Genomic Acquisition and Analysis (GAA)

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ABSTRACT: GASP CORE Genetic studies have provided clear evidence that virtually all human traits studied in biomedical research, including disease susceptibility, treatment responses, relapses and side effects, are influenced by genetic makeup. It is, therefore, essential to incorporate genetic information in medical research and practice to achieve optimal outcome. As genetic information is encoded in genomic DNA, to understand the genetic architecture of a disease or trait, or to dissect the genetic makeup of an individual, we have to conduct DNA sequencing of the genome of that individual. In this personalized medicine focused COBRE application, we intend to integrate and disseminate genetic and genomic data, and apply them to personalize health issues proposed by individual projects. The genome analysis and sequencing pipeline (GASP) core is designed to support individual projects by providing services for DNA/RNA sequencing, data integration, dissemination and analyses. Since bioinformatics and biostatistics have become a critical component in genomic and genetic studies, the core will also provide expertise and services to support each project to accomplish its goals. The specific aims of the core are: 1. To conduct genomic experiments to acquire data required by each individual project. These experiments could be the sequencing of exome/whole genome, or enriched portion of genome (methylation or targeted genes/pathways), genotyping of specified genetic variants or profiling of gene expression. 2. To provide bioinformatics support for individual projects. This service includes data quality control, the establishment of analytic and annotation pipelines and the generation of analysis-ready data sets for downstream analyses. 3. To provide genetic analysis service to individual projects. These services include the identification, annotation and characterization of genetic variants, evaluation of genetic risks, and genetic association analyses. 4. To assist and coordinate other omics services required by individual projects. Project 3 will analyze blood samples for protein components and metabolites. We do not have sufficient resource in this COBRE to conduct these proteomics and metabolomics analyses. Other projects and pilot studies may need other omics services as well. Therefore, we propose to coordinate with the project leaders and help them to find appropriate vendors for these services.