis tools do exist for generic NGS applications, but a technology gap remains for specialized applications such as TCR repertoire sequencing. GigaGen performs TCR repertoire sequencing as a service, and offering analysis tools would give us a competitive advantage over other providers while broadening the market for immune signature profiling methods in general. We have already developed a computational pipeline to process raw sequencer output, but we see a clear customer need for tools to interpret and analyze TCR repertoire data. In this Phase I grant, we will: (1) expand our existing pipeline to fully automate NGS data processing and transfer; (2) build a website for users to access and manage their data; and (3) develop algorithms, tools, and workflows that allow users to analyze complex data using cloud computing. The test of feasibility will be for immunology researchers with little computational expertise or resources to perform the following operations on their data through a standard web browser: (1) track abundance and expansion of user-specified TCR sequences across multiple data sets; (2) compare TCR repertoire data sets using resampling-based statistical tests that run in the cloud; and (3) create and configure informative, publication-quality data visualizations. The infrastructure we develop in Phase I will enable broad commercialization of TCR repertoire sequencing in Phase II. We also plan to use the infrastructure we develop as the basis for building a public website and repository for immune sequencing data, to be co-hosted with an educational institution or government entity. PUBLIC HEALTH RELEVANCE: New DNA sequencing methods have the potential to revolutionize how we monitor a patient's immune system during disease progression and treatment. We are building web-based data processing and analysis tools that allow clinicians and researchers to use DNA sequencing data to better understand the immune system.