Core F- Bioinformatics and Data Analysis

核心F-生物信息学和数据分析

• 批准号: 7174735
• 负责人: AVITAL CNAAN
• 金额: $ 29.94万
• 依托单位: CHILDREN'S HOSP OF PHILADELPHIA
• 依托单位国家: 美国
• 财政年份: 2006
• 资助国家: 美国
• 起止时间: 2006-02-01 至 2009-01-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7174735
• 关键词: bioinformatics; biomedical facility; cardiogenesis; clinical research; congenital heart disorder; data management; functional /structural genomics; gene expression; human data; statistics /biometry

DESCRIPTION (provided by applicant): The purpose of this Core is to provide state-of-the-art bioinformatics resources, experimental design and analysis expertise, database development and data management support to all projects in the SCCOR. To achieve this purpose, Core F is organized as three complementary functional components: bioinformatics, biostatistical design and analysis, and data management. The first component is bioinformatics. Each project will conduct molecular experiments designed to determine genetic, genomic, and/or functional genomic associations with abnormal cardiac developmental processes. These projects will require efficient integrative technologies for the identification, management, visualization, and analysis of the data generated from these experiments. The bioinformatics staff will take advantage of the fact that there is substantial duplication in the experimental designs among the projects, to achieve data handling efficiencies. For example, several projects propose similar designs from a bioinformatics standpoint involving sample tracking, genotyping, and mutation screening, along with subsequent expression microarray studies in certain cases. This similarity in approach will allow the bioinformatics staff of the Core to design a shared infrastructure and toolkit to optimize interactions and take advantage of economies of scale. The availability of cDNA and oligonucleotide microarrays have made possible the simultaneous acquisition of data on the expression levels of thousands of genes, a fact that accelerates the research process, but presents new challenges in database development, data processing, and visualization. The second functional component is biostatistics, which will involve design and analysis support to investigators in the SCCOR. Most projects have experiments that combine deterministic science as well as experiments with elements of variability in results. For those components of a study where there is variability in the results, appropriate statistical methods need to be employed. For example, Project 1, which is translational in nature, has statistical experimental design considerations in its pre-clinical studies, while Project 3, which is an in-depth cohort study, requires substantial use of regressions analyses, both linear and logistic. Several projects have microarray experiments. While the Cell Culture and DNA Core (Core D) is responsible for conducting these experiments, Core F will be responsible for analyzing the data beyond the imaging phase. Methods for handling microarray data are now much improved, providing greater control and definition of outcomes, and the statistical approaches to both the experimental design of these studies and analyses methods are developing rapidly. The Core's biostatistics staff will focus on determining the most appropriate approaches to these analyses and also will acquire and apply the most up-to-date analysis technology. The biostatisticians of Core F will work closely with Core D on these aspects. The third functional component of Core F is data management, which will include responsibility for all clinical data management. The data management staff of Core F will work closely with the Clinical Core (Core C). Patients will be recruited into all studies within the SCCOR, except Project 1, which is not clinical. Subject enrollment will include both new patients and patients identified from the ongoing SCOR and invited for repeat visits. All clinical data will be collected on case report forms or directly stored for download from instruments by the Clinical Core (Core C). This Core will be responsible for revising and updating the clinical database of the original SCOR to meet the needs of the new SCCOR's scientific agenda, including the development of the ability to receive and manage all relevant information from the previously performed bioinformatics analyses, and clinical data collection. The Core's data management staff also will provide prospective data processing, data management and quality assurance of all new data collected on enrolled subjects.

描述（由申请人提供）： 该核心的目的是为SCCOR中的所有项目提供最先进的生物信息学资源，实验设计和分析专业知识，数据库开发和数据管理支持。为了实现此目的，核心F被组织为三个互补功能组成部分：生物信息学，生物统计学设计和分析以及数据管理。 第一个组件是生物信息学。每个项目将进行旨在确定与心脏异常的遗传，基因组和/或功能性基因组关联的分子实验 发展过程。这些项目将需要有效的集成技术 对这些实验产生的数据的识别，管理，可视化和分析。生物信息学人员将利用这一事实，即项目之间的实验设计有实质性的重复，以实现数据处理效率。例如，几个项目从生物信息学的角度提出了类似的设计，涉及样品跟踪，基因分型和突变筛选，以及在某些情况下随后的表达微阵列研究。这种方法的相似性将使核心的生物信息学人员能够设计共享的基础架构和工具包，以优化交互并利用规模经济。 cDNA和寡核苷酸微阵列的可用性使同时获得了数千个基因表达水平的数据，这一事实加速了研究过程，但在数据库开发，数据处理和可视化中提出了新的挑战。第二个功能成分是生物统计学，它将涉及SCCOR研究人员的设计和分析支持。大多数项目的实验将确定性科学以及实验与结果变异性要素结合在一起。对于研究结果有差异的研究组成部分，需要采用适当的统计方法。例如，项目1， 本质上是翻译的，在其临床前研究中具有统计的实验设计考虑因素，而项目3是一项深入的队列研究，需要大量使用线性和逻辑分析的回归分析。几个项目都有微阵列实验。尽管细胞培养和DNA核心（核心D）负责进行这些实验，但核心F将负责分析成像阶段的数据。现在，用于处理微阵列数据的方法现在得到了很大的改进，提供了对结果的更大控制和定义，并且这些研究的实验设计和分析方法的统计方法正在迅速发展。核心的生物统计学人员将专注于确定这些分析最合适的方法，并将获取和应用最新的分析技术。核心F的生物统计学家将在这些方面与核心D紧密合作。核心F的第三个功能组成部分是数据管理，其中包括对所有临床数据管理的责任。核心F的数据管理人员将与临床核心（核心C）紧密合作。除非临床的项目1，否则患者将被招募到SCCOR内的所有研究中。受试者的入学率将包括新患者和正在进行的SCOR中确定的患者，并邀请重复就诊。所有临床数据将在病例报告表上收集或直接存储通过临床核心（Core C）从工具下载。该核心将负责修改和更新原始SCOR的临床数据库，以满足新SCCOR的科学议程的需求，包括开发从先前执行的生物信息学分析中接收和管理所有相关信息的能力，以及临床数据收集。核心的数据管理人员还将提供所有针对注册受试者收集的新数据的预期数据处理，数据管理和质量保证。