Core F- Bioinformatics and Data Analysis

Childrens Hospital Of Philadelphia, Philadelphia PA

Investigators

Linked publications & trials

Abstract

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.