Developing the JBrowse Genome Browser to Visualize Structural Variants and Cancer Genomics Data

开发 JBrowse 基因组浏览器以可视化结构变异和癌症基因组数据

• 批准号: 9390007
• 负责人: Ian H Holmes
• 金额: $ 70.03万
• 依托单位: UNIVERSITY OF CALIFORNIA BERKELEY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-01 至 2021-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9390007
• 关键词: Animal Model; Area; Back; Chromosomes; Client; Communities; Computer software; DNA; DNA sequencing; Data; Data Set; Databases; Education and Outreach; Educational workshop; Funding; Galaxy; Gene Expression Regulation; Gene Fusion; Genes; Genetic Transcription; Genome; Genomic Data Commons; Human; Human Genome; Image; Imagery; Individual; Informatics; International; Internet; Intuition; Language; Malignant Neoplasms; Mutation; Online Systems; Organism; Population; Research Personnel; Resources; Rest; Running; Scientist; Side; Slice; Source; Structure; Synteny; System; Techniques; Technology; Tissues; Training; Validation; Variant; Visualization software; base; cancer genome; cancer genomics; carcinogenesis; data portal; duplicate genes; functional genomics; genome analysis; genome annotation; genome browser; genomic data; genomic tools; human reference genome; indexing; insertion/deletion mutation; insight; interest; navigation aid; outreach; prototype; reference genome; tool; transcriptome sequencing; tumor; whole genome

Cancer begins with mutations of the genome that can include substitutions, indels, duplications, gene fusions, and genome rearrangements. These mutational signatures vary widely between tissues and, often, between individual tumors. To understand this mutational landscape, cancer researchers need tools for visualizing the structural variation in cancer DNA, and its impact on gene transcription and regulation. For greater insight, these data should be augmented with gene annotations, results from functional genomics project like ENCODE, and population-level data. The classic tool for visualizing human gene annotations is the web-based genome browser. However, genome browsers are not generally well-suited to visualizing large-scale structural variation: for that, circular visualization tools (such as Circos) are often used, but those tools are not very interactive (or web-based). Additionally, few genome browsers allow analysis to be performed within the application itself. JBrowse is the most popular genome browser built using JavaScript and dynamic web technology. Originally aimed at model organism genome projects, it is the web-based browser predominantly used by such projects, and yet its single largest user is now the UK-based Cancer Genome Project. We have developed prototypes of an interactive circular view for JBrowse, a data loading pipeline to import human genome annotations, a framework for running interactive analyses from within the browser. We plan to extend these prototypes to a fully-fledged system for visualizing structural variants and other mutations in cancer genomes, and running analyses on those data. We will integrate this software with the systems of the Cancer Genome Project, the International Cancer Genome Consortium, and the Genomic Data Commons.

癌症始于基因组突变，包括替换、插入缺失、 重复、基因融合和基因组重排。这些突变特征 组织之间、个体肿瘤之间的差异很大。要了解这一点 突变景观，癌症研究人员需要工具来可视化结构 癌症 DNA 的变异及其对基因转录和调控的影响。为了更大 洞察力，这些数据应该通过基因注释、功能结果来增强 基因组学项目（如 ENCODE）和人口水平数据。 可视化人类基因注释的经典工具是基于网络的基因组 浏览器。然而，基因组浏览器通常不太适合可视化 大规模的结构变化：为此，圆形可视化工具（例如 Circos） 经常使用，但这些工具的交互性不强（或基于网络）。此外，很少有 基因组浏览器允许在应用程序本身内执行分析。 JBrowse 是使用 JavaScript 和动态 Web 构建的最流行的基因组浏览器 技术。它最初针对模式生物基因组项目，是基于网络的 此类项目主要使用的浏览器，但其最大的用户现在是 英国癌症基因组计划。我们开发了一个交互式的原型 JBrowse 的圆形视图，一个用于导入人类基因组注释的数据加载管道， 用于在浏览器内运行交互式分析的框架。我们计划延长 这些原型是一个成熟的系统，用于可视化结构变体和其他 癌症基因组的突变，并对这些数据进行分析。我们将整合 该软件与癌症基因组计划、国际癌症研究中心的系统相结合 基因组联盟和基因组数据共享。