{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,15]],"date-time":"2026-07-15T05:28:14Z","timestamp":1784093294955,"version":"3.55.0"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2384,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,5,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Motivation: Emergence of genetic data coupled to longitudinal electronic medical records (EMRs) offers the possibility of phenome-wide association scans (PheWAS) for disease\u2013gene associations. We propose a novel method to scan phenomic data for genetic associations using International Classification of Disease (ICD9) billing codes, which are available in most EMR systems. We have developed a code translation table to automatically define 776 different disease populations and their controls using prevalent ICD9 codes derived from EMR data. As a proof of concept of this algorithm, we genotyped the first 6005 European\u2013Americans accrued into BioVU, Vanderbilt's DNA biobank, at five single nucleotide polymorphisms (SNPs) with previously reported disease associations: atrial fibrillation, Crohn's disease, carotid artery stenosis, coronary artery disease, multiple sclerosis, systemic lupus erythematosus and rheumatoid arthritis. The PheWAS software generated cases and control populations across all ICD9 code groups for each of these five SNPs, and disease-SNP associations were analyzed. The primary outcome of this study was replication of seven previously known SNP\u2013disease associations for these SNPs.<\/jats:p>\n                  <jats:p>Results: Four of seven known SNP\u2013disease associations using the PheWAS algorithm were replicated with P-values between 2.8 \u00d7 10\u22126 and 0.011. The PheWAS algorithm also identified 19 previously unknown statistical associations between these SNPs and diseases at P &amp;lt; 0.01. This study indicates that PheWAS analysis is a feasible method to investigate SNP\u2013disease associations. Further evaluation is needed to determine the validity of these associations and the appropriate statistical thresholds for clinical significance.<\/jats:p>\n                  <jats:p>Availability:The PheWAS software and code translation table are freely available at http:\/\/knowledgemap.mc.vanderbilt.edu\/research.<\/jats:p>\n                  <jats:p>Contact: \u00a0josh.denny@vanderbilt.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btq126","type":"journal-article","created":{"date-parts":[[2010,3,24]],"date-time":"2010-03-24T22:48:28Z","timestamp":1269470908000},"page":"1205-1210","source":"Crossref","is-referenced-by-count":1106,"title":["PheWAS: demonstrating the feasibility of a phenome-wide scan to discover gene\u2013disease associations"],"prefix":"10.1093","volume":"26","author":[{"given":"Joshua C.","family":"Denny","sequence":"first","affiliation":[{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"},{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marylyn D.","family":"Ritchie","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Melissa A.","family":"Basford","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jill M.","family":"Pulley","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"},{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lisa","family":"Bastarache","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kristin","family":"Brown-Gentry","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Deede","family":"Wang","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan R.","family":"Masys","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dan M.","family":"Roden","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine, Nashville, TN, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dana C.","family":"Crawford","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, 2 Department of Medicine, Vanderbilt University and 3 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