Proposal for the AMP T2D-GENES Data Coordination Center and Web Portal

关于 AMP T2D-GENES 数据协调中心和门户网站的提案

• 批准号: 9337140
• 负责人: JOSE CARLOS FLOREZ
• 金额: $ 17.35万
• 依托单位: BROAD INSTITUTE, INC.
• 依托单位国家: 美国
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-05-01 至 2020-04-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9337140
• 关键词: Base Sequence; Biological; Chromatin; Collaborations; Communication; Communities; Complex; Computer software; Crowding; Data; Data Aggregation; Data Analyses; Data Coordinating Center; Data Quality; Data Set; Databases; Deposition; Development; Diabetic Nephropathy; Diabetic Retinopathy; Discipline; Disease; Educational workshop; Ensure; Feedback; Functional disorder; Future; Gene Expression; Genes; Genetic; Genetic study; Genotype; Goals; Health; Human; Human Genetics; Human Resources; Imagery; Industry; Information Dissemination; Knowledge; Medicine; Meta-Analysis; Methods; Myocardial Infarction; National Institute of Diabetes and Digestive and Kidney Diseases; Non-Insulin-Dependent Diabetes Mellitus; Online Systems; Output; Phenotype; Population; Procedures; Process; Quality Control; Research; Research Design; Research Infrastructure; Research Personnel; Resources; Running; Sampling; Scientist; Series; Services; Sorting - Cell Movement; Statistical Methods; Teleconferences; Text; Therapeutic; Translations; United States National Institutes of Health; Variant; Work; analytical tool; computer infrastructure; data portal; design; diabetes mellitus genetics; empowered; exome; exome sequencing; genetic analysis; genetic variant; genome wide association study; knowledge base; meetings; member; programs; prototype; repository; response; software development; trait; user-friendly; web portal; web site; working group

 DESCRIPTION (provided by applicant): In response to RFA NIDDK RFA-DK-14-503, we propose to develop a public web portal that will aggregate data on human genotypes, phenotypes, and annotations relevant to type 2 diabetes (T2D) and related traits, automate the analysis and interpretation of these data, communicate the results clearly and comprehensively to scientists across biomedical disciplines, and provide an organizational infrastructure for the Accelerating Medicines Partnership in T2D (AMP T2D), a new consortium aiming to empower a wide range of biomedical investigators to use human genetic analysis to accelerate biological understanding and development of new treatments for T2D. As Director of the Data Coordinating Center and Chair of the Steering Committee of the T2D-GENES Consortium, the applicants (Altshuler and Boehnke) have been leaders of the T2D-GENES Consortium, which built a prototype T2D portal that provides access to results and explanations of underlying methods. This prototype includes data on 13,000 exome sequences, 80,000 samples genotyped on the exome array, and meta analyses of 25 genome-wide association studies, allowing users to fetch, filter, sort, and view results from these studies via an intuitive interfae. To expand the portal's data, we will work with the AMP T2D consortium to identify high-quality datasets relevant to T2D, related phenotypes, and functional annotations; develop an administrative and computational infrastructure to collate, store, and manage these datasets; and ensure the data are deposited in this infrastructure. To automate analyses of the data, we will form a group to identify best-practice methods and, where needed, develop new ones; build a software platform to run a series of complex analyses and store their inputs and outputs; and implement these codified statistical methods on the platform. To communicate the results, we will gather user requirements for portal functions; develop a web-based platform and software widgets to facilitate these functions; and design user-friendly queries, visualizations, text, and other features to serve these functions, instantiating them on the portal. To enable collaboration within AMP T2D, we will help define goals for communication and engagement; instantiate standard operating procedures and personnel; and perform administrative functions to support the consortium.

 描述（申请人提供）：作为对RFA NIDDK RFA-DK-14-503的回应，我们建议开发一个公共门户网站，该网站将汇总与2型糖尿病（T2 D）和相关性状相关的人类基因型、表型和注释数据，自动分析和解释这些数据，将结果清晰全面地传达给生物医学学科的科学家，并为T2 D加速药物伙伴关系（AMP T2 D）提供组织基础设施，这是一个新的联盟，旨在使广泛的生物医学研究人员能够使用人类遗传分析来加速T2 D的生物学理解和新疗法的开发。作为数据协调中心主任和T2 D-GENES联盟指导委员会主席，申请人（Altshirt和Boehnke）一直是T2 D-GENES联盟的领导人，该联盟建立了一个原型T2 D门户网站，提供对基础方法的结果和解释的访问。该原型包括13，000个外显子组序列的数据，外显子组阵列上的80，000个样本基因分型，以及25个全基因组关联研究的Meta分析，允许用户通过直观的界面获取，过滤，排序和查看这些研究的结果。为了扩展门户网站的数据，我们将与AMP T2 D联盟合作，识别与T2 D相关的高质量数据集、相关表型和功能注释;开发管理和计算基础设施，以整理、存储和管理这些数据集;并确保数据存储在该基础设施中。为了实现数据分析的自动化，我们将成立一个小组，以确定最佳实践方法，并在需要时开发新的方法;建立一个软件平台，以运行一系列复杂的分析并存储其输入和输出;并在平台上实施这些编码的统计方法。为了传达结果，我们将收集用户对门户功能的需求;开发基于Web的平台和软件小部件来促进这些功能;设计用户友好的查询、可视化、文本和其他功能来服务这些功能，并在门户上实例化它们。为了实现AMP T2 D内部的协作，我们将帮助定义沟通和参与的目标;实施标准操作程序和人员;并执行行政职能以支持联盟。