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: 9294071
• 负责人: JOSE CARLOS FLOREZ
• 金额: $ 263.33万
• 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/9294071
• 关键词: Base Sequence; Biological; Chromatin; Collaborations; Communication; Communities; Complex Analysis; Computer software; 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; Human; Human Genetics; Human Resources; Imagery; Industry; Information Dissemination; Intuition; 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; Statistical Methods; Teleconferences; Text; Therapeutic; Translations; United States National Institutes of Health; Variant; Work; analytical tool; computer infrastructure; crowdsourcing; data portal; data sharing; database of Genotypes and Phenotypes; design; diabetes mellitus genetics; exome; genetic analysis; genetic variant; genome wide association study; knowledge base; meetings; member; phenotypic data; programs; prototype; public health relevance; 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.