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BUSH WILLIAMS, BOSTON JONATHAN, PENDERGRASS SARAHA, DUMITRESCU LOGAN, GOODLOE ROBERT, BROWN-GENTRY KRISTIN, WILSON SARAH, MCCLELLAN BOB, TORSTENSON ERIC, BASFORD MELISSAA, SPENCER KYLEEL, RITCHIE MARYLYND, CRAWFORD DANAC. Enabling high-throughput genotype-phenotype associations in the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) project as part of the Population Architecture using Genomics and Epidemiology (PAGE) study. Pac Symp Biocomput 2013:373-84. [PMID: 23424142 PMCID: PMC3579641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Genetic association studies have rapidly become a major tool for identifying the genetic basis of common human diseases. The advent of cost-effective genotyping coupled with large collections of samples linked to clinical outcomes and quantitative traits now make it possible to systematically characterize genotype-phenotype relationships in diverse populations and extensive datasets. To capitalize on these advancements, the Epidemiologic Architecture for Genes Linked to Environment (EAGLE) project, as part of the collaborative Population Architecture using Genomics and Epidemiology (PAGE) study, accesses two collections: the National Health and Nutrition Examination Surveys (NHANES) and BioVU, Vanderbilt University's biorepository linked to de-identified electronic medical records. We describe herein the workflows for accessing and using the epidemiologic (NHANES) and clinical (BioVU) collections, where each workflow has been customized to reflect the content and data access limitations of each respective source. We also describe the process by which these data are generated, standardized, and shared for meta-analysis among the PAGE study sites. As a specific example of the use of BioVU, we describe the data mining efforts to define cases and controls for genetic association studies of common cancers in PAGE. Collectively, the efforts described here are a generalized outline for many of the successful approaches that can be used in the era of high-throughput genotype-phenotype associations for moving biomedical discovery forward to new frontiers of data generation and analysis.
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Affiliation(s)
- WILLIAM S. BUSH
- Department of Biomedical Informatics, Center for Human Genetics Research, Vanderbilt University, 2215 Garland, Avenue, 519 Light Hall, Nashville, TN 37232, USA
| | - JONATHAN BOSTON
- Center for Human Genetics Research, Vanderbilt University, 1207 17 Avenue, Suite 300, Nashville, TN 37232, USA
| | - SARAH A. PENDERGRASS
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, 503 Wartik Lab, University Park, PA 16802, USA
| | - LOGAN DUMITRESCU
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, 2215 Garland Avenue, 519 Light Hall, Nashville, TN 37232, USA
| | - ROBERT GOODLOE
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, 2215 Garland Avenue, 519 Light Hall, Nashville, TN 37232, USA
| | - KRISTIN BROWN-GENTRY
- Center for Human Genetics Research, Vanderbilt University, 1207 17Avenue, Suite 300, Nashville, TN 37232, USA
| | - SARAH WILSON
- Center for Human Genetics Research, Vanderbilt University, 1207 17Avenue, Suite 300, Nashville, TN 37232, USA
| | - BOB MCCLELLAN
- Center for Human Genetics Research, Vanderbilt University, 1207 17Avenue, Suite 300, Nashville, TN 37232, USA
| | - ERIC TORSTENSON
- Center for Human Genetics Research, Vanderbilt University, 2215 Garland Avenue, 519 Light Hall, Nashville, TN 37232, USA
| | - MELISSA A. BASFORD
- Office of Research, Office of Personalized Medicine, Vanderbilt University, 2525 West End Avenue, Nashville, TN 37203, USA
| | - KYLEE L. SPENCER
- Biology and Environmental Science, Heidelberg University, Bareis Hall 131, 310 East Market Street, Tiffin, OH 44883, USA
| | - MARYLYN D. RITCHIE
- Center for System Genomics, Department of Biochemistry and Molecular Biology,, Pennsylvania State University, 512 Wartik Lab, University Park, PA 16802, USA
| | - DANA C. CRAWFORD
- Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, 2215 Garland Avenue, 519 Light Hall, Nashville, TN 37232, USA
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