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

William S. Bush, Jonathan Boston, Sarah A. Pendergrass, Logan Dumitrescu, Robert Goodloe, Kristin Brown-Gentry, Sarah Wilson, Bob McClellan, Eric Torstenson, Melissa A. Basford, Kylee L. Spencer, Marylyn D. Ritchie, Dana C. Crawford

Research output: Contribution to journalConference article

11 Scopus citations

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 metaanalysis 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.

Original languageEnglish (US)
Pages (from-to)373-384
Number of pages12
JournalPacific Symposium on Biocomputing
StatePublished - Jan 1 2013
Event18th Pacific Symposium on Biocomputing, PSB 2013 - Kohala Coast, United States
Duration: Jan 3 2013Jan 7 2013

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Computational Theory and Mathematics

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    Bush, W. S., Boston, J., Pendergrass, S. A., Dumitrescu, L., Goodloe, R., Brown-Gentry, K., Wilson, S., McClellan, B., Torstenson, E., Basford, M. A., Spencer, K. L., Ritchie, M. D., & Crawford, D. C. (2013). 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. Pacific Symposium on Biocomputing, 373-384.