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 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。为了实现这一目的，Core F 被组织为三个互补的功能组件：生物信息学、生物统计设计和分析以及数据管理。 第一个组成部分是生物信息学。每个项目将进行分子实验，旨在确定遗传、基因组和/或功能基因组与异常心脏的关联 发展过程。这些项目将需要高效的集成技术 识别、管理、可视化和分析这些实验生成的数据。生物信息学工作人员将利用项目之间实验设计存在大量重复的事实来实现数据处理效率。例如，几个项目从生物信息学的角度提出了类似的设计，涉及样本跟踪、基因分型和突变筛选，以及某些情况下的后续表达微阵列研究。这种方法的相似性将使核心的生物信息学工作人员能够设计一个共享的基础设施和工具包，以优化交互并利用规模经济。 cDNA 和寡核苷酸微阵列的出现使得同时采集数千个基因表达水平的数据成为可能，这一事实加速了研究进程，但也给数据库开发、数据处理和可视化带来了新的挑战。第二个功能部分是生物统计学，它将为 SCCOR 的研究人员提供设计和分析支持。大多数项目的实验都结合了确定性科学以及结果可变因素的实验。对于结果存在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， 本质上是转化性的，在临床前研究中考虑了统计实验设计，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回归分析。几个项目有微阵列实验。细胞培养和 DNA 核心 (Core D) 负责进行这些实验，而 Core F 将负责分析成像阶段之外的数据。处理微阵列数据的方法现已得到很大改进，可以更好地控制和定义结果，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。核心的生物统计人员将专注于确定最合适的分析方法，并将获取和应用最新的分析技术。 Core F 的生物统计学家将与 Core D 在这些方面密切合作。 Core F 的第三个功能组件是数据管理，其中包括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）密切合作。 SCCOR 内的所有研究都将招募患者，但项目 1 除外，该项目不是临床研究。受试者登记将包括新患者和从正在进行的 SCOR 中确定并邀请重复访问的患者。所有临床数据将收集在病例报告表中或直接存储以供临床核心（核心 C）从仪器中下载。该核心将负责修订和更新原始 SCOR 的临床数据库，以满足新 SCCOR 科学议程的需求，包括开发接收和管理来自先前进行的生物信息学分析和临床数据的所有相关信息的能力收藏。核心的数据管理人员还将为登记受试者收集的所有新数据提供前瞻性数据处理、数据管理和质量保证。