Document Detail

Leveraging informatics for genetic studies: use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease.
MedLine Citation:
PMID:  20819866     Owner:  NLM     Status:  MEDLINE    
BACKGROUND: There is significant interest in leveraging the electronic medical record (EMR) to conduct genome-wide association studies (GWAS).
METHODS: A biorepository of DNA and plasma was created by recruiting patients referred for non-invasive lower extremity arterial evaluation or stress ECG. Peripheral arterial disease (PAD) was defined as a resting/post-exercise ankle-brachial index (ABI) less than or equal to 0.9, a history of lower extremity revascularization, or having poorly compressible leg arteries. Controls were patients without evidence of PAD. Demographic data and laboratory values were extracted from the EMR. Medication use and smoking status were established by natural language processing of clinical notes. Other risk factors and comorbidities were ascertained based on ICD-9-CM codes, medication use and laboratory data.
RESULTS: Of 1802 patients with an abnormal ABI, 115 had non-atherosclerotic vascular disease such as vasculitis, Buerger's disease, trauma and embolism (phenocopies) based on ICD-9-CM diagnosis codes and were excluded. The PAD cases (66+/-11 years, 64% men) were older than controls (61+/-8 years, 60% men) but had similar geographical distribution and ethnic composition. Among PAD cases, 1444 (85.6%) had an abnormal ABI, 233 (13.8%) had poorly compressible arteries and 10 (0.6%) had a history of lower extremity revascularization. In a random sample of 95 cases and 100 controls, risk factors and comorbidities ascertained from EMR-based algorithms had good concordance compared with manual record review; the precision ranged from 67% to 100% and recall from 84% to 100%.
CONCLUSION: This study demonstrates use of the EMR to ascertain phenocopies, phenotype heterogeneity and relevant covariates to enable a GWAS of PAD. Biorepositories linked to EMR may provide a relatively efficient means of conducting GWAS.
Iftikhar J Kullo; Jin Fan; Jyotishman Pathak; Guergana K Savova; Zeenat Ali; Christopher G Chute
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Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Journal of the American Medical Informatics Association : JAMIA     Volume:  17     ISSN:  1527-974X     ISO Abbreviation:  J Am Med Inform Assoc     Publication Date:    2010 Sep-Oct
Date Detail:
Created Date:  2010-09-07     Completed Date:  2010-11-15     Revised Date:  2014-04-08    
Medline Journal Info:
Nlm Unique ID:  9430800     Medline TA:  J Am Med Inform Assoc     Country:  United States    
Other Details:
Languages:  eng     Pagination:  568-74     Citation Subset:  IM    
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MeSH Terms
Case-Control Studies
Databases, Factual
Electronic Health Records*
Genome-Wide Association Study / methods*
Medical Records
Middle Aged
Natural Language Processing
Peripheral Vascular Diseases / epidemiology,  genetics*
Risk Factors
United States / epidemiology
Grant Support

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine

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