Genomic medicine offers hope for improved diagnostic methods and for more effective, patient-specific therapies. Genome-wide associated studies (GWAS) elucidate genetic markers that improve clinical understanding of risks and mechanisms for many diseases and conditions and that may ultimately guide diagnosis and therapy on a patient-specific basis. This project will expand on existing work to identify gene-phenotype associations across the genome and phenome, deploying new phenome-wide associations study (PheWAS) methods to deeply investigate electronic medical record (EMR)-derived phenotypes across common and rare variants across the genome. The project is enabled by large DNA biobanks coupled to de-identified copies of EMR. This project has three specific aims. First, we will expand the PheWAS phenotype library to include both binary traits and continuous variables incorporating about 7000 phenotypes derived from natural language processing, laboratory data, and report data.
The second aim i s to perform a PheWAS for common and rare variants using extant genome-wide and exome variant data and the broader set of phenotypes derived in Aim 1. We will analyze associations using single variant and multi-variant aggregation methods. We will validate the efficacy of our methods in Aim 2 by comparing to known associations.
The third aim i s to develop a standards-based infrastructure to share PheWAS results and develop tools to enable others to perform PheWAS. The tools generated from this project will not only expand the capabilities of the current PheWAS methodology, but will also broadly enable clinical research and subsequent genetic studies.

Public Health Relevance

Genomic medicine offers hope for improved diagnosis and for more effective, patient- specific therapies. This PheWAS proposal will develop new methods to identify detailed phenotypes and diseases from electronic medical records and then find novel genetic associations from existing genomic data.

Agency
National Institute of Health (NIH)
Institute
National Library of Medicine (NLM)
Type
Research Project (R01)
Project #
2R01LM010685-04
Application #
8816305
Study Section
Biomedical Library and Informatics Review Committee (BLR)
Program Officer
Ye, Jane
Project Start
2010-04-01
Project End
2018-08-31
Budget Start
2014-09-01
Budget End
2015-08-31
Support Year
4
Fiscal Year
2014
Total Cost
Indirect Cost
Name
Vanderbilt University Medical Center
Department
Internal Medicine/Medicine
Type
Schools of Medicine
DUNS #
City
Nashville
State
TN
Country
United States
Zip Code
37212
Mosley, Jonathan D; van Driest, Sara L; Wells, Quinn S et al. (2016) Defining a Contemporary Ischemic Heart Disease Genetic Risk Profile Using Historical Data. Circ Cardiovasc Genet 9:521-530
Wei, Wei-Qi; Teixeira, Pedro L; Mo, Huan et al. (2016) Combining billing codes, clinical notes, and medications from electronic health records provides superior phenotyping performance. J Am Med Inform Assoc 23:e20-7
Doss, Jayanth; Mo, Huan; Carroll, Robert J et al. (2016) Phenome-Wide Association Study of Rheumatoid Arthritis Subgroups Identifies Association between Seronegative Disease and Fibromyalgia. Arthritis Rheumatol :
Claar, Dru D; Larkin, Emma K; Bastarache, Lisa et al. (2016) A Phenome-Wide Association Study Identifies a Novel Asthma Risk Locus Near TERC. Am J Respir Crit Care Med 193:98-100
Heatherly, Raymond; Rasmussen, Luke V; Peissig, Peggy L et al. (2016) A multi-institution evaluation of clinical profile anonymization. J Am Med Inform Assoc 23:e131-7
Simonti, Corinne N; Vernot, Benjamin; Bastarache, Lisa et al. (2016) The phenotypic legacy of admixture between modern humans and Neandertals. Science 351:737-41
Mosley, Jonathan D; Witte, John S; Larkin, Emma K et al. (2016) Identifying genetically driven clinical phenotypes using linear mixed models. Nat Commun 7:11433
Li, Haiquan; Achour, Ikbel; Bastarache, Lisa et al. (2016) Integrative genomics analyses unveil downstream biological effectors of disease-specific polymorphisms buried in intergenic regions. NPJ Genom Med 1:
Wang, Xusheng; Pandey, Ashutosh K; Mulligan, Megan K et al. (2016) Joint mouse-human phenome-wide association to test gene function and disease risk. Nat Commun 7:10464
Mosley, Jonathan D; Brittain, Evan L; Loyd, James E et al. (2015) Letter by Mosley Regarding Article, ""Iron Homeostasis and Pulmonary Hypertension: Iron Deficiency Leads to Pulmonary Vascular Remodeling in the Rat"". Circ Res 117:e56-7

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