An Integrative Genomics Data Viewer to Support the TCGA Project

项目摘要/摘要： 基因组研究，如癌症基因组图谱(TCGA)项目的研究，是 准备彻底改变我们研究癌症的方式，并绘制出 治疗这种疾病的新疗法。它们需要高吞吐量的产品 以及多种类型的基因组数据的分析。这项工作的关键是有能力 (1)在锚定所有数据类型的同时查看并与其交互 到基因组，并突出重要的关系， (2)处理兆兆字节的数据， (3)平稳快速地从碱基对缩放到全基因组规模，就像 谷歌地图可以从一条街到另一座城市，从一个国家到另一个世界， (4)轻松集成新的数据类型、视图和布局。 目前，没有一种基因组浏览器或其他软件工具能完全满足这一挑战。 该方案的目标是设计和开发一个完整的基因组数据查看器 (IGV)，以满足所有这些关键需求，并使其可用于癌症研究 社区。该提案的具体目标集中在： 目标1.开发一个集成的数据查看器，允许快速、同步 多种数据类型的导航， 目标2.提供数据表示和工具，以确保最大限度地响应 用户与非常大的(TB+)数据集的交互，包括实时 从碱基对到全基因组视图进行缩放和平移， 目标3.软件分发和支持。 我们是TCGA基因组测序中心和TCGA癌症基因组的一部分 角色中心。我们在软件工程方面有丰富的经验， 包括开发和分发5500多名科学家使用的软件 世界范围内。所有这些，加上我们最初的IGV原型，使我们做好了携带 这项提议的目的是什么。项目说明： 我们建议设计和开发一个集成基因组数据查看器(IGV)来支持 TCGA项目。IGV将提供灵活显示多种数据类型和分析的能力 对照基因组坐标的结果，从单碱基对到 全基因组观察并将扩展到数TB的数据集。

Project Summary/Abstract: Genomic studies, such as those for the Cancer Genome Atlas (TCGA) project, are poised to revolutionize the way we approach the study of cancer and chart the way to novel treatment regimens for the disease. They require the high-throughput generation and analysis of multiple types of genomic data. Key to this work is the ability to (1) Simultaneously view and interact with all the data types while anchoring them to the genome and highlighting the important relationships, (2) Handle terabytes of data, (3) Smoothly and rapidly zoom from base-pair to whole-genome scale just as Google Maps can zoom from street to city to country to the world, (4) Easily integrate new data types, views, and layouts. No current genome browser or other software tool fully meets this challenge. The goal of this proposal is to design and develop an Integrative Genomics Data Viewer (IGV) that meets all these key needs and to make it available to the cancer research community. The specific aims of the proposal focus on: Aim 1. Developing an integrative data viewer allowing rapid, simultaneous navigation of multiple data types, Aim 2. Providing data representations and tools to insure maximally responsive user interaction with very large (terabyte+) data sets, including real time zoom and pan from base-pair to whole-genome views, Aim 3. Software distribution and support. We are part of both a TCGA Genome Sequencing Center and TCGA Cancer Genome Characterization Center. We have extensive experience in software engineering, including the development and distribution of software used by over 5500 scientists world-wide. All this, together with our initial IGV prototype, makes us well poised to carry out the aims of this proposal. Project narrative: We propose to design and develop an Integrative Genomics Data Viewer (IGV) to support the TCGA project. The IGV will provide the ability to flexibly display multiple data types and analytic results against genomic coordinates with near-immediate response time from single base-pair to the whole-genome views and will scale to multi-terabyte data sets.