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

 描述(由申请人提供)：针对RFA NIDDK RFA-DK-14-503，我们建议开发一个公共门户网站，收集与2型糖尿病(T2D)和相关特征相关的人类基因型、表型和注释的数据，自动化这些数据的分析和解释，将结果清楚和全面地传达给跨生物医学学科的科学家，并为T2D加速药物伙伴关系(AMP T2D)提供组织基础设施，AMP T2D是一个新的联盟，旨在授权广泛的生物医学研究人员使用人类基因分析来促进对T2D的生物学理解和新疗法的开发。作为数据协调中心主任和T2D基因联盟指导委员会主席，申请者(Altshuler和Boehnke)一直是T2D基因联盟的领导人，该联盟建立了一个原型T2D门户，提供对潜在方法的结果和解释。这个原型包括13,000个外显子组序列的数据，80,000个外显子组阵列上的基因分型样本，以及25个全基因组关联研究的荟萃分析，允许用户通过直观的界面获取、筛选、分类和查看这些研究的结果。为了扩展门户的数据，我们将与AMP T2D联盟合作，确定与T2D、相关表型和功能注释相关的高质量数据集；开发行政和计算基础设施来整理、存储和管理这些数据集；并确保数据存储在此基础设施中。为了使数据分析自动化，我们将成立一个小组，以确定最佳做法方法，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；并在该平台上实施这些编码化的统计方法。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；并设计用户友好的查询、可视化、文本和其他功能来提供这些功能，并在门户上实例化它们。为了在AMP T2D内实现协作，我们将帮助定义沟通和参与的目标；实例化标准操作程序和人员；并执行行政职能以支持财团。

 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.