Visualization hub for genomics data exploration and translational discovery

项目摘要/摘要 NCI的大型临床试验和研究项目已经在一个 史无前例的速度，阐明了癌症的启动和演变机制，以及对 心理治疗。为了充分利用这一已超过1PB(1015字节)数据的综合数据资源， 科学界需要深入的、用户友好的交互式计算机数据可视化。这些遗嘱 使研究人员能够发现导致每个患者癌症的分子过程，并确定 可能将这种知识转化为新的治疗方法，最终促进我们对癌症的了解 机制和患者结局。 我们建议开发一个基于Web的数据中心和Viz Hub平台，使研究人员能够将 来自单一网络界面的NCI癌症基因组数据的丰富性。可视化将由一个 由生物信息学社区开发并在BioJS中提供的一套“以生物为中心”的观点，这是一个开放的 表示生物数据的工具的源库。这将建立一种新的基于Web的 以可共享和可重用的模块化开源组件的方式开发生物数据可视化。 为了启动Viz Hub平台，我们将把七个流行的第三方生物信息学可视化集成到 使用即插即用框架的现有UCSC Xena浏览器。然后我们将与几家公司密切合作 临床实验室为下一代基因组医学开发两种新的翻译可视化。一 将是一个纵向Omics集成器，使研究人员在钻探时突出显示患者的概况 在整个治疗过程中收集到的基因组和功能数据。另一项将帮助研究人员 调查对各种新型免疫疗法的反应，这些疗法有望给癌症带来革命性的变化 治疗。这个免疫追踪器和免疫编辑查看器将显示免疫原性新抗原，T细胞 受体和B细胞受体随着疾病的进展和治疗的反应而变化。 科学界、NCI基因组数据分析网络和疾病的可视化需求 工作组将通过我们的公共和受限数据中心系统得到充分支持。我们的高中- 性能数据中心将很容易安装在各种计算环境中。用户将成为 能够集成来自大型财团和个人研究人员(包括他们自己的)的公开和受限数据 实验室)，在我们基于网络的Viz Hub上无缝连接。我们对生物信息学社区标准的承诺，例如 GA4GH和BioJS，确保我们的贡献将是可互操作的。我们的设计将接受用户的审查 通过在肿瘤委员会和国际癌症会议的指定展位上进行测试。这将确保 我们的平台将有效地服务于现在和未来的研究人员、生物学家和临床医生 医药。

Project Summary/Abstract Large NCI clinical trials and research projects have been generating data on cancer genomes at an unprecedented rate, elucidating the mechanisms of cancer initiation and evolution, as well as resistance to therapy. To fully utilize this comprehensive data resource, which has exceeded a petabyte (1015 bytes) of data, the scientific community needs deep, user-friendly interactive computer visualizations of the data. These will empower investigators to discover the molecular processes driving each patient's cancer, and to identify potential translations of this knowledge into new therapies, ultimately advancing both our knowledge of cancer mechanisms and patient outcomes. We propose to develop a web-based Data Hub and Viz Hub platform to allow researchers to visualize the richness of the NCI's cancer genomics data from a single web interface. Visualizations will be composed of a set of “bio-centric” views developed by the bioinformatics community and made available in BioJS, an open- source repository of tools to represent biological data. This will establish a new paradigm of web-based biological data visualization development by way of sharable and reusable modular open source components. To initiate the Viz Hub platform, we will integrate seven popular 3rd-party bioinformatics visualizations into the existing UCSC Xena Browser utilizing a plug-and-play framework. We will then work closely with several clinical labs to develop two new translational visualizations for the next generation of genomic medicine. One will be a Longitudinal Omics Integrator, giving researchers a highlighted overview of a patient while drilling down into genomic and functional data collected throughout treatment. Another will help researchers investigate responses to various new types of immunotherapy, which promise to revolutionize cancer treatment. This Immuno-Tracker and Immunoediting Viewer will show how immunogenic neoantigens, T-cell receptors, and B-cell receptors change over disease progression and in response to treatment. The visualization needs of the scientific community, NCI's Genomic Data Analysis Network, and Disease Working groups will be fully supported through our system of public and restricted Data Hubs. Our high- performance Data Hubs will be easy to install on a diverse range of computing environments. Users will be able to integrate public and restricted data, from large consortia and individual researchers (including their own labs), seamlessly on our web-based Viz Hub. Our commitment to bioinformatics community standards, such as GA4GH and BioJS, ensures that our contributions will be interoperable. Our designs will be vetted by users through testing in tumor boards and at designated booths at international cancer meetings. This will ensure that our platform will effectively serve researchers, biologists and clinicians now and into the future of precision medicine.