Visualization of (Epi)Genomic Data for Discovery of Disease-Associated Variants

(Epi)基因组数据可视化以发现疾病相关变异

基本信息

  • 批准号:
    8633263
  • 负责人:
  • 金额:
    $ 8.86万
  • 依托单位:
  • 依托单位国家:
    美国
  • 项目类别:
  • 财政年份:
    2014
  • 资助国家:
    美国
  • 起止时间:
    2014-01-01 至 2015-12-31
  • 项目状态:
    已结题

项目摘要

DESCRIPTION (provided by applicant): This proposal combines an extensive mentored training program for the PI with a research project that aims to develop novel approaches for visualization and exploration that will accelerate the identification and validation of disease-associated variants in large and complex genomics and epigenomics data sets. An increasing number of such variants are discovered in studies that generate and analyze a wide range of molecular data types for thousands of patients or samples. This progress is enabled by the availability of computational analysis pipelines that employ sophisticated statistical methods for next-generation sequencing (NGS) data. Interpretation of analysis results by biological and clinical domain experts, however, is emerging as a major bottle- neck due to the amount and complexity of the pipeline outputs. To address this, we propose to develop inter- active visualization methods and a web-based infrastructure that will enable domain experts to identify disease-associated variants in large (epi)genomic data sets through visual exploration of computational predictions and the underlying data. This will have a significant impact on the rate at which predictions can be verified, interpreted and translated into clinically actionable finding. Our first priority is the design of methods and tools to visualize (epi) genomic data in a range of different contexts, for instance by grouping and representing features based on their function, chromatin state, transcriptional activity or genomic coordinates. We will also develop new non-linear genome representations to compare structural variants across genomes, complementing the functionality of the highly successful genome browsers. We then investigate how information external to the primary data - for instance from other studies, drug target or biomarker databases - can be applied to guide investigators through the data set. Finally, we implement a web-based exploration system for biological and clinical domain an expert that combines our interactive visualizations with large-scale public (epi) genomic data sets. The methods and tools developed under this proposal will be generally applicable and driving biological examples are chosen from The Cancer Genome Atlas (TCGA) and the Encyclopedia of DNA Elements (ENCODE and modENCODE).
描述(由申请人提供):该提案将针对PI的广泛指导培训计划与一个研究项目相结合,该项目旨在开发可视化和探索的新方法,以加速在大型和复杂的基因组学和表观基因组学数据集中识别和验证与疾病相关的变异。在为数千名患者或样本生成和分析广泛的分子数据类型的研究中,发现了越来越多的此类变异。这一进展得益于计算分析管道的可用性,这些管道使用复杂的统计方法来处理下一代测序(NGS)数据。然而,由于管道输出的数量和复杂性,生物和临床领域专家对分析结果的解释正成为一个主要瓶颈。为了解决这个问题,我们建议开发交互式可视化方法和基于网络的基础设施,使领域专家能够通过对计算预测和基础数据的可视探索,在大型(EPI)基因组数据集中识别与疾病相关的变异。这将对验证、解释预测并将其转化为临床上可操作的发现的速度产生重大影响。我们的首要任务是设计方法和工具来可视化(Epi)一系列 不同的背景,例如通过基于其功能、染色质状态、转录活性或基因组坐标对特征进行分组和表示。我们还将开发新的非线性基因组表示,以比较基因组中的结构变异,补充非常成功的基因组浏览器的功能。然后,我们调查初级数据之外的信息--例如来自其他研究、药物靶标或生物标记物数据库的信息--如何应用于指导调查人员通过数据集。最后,我们实现了一个基于Web的生物和临床领域的探索系统,专家将我们的交互式可视化与大规模公共(EPI)基因组数据集相结合。根据这一提议开发的方法和工具将普遍适用,并从癌症基因组图谱(TCGA)和DNA元素百科全书(ENCODE和modENCODE)中选择具有推动作用的生物学例子。

项目成果

期刊论文数量(0)
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Nils Gehlenborg其他文献

Nils Gehlenborg的其他文献

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{{ truncateString('Nils Gehlenborg', 18)}}的其他基金

Data Exploration and Visualization Tools for HuBMAP and a Human Reference Atlas
HuBMAP 和人类参考图集的数据探索和可视化工具
  • 批准号:
    10886906
  • 财政年份:
    2023
  • 资助金额:
    $ 8.86万
  • 项目类别:
Data Exploration and Visualization Tools for HuBMAP and a Human Reference Atlas
HuBMAP 和人类参考图集的数据探索和可视化工具
  • 批准号:
    10534328
  • 财政年份:
    2022
  • 资助金额:
    $ 8.86万
  • 项目类别:
Grammar-Driven Genomic Data Visualization
语法驱动的基因组数据可视化
  • 批准号:
    10452031
  • 财政年份:
    2022
  • 资助金额:
    $ 8.86万
  • 项目类别:
Grammar-Driven Genomic Data Visualization
语法驱动的基因组数据可视化
  • 批准号:
    10646478
  • 财政年份:
    2022
  • 资助金额:
    $ 8.86万
  • 项目类别:
HuBMAP HIVE Tools Component
HuBMAP HIVE 工具组件
  • 批准号:
    10396856
  • 财政年份:
    2021
  • 资助金额:
    $ 8.86万
  • 项目类别:
Integrative Visualization of Spatiotemporal Tumor Atlases
时空肿瘤图谱的综合可视化
  • 批准号:
    10293808
  • 财政年份:
    2021
  • 资助金额:
    $ 8.86万
  • 项目类别:
HuBMAP HIVE Tools Component
HuBMAP HIVE 工具组件
  • 批准号:
    9988042
  • 财政年份:
    2019
  • 资助金额:
    $ 8.86万
  • 项目类别:
HuBMAP HIVE Tools Component Supplement
HuBMAP HIVE 工具组件补充
  • 批准号:
    9919980
  • 财政年份:
    2019
  • 资助金额:
    $ 8.86万
  • 项目类别:
Visualization of (Epi)Genomic Data for Discovery of Disease-Associated Variants
(Epi)基因组数据可视化以发现疾病相关变异
  • 批准号:
    9128459
  • 财政年份:
    2015
  • 资助金额:
    $ 8.86万
  • 项目类别:
Visualization of (Epi)Genomic Data for Discovery of Disease-Associated Variants
(Epi)基因组数据可视化以发现疾病相关变异
  • 批准号:
    9123773
  • 财政年份:
    2015
  • 资助金额:
    $ 8.86万
  • 项目类别:

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