Interactive Browser-Based Genomics Data Visualization Tools for Translational and Clinical Laboratory Applications
Interactive Browser-Based Genomics Data Visualization Tools for Translational and Clinical Laboratory Applications
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DOI：
10.1016/j.jmoldx.2019.06.005
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发表时间：
2019-11-01
影响因子：
4.1
通讯作者：
Roy, Somak
中科院分区：
文献类型：
--
作者：
Pearce, Thomas M.;Nikiforova, Marina N.;Roy, Somak
可视化驱动的数据探索是解释和发现高通量基因组数据集见解的一种非常有效的模式；然而，它在临床和翻译设置的日常工作流程中被大大低估。我们已经开发了三个开源的，基于浏览器的交互式基因组数据可视化小部件，可以作为直观的独立应用程序或与现有的基于web的实验室信息解决方案集成。这些小部件是使用D3.js库用JavaScript开发的。这些小部件可以在桌面和移动设备上的任何现代web浏览器中运行，以方便访问，但它们是为客户端数据处理而设计的，以解决数据隐私问题。jsProteinMapper绘制了与蛋白质结构域和多个变体数据库相关的感兴趣的变体的位置，协助序列变体的临床解释。jsComut生成一个高度交互式和可定制的计算图，用于对基因组数据集进行视觉探索，并带有临床病理注释，以揭示独特的分子特征和临床相关性。jsCodonWheel是无处不在的环状密码子到氨基酸翻译表的交互式版本，它允许用户快速将核苷酸变化映射到产生的氨基酸差异上。这些开源可视化工具可以改善一些关键的实验室工作流程，这些工作流程涉及在大容量环境中审查大规模基因组学数据集。直观和响应的用户界面，高度可定制的可视化，以及与现有的基于web的实验室软件的轻松集成是这些工具的重要亮点。
Visualization-driven data exploration is a highly effective modality for interpreting and discovering insights from high-throughput genomics data sets; however, it is vastly underutilized in routine workflows in clinical and translation settings. We have developed three open-source, browser-based, interactive genomics data visualization widgets that can be used as intuitive stand-alone applications or integrated with existing web-based laboratory information solutions. The widgets were developed in JavaScript using the D3.js library. These widgets run in any modern web browser across desktop and mobile devices for easy accessibility but are designed for client-side data processing to address data privacy concerns. jsProteinMapper plots the location of a variant of interest relative to the protein domains and multiple variant databases, assisting with clinical interpretation of sequence variants. jsComut generates a highly interactive and customizable comutation plot for visual exploration of genomic data sets with clinicopathologic annotations to reveal unique molecular profiles and clinical correlates. jsCodonWheel is an interactive version of the ubiquitous circular codon-to-amino acid translation table, which lets users quickly map nucleotide changes onto resulting amino acid differences. These open-source visualization tools may improve some of the key Laboratory workflows that involve the review of large-scale genomics data sets in a high-volume setting. The intuitive and responsive user interface, highly customizable visualizations, and easy integration with existing web-based laboratory software are significant highlights of these tools.