Genomics, Biostatistics and Bioinformatics Core

基因组学、生物统计学和生物信息学核心

• 批准号: 9980279
• 负责人: Shannon K. McWeeney
• 金额: $ 21.24万
• 依托单位: OREGON HEALTH & SCIENCE UNIVERSITY
• 依托单位国家: 美国
• 财政年份: 2017
• 资助国家: 美国
• 起止时间: 2017-08-15 至 2022-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9980279
• 关键词: Back; Bioinformatics; Biometry; CD34 gene; Candidate Disease Gene; Computer software; Cytomegalovirus; DNA Sequencing Facility; Data; Data Security; Data Set; Detection; Development; Dideoxy Chain Termination DNA Sequencing; Ensure; Evaluation; Experimental Designs; Generations; Genes; Genomics; Goals; Hematopoiesis; Hematopoietic stem cells; Human; Infection; Libraries; Life Cycle Stages; Maintenance; Maps; Massive Parallel Sequencing; Metadata; Methodology; Methods; Modeling; Molecular; Multiomic Data; Pathway interactions; Play; Poly A; Preparation; Process; Program Research Project Grants; Protocols documentation; RNA; Reproducibility; Research; Research Design; Research Personnel; Research Project Grants; Resource Sharing; Role; Running; Sampling; Signal Pathway; Signal Transduction; Standardization; Technology; Testing; Time; Transplantation; Validation; Viral; Virus; Virus Latency; Visualization; base; candidate validation; cell growth regulation; data integration; data integrity; data management; differential expression; experimental study; follow-up; genetic signature; mutant; novel; phosphoproteomics; transcriptome sequencing; transcriptomics; validation studies

CORE B PROJECT SUMMARY/ABSTRACT Consistent with the Overall aims of the PPG, the Genomics, Biostatistics and Bioinformatics core (Core B) will play a central role focused on robust identification and prioritization of candidate genes, pathways and gene signatures in order to elucidate how HCMV encoded genes regulate cellular signaling in HPCs to contribute to the establishment and maintenance of viral latency as well as hematopoiesis. Core B will support all five projects and will provide biostatistics and bioinformatics assistance, as well as critical expertise and standardization in sample and library preparation and initial confirmation to aid in prioritization of targets. Core B is responsible for the pre-processing, integration and modeling of the diverse readouts (e.g., transcriptomics, phosphoproteomics, secretomics etc.) generated by each project as well as across projects within the PPG. These data will be incorporated into probabilistic pathway models to provide a rigorous and reproducible framework for hypothesis testing. Follow-up validation and perturbation experiments will aid in the evaluation and refinement of the modeling in an iterative manner. To ensure the data from all PPG research projects will be generated in a standardized manner, the GBBC will play a critical role in facilitating PPG studies, managing and integrating the diverse experimental read-outs, assessing reproducibility and guiding identification of the most promising candidates for validation. The GBBC will regulate consistency and quality of the samples to be sequenced by performing both CD34+ HPC infection experiments with virus mutants generated by the different projects, and subsequent RNA isolations for RNA-seq to allow for cross-comparisons of datasets. This core will assist in prioritization of candidates for further perturbation and validation studies. Finally, the GBBC will provide bioinformatics and biostatistics support for PPG components throughout the “data life cycle” including assistance with experimental design, data pre-processing, QA/QC, analysis, modeling and visualization as well as data integration, storage, management, standards and dissemination for all data types utilized in the PPG.

核心 B 项目摘要/摘要 与 PPG 的总体目标一致，基因组学、生物统计学和生物信息学核心（核心 B）将 发挥核心作用，专注于候选基因、途径和基因的稳健识别和优先排序 特征，以​​阐明 HCMV 编码基因如何调节 HPC 中的细胞信号传导，从而有助于 病毒潜伏期以及造血作用的建立和维持。 Core B 将支持所有五个 项目并将提供生物统计学和生物信息学援助，以及关键的专业知识和 样品和文库制备以及初步确认的标准化有助于确定目标的优先顺序。核 B 负责不同读数的预处理、整合和建模（例如转录组学、 每个项目以及 PPG 内的跨项目生成的（磷酸蛋白质组学、分泌组学等）。 这些数据将被纳入概率路径模型中，以提供严格且可重复的 假设检验的框架。后续验证和扰动实验将有助于评估 并以迭代方式细化建模。确保所有 PPG 研究项目的数据 如果以标准化方式生成，GBBC 将在促进 PPG 研究、管理 并整合不同的实验读数，评估再现性并指导识别 最有希望进行验证的候选者。 GBBC 将规范样品的一致性和质量 通过使用不同病毒产生的病毒突变体进行 CD34+ HPC 感染实验来测序 项目，以及随后用于 RNA-seq 的 RNA 分离，以允许数据集的交叉比较。该核心将 协助确定进一步扰动和验证研究候选者的优先顺序。最后，GBBC 将 在整个“数据生命周期”中为 PPG 组件提供生物信息学和生物统计学支持，包括 协助实验设计、数据预处理、QA/QC、分析、建模和可视化 PPG 中使用的所有数据类型的数据集成、存储、管理、标准和传播。