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 #
6R01LM010685-06
Application #
9302039
Study Section
Biomedical Library and Informatics Review Committee (BLR)
Project Start
2010-04-01
Project End
2018-08-31
Budget Start
2016-04-30
Budget End
2016-08-31
Support Year
6
Fiscal Year
2015
Total Cost
Indirect Cost
Name
Vanderbilt University Medical Center
Department
Type
DUNS #
079917897
City
Nashville
State
TN
Country
United States
Zip Code
37232
Rhoades, Seth D; Bastarache, Lisa; Denny, Joshua C et al. (2018) Pulling the covers in electronic health records for an association study with self-reported sleep behaviors. Chronobiol Int 35:1702-1712
Barnado, April; Carroll, Robert J; Casey, Carolyn et al. (2018) Phenome-wide association study identifies marked increased in burden of comorbidities in African Americans with systemic lupus erythematosus. Arthritis Res Ther 20:69
Bastarache, Lisa; Hughey, Jacob J; Hebbring, Scott et al. (2018) Phenotype risk scores identify patients with unrecognized Mendelian disease patterns. Science 359:1233-1239
Robinson, Jamie R; Denny, Joshua C; Roden, Dan M et al. (2018) Genome-wide and Phenome-wide Approaches to Understand Variable Drug Actions in Electronic Health Records. Clin Transl Sci 11:112-122
Zhao, Junfei; Cheng, Feixiong; Jia, Peilin et al. (2018) An integrative functional genomics framework for effective identification of novel regulatory variants in genome-phenome studies. Genome Med 10:7
Mosley, Jonathan D; Feng, QiPing; Wells, Quinn S et al. (2018) A study paradigm integrating prospective epidemiologic cohorts and electronic health records to identify disease biomarkers. Nat Commun 9:3522
Bloodworth, Melissa H; Rusznak, Mark; Bastarache, Lisa et al. (2018) Association of ST2 polymorphisms with atopy, asthma, and leukemia. J Allergy Clin Immunol 142:991-993.e3
Denny, Joshua C; Van Driest, Sara L; Wei, Wei-Qi et al. (2018) The Influence of Big (Clinical) Data and Genomics on Precision Medicine and Drug Development. Clin Pharmacol Ther 103:409-418
Dahir, Kathryn M; Tilden, Daniel R; Warner, Jeremy L et al. (2018) Rare Variants in the Gene ALPL That Cause Hypophosphatasia Are Strongly Associated With Ovarian and Uterine Disorders. J Clin Endocrinol Metab 103:2234-2243
Barnado, A; Carroll, R J; Casey, C et al. (2018) Phenome-wide association study identifies dsDNA as a driver of major organ involvement in systemic lupus erythematosus. Lupus :961203318815577

Showing the most recent 10 out of 76 publications