Core B: Genomics and Bioinformatics Core

核心 B：基因组学和生物信息学核心

• 批准号: 10584529
• 负责人: Jorge A Di Paola
• 金额: $ 34.3万
• 依托单位: VERSITI WISCONSIN, INC.
• 依托单位国家: 美国
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-03-15 至 2025-02-28
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10584529
• 关键词: Address; Bioinformatics; Biology; Code; Colorado; Communities; Complex; Core Facility; Data; Data Analyses; Data Set; Data Storage and Retrieval; Databases; Dedications; Deposition; Ensure; Epigenetic Process; Experimental Designs; Gene Expression Regulation; Genes; Genetic; Genomics; Goals; Human Resources; Libraries; Link; Manuscripts; Medical; Molecular; Mutation; Outcome; Patients; Phenotype; Policies; Post-Translational Protein Processing; Process; Research; Research Personnel; Sample Size; Sampling; Secure; Statistical Data Interpretation; Text; Translations; United States National Institutes of Health; Universities; Untranslated RNA; Variant; Work; clinical database; data exchange; data sharing; data submission; deep sequencing; design; experimental study; follow-up; genome-wide; genomic data; next generation sequencing; phenotypic data; programs; repository; transcription factor; transcriptome sequencing; user-friendly; von Willebrand Disease; von Willebrand Factor; web site; web-based tool

PROJECT SUMMARY: CORE B The overall theme of this PPG is to further understand the molecular mechanisms of von Willebrand Disease (VWD). Each Project will study unique quantitative and qualitative aspects of von Willebrand factor (VWF) and VWD which will involve many next-generation sequencing (NGS) experiments. Since the sequence data will require extensive computational, bioinformatic and statistical analyses, we have established a Genomics and Bioinformatics Core to serve these critical needs. In addition, this Core will provide a major data-storage and data-sharing function for both this PPG and for investigators worldwide. This Core will have three Specific Aims. Aim 1 will focus on performing all the NGS and analysis for this PPG. The Core personnel will work closely with Project investigators in the design of proposed experiments, and will provide standard analysis of both coding and noncoding sequences for each project. Core B will produce extensive upstream analyses of VWF, RNA seq, genetic and epigenetic genome wide sequences and thorough genomic analyses of patients with low VWF levels but no mutations in VWF. Critical to this application, the Core personnel will also provide data interpretation and additional follow-up data-driven iterative analyses as are often required. This will permit major increase in efficiency by having computational biologists dedicated to this PPG; will offer an iterative approach since analysis of NGS data is complex and experiment driven and will provide consistency regarding analytic approaches. Aim 2 will guarantee data storage, management and transfer. The Genomics and Bioinformatics Core will utilize a newly generated genomic Analytic Platform, which will be exclusive to this application. This platform will be the input conduit and repository for all raw sequencing data and for all NGS analyses in this PPG. All relevant genomic results will be transferred to the Velos clinical database in Core A, where they will be incorporated with phenotype/outcome data to generate a user-friendly interface that enables the simultaneous queries by PPG investigators of phenotype and VWF sequence variants, as well as other genes involved in VWD. Aim 3 will be focused on providing local and public data sharing. We will ensure that raw and analyzed sequencing data are submitted to stable repositories that are accepted by the research community and in accordance with NIH Data Sharing policy. Therefore, a major goal of the Genomics and Bioinformatics Core will be to expand public access to the generated genomic data by interactive public web tools. Within the last year of the PPG we will generate a public web site with a user-friendly interface that enables queries on multiple VWF sequence variants, other genes involved in VWD, and phenotype datasets simultaneously. Ultimately Core B represents a central conduit for genomic and bioinformatics flow of data of this PPG therefore contributing significantly to further understanding the genetics basis of VWD.

项目总结：核心B 本PPG的总体主题是进一步了解血管性血友病的分子机制 （VWD）。每个项目将研究血管性血友病因子（VWF）的独特定量和定性方面， VWD将涉及许多下一代测序（NGS）实验。由于序列数据将 需要广泛的计算，生物信息学和统计分析，我们已经建立了一个基因组学， 生物信息学核心服务于这些关键需求。此外，这一核心将提供一个主要的数据存储， 该PPG和全球研究者的数据共享功能。该核心将有三个具体的 目标。目标1将侧重于执行本PPG的所有NGS和分析。核心人员将在 与项目研究人员密切合作，设计拟议的实验，并将提供标准的分析， 每个项目的编码和非编码序列。岩芯B将产生大量上游分析， VWF、RNA seq、遗传和表观遗传全基因组序列以及对患者的全面基因组分析 VWF水平较低但没有突变对于此应用程序至关重要，核心人员还将提供 数据解释和额外的后续数据驱动的迭代分析，这是经常需要的。这将允许 通过让计算生物学家致力于这一PPG，大大提高了效率;将提供一个迭代的 由于NGS数据的分析是复杂的和实验驱动的， 分析方法。目标2将保证数据的存储、管理和传输。基因组学和 生物信息学核心将利用新生成的基因组分析平台，这将是独家的， 应用程序.该平台将成为所有原始测序数据和所有NGS的输入管道和储存库 分析了这个PPG。所有相关基因组结果将转移至核心A中的Velos临床数据库， 在那里，它们将与表型/结果数据相结合，以生成用户友好的界面， PPG研究者同时询问表型和VWF序列变异体，以及其他 与VWD有关的基因目标3将侧重于提供本地和公共数据共享。我们将确保 原始和分析的测序数据被提交到研究所接受的稳定存储库， 根据NIH数据共享政策。因此，基因组学的一个主要目标， 生物信息学的核心将是通过交互式公共网络扩大公众对生成的基因组数据的访问 工具.在PPG的最后一年内，我们将创建一个具有用户友好界面的公共网站， 允许查询多个VWF序列变体、VWD中涉及的其他基因和表型数据集 同步最终，核心B代表基因组和生物信息学数据流的中心管道， 因此，该PPG对进一步理解VWD的遗传学基础有重要贡献。