Global Infrastructure for Collaborative High-throughput Cancer Genomics Analysis

协作高通量癌症基因组分析的全球基础设施

• 批准号: 9211085
• 负责人: GAD A GETZ
• 金额: $ 96.27万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2016
• 资助国家: 美国
• 起止时间: 2016-09-20 至 2021-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9211085
• 关键词: Address; Algorithms; Attention; Bioinformatics; Biological; Biomedical Research; Categories; Classification; Clinic; Clinical; Clinical Data; Clinical Trials; Code; Collaborations; Communities; Complex; Consensus; Correlative Study; Custom; Data; Data Aggregation; Data Analyses; Data Set; Databases; Deposition; Development; Diagnostic; Documentation; Ensure; Evolution; Freezing; Future; General Population; Genome Data Analysis Center; Genome Data Analysis Network; Genomic Data Commons; Goals; Institutes; Knowledge; Learning; Left; Link; Malignant Neoplasms; Manuscripts; Mission; Modeling; Molecular; Morphologic artifacts; National Cancer Institute; Oncogenes; Paper; Pathway Analysis; Patient-Focused Outcomes; Patients; Phase; Process; Production; Publications; Publishing; Reporting; Reproducibility; Research Infrastructure; Research Personnel; Running; Sampling; Science; Scientist; Services; Structure; Suggestion; Summary Reports; System; The Cancer Genome Atlas; Time; TimeLine; Tumor Subtype; Update; Vertebral column; Work; Writing; abstracting; base; cancer genome; cancer genomics; clinically relevant; cost; disorder subtype; experience; genome analysis; high standard; improved; innovation; insight; member; molecular subtypes; operation; prevent; repository; research study; tool; treatment response; user-friendly; whole genome; working group

Abstract The Cancer Genome Atlas (TCGA) set the standards for large-scale cancer genome projects worldwide. In the next phase, the National Cancer Institute and its Center for Cancer Genomics are planning large-scale projects closely tied to clinical questions and trials. In order to perform the analysis of these data, the NCI is creating a Genome Data Analysis Network (GDAN) of different types of Genome Data Analysis Centers (GDACs). Central to this Network is a single Processing GDAC, which will take all the harmonized data, as stored in the NCI's Genomics Data Commons, and perform higher level integrated analyses on these data to support both the Analysis Working Groups (AWGs) within the Network (which will be formed for each project to perform special analyses of the data and write manuscripts) as well as the entire biomedical research community. Herein we propose to build the centralized Processing GDAC on top of our FireCloud platform, an infrastructure to run large scale computation on the cloud in a fully rigorous and reproducible fashion. FireCloud development was based on our experience with Firehose, the Broad internal platform on which the standard TCGA data and analyses currently run. We propose to create and operate the GDAN Standard Workflow, incorporating tools actively developed and used within the GDAN and across the entire field, with particular emphasis on clinical tools. This Workflow will serve as the starting point for AWGs and set the highest standards of transparency, reproducibility and rigor for cancer genome analysis. The results of the Standard Workflow will be stored in a public database, and accessible via standard APIs, and used together with a continuously updated database of prior knowledge to create scientific reports that will be made available to the community, in a pre-publication manner. Finally, a major innovation is that AWG members will be able to login into FireCloud and rerun the entire workflow, or parts of it, with their own parameters and subsets of the data – thus making the entire GDAN analysis fully reproducible and scalable. Our goals are therefore: (1) To create a global infrastructure for collaborative extreme- scale cancer analysis; (2) Operate the Standard Workflows at scale; (3) Rapidly and continuously evolve the Standard Workflows; and (4) created improved capabilities for reporting, exploring the results, clinical diagnostics and reproducibility.

抽象的 癌症基因组图集（TCGA）设定了大规模癌症基因组的标准 全球项目。在下一个阶段，国家癌症研究所及其中心 癌症基因组学计划与临床问题紧密相关的大规模项目和 试验。为了对这些数据进行分析，NCI正在创建基因组数据 不同类型的基因组数据分析中心（GDAC）的分析网络（GDAN）。 该网络的核心是单个处理GDAC，它将采用所有协调 数据存储在NCI的基因组数据共享中，并执行更高级别的集成 对这些数据进行分析，以支持两个分析工作组（AWG） 网络（将为每个项目组成，以执行数据的特殊分析和 写手稿）以及整个生物医学研究界。 在此，我们建议在我们的Firecloud上构建集中的加工GDAC 平台，一个完全严格的基础架构，可以在云上运行大规模计算 和可重现的时尚。 FireCloud开发是根据我们在 Firehose，标准TCGA数据和分析的广泛内部平台 目前运行。我们建议创建和操作GDAN标准工作流程， 将积极开发和使用的工具合并在GDAN和整个中 领域，特别着重于临床工具。此工作流将作为起始 AWG的观点，并设定了最高的透明度，繁殖和严格的标准 癌症基因组分析。标准工作流的结果将存储在公众中 数据库，可通过标准API访问，并与连续 更新的先验知识数据库，以创建科学报告 向社区出版前的方式。最后，一个主要的创新是AWG 成员将能够登录FireCloud并重新运行整个工作流程，或者部分的一部分 凭借其自己的数据和数据子集 - 从而使整个GDAN分析 完全可重现和可扩展。 因此，我们的目标是：（1）为协作极端建立全球基础架构 - 比例癌分析； （2）大规模操作标准工作流； （3）迅速和 不断发展标准工作流； （4）创造了改进的功能 报告结果，探索结果，临床诊断和可重复性。