Leveraging informatics for genetic studies

Use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease

Iftikhar Jan Kullo, Jin Fan, Jyotishman Pathak, Guergana K. Savova, Zeenat Ali, Christopher G. Chute

Research output: Contribution to journalArticle

90 Citations (Scopus)

Abstract

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.

Original languageEnglish (US)
Pages (from-to)568-574
Number of pages7
JournalJournal of the American Medical Informatics Association
Volume17
Issue number5
DOIs
StatePublished - Sep 2010

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Informatics
Electronic Health Records
Genome-Wide Association Study
Peripheral Arterial Disease
Ankle Brachial Index
Lower Extremity
International Classification of Diseases
Comorbidity
Arteries
Natural Language Processing
Thromboangiitis Obliterans
Vasculitis
Embolism
Vascular Diseases
Leg
Electrocardiography
Smoking
Demography
Exercise
Phenotype

ASJC Scopus subject areas

  • Health Informatics
  • Medicine(all)

Cite this

Leveraging informatics for genetic studies : Use of the electronic medical record to enable a genome-wide association study of peripheral arterial disease. / Kullo, Iftikhar Jan; Fan, Jin; Pathak, Jyotishman; Savova, Guergana K.; Ali, Zeenat; Chute, Christopher G.

In: Journal of the American Medical Informatics Association, Vol. 17, No. 5, 09.2010, p. 568-574.

Research output: Contribution to journalArticle

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abstract = "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.",
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