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Defining disease phenotypes using national linked electronic health records: a case study of atrial fibrillation.

Morley KI, Wallace J, Denaxas SC, Hunter RJ, Patel RS, Perel P, Shah AD, Timmis AD, Schilling RJ, Hemingway H - PLoS ONE (2014)

Bottom Line: The proportion of cases identified from each source differed by diagnosis age; inferred diagnoses contributed a greater proportion of younger cases (≤ 60 years), while older patients (≥ 80 years) were mainly diagnosed in SC.Associations of risk factors (hypertension, myocardial infarction, heart failure) with incident AF defined using different EHR sources were comparable in magnitude to those from traditional consented cohorts.A single EHR source is not sufficient to identify all patients, nor will it provide a representative sample.

View Article: PubMed Central - PubMed

Affiliation: Farr Institute of Health Informatics Research, University College London, London, United Kingdom, and Clinical Epidemiology, Department of Epidemiology and Public Health, University College London, London, United Kingdom; Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; Melbourne School of Global and Population Health, The University of Melbourne, Melbourne, Australia.

ABSTRACT

Background: National electronic health records (EHR) are increasingly used for research but identifying disease cases is challenging due to differences in information captured between sources (e.g. primary and secondary care). Our objective was to provide a transparent, reproducible model for integrating these data using atrial fibrillation (AF), a chronic condition diagnosed and managed in multiple ways in different healthcare settings, as a case study.

Methods: Potentially relevant codes for AF screening, diagnosis, and management were identified in four coding systems: Read (primary care diagnoses and procedures), British National Formulary (BNF; primary care prescriptions), ICD-10 (secondary care diagnoses) and OPCS-4 (secondary care procedures). From these we developed a phenotype algorithm via expert review and analysis of linked EHR data from 1998 to 2010 for a cohort of 2.14 million UK patients aged ≥ 30 years. The cohort was also used to evaluate the phenotype by examining associations between incident AF and known risk factors.

Results: The phenotype algorithm incorporated 286 codes: 201 Read, 63 BNF, 18 ICD-10, and four OPCS-4. Incident AF diagnoses were recorded for 72,793 patients, but only 39.6% (N = 28,795) were recorded in primary care and secondary care. An additional 7,468 potential cases were inferred from data on treatment and pre-existing conditions. The proportion of cases identified from each source differed by diagnosis age; inferred diagnoses contributed a greater proportion of younger cases (≤ 60 years), while older patients (≥ 80 years) were mainly diagnosed in SC. Associations of risk factors (hypertension, myocardial infarction, heart failure) with incident AF defined using different EHR sources were comparable in magnitude to those from traditional consented cohorts.

Conclusions: A single EHR source is not sufficient to identify all patients, nor will it provide a representative sample. Combining multiple data sources and integrating information on treatment and comorbid conditions can substantially improve case identification.

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Related in: MedlinePlus

Proportion of incident atrial fibrillation cases identified in each source by age at diagnosis.
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pone-0110900-g004: Proportion of incident atrial fibrillation cases identified in each source by age at diagnosis.

Mentions: The proportion of cases contributed by each source differed by age at diagnosis; individuals identified by inferred diagnosis criteria made up a greater proportion of cases diagnosed at younger ages (≤60 years), while cases diagnosed at older ages (≥80 years) were mostly identified from secondary care data (see Figure 4). The proportion of cases identified in primary care was highest for ages 60–80 years, but for all age groups primary care contributed fewer cases than secondary care. For patients diagnosed in secondary care, AF was more likely to be the main diagnosis for the hospital episode when individuals were younger (≤50 years), whereas amongst those diagnosed at older ages AF was much more likely to be a secondary diagnosis made during admission for another condition. Patients with diagnoses recorded only in secondary care were slightly more likely to be female compared to those with diagnoses in both data sources, primary care only, or inferred diagnoses (51.3%, 48.2%, 48.8% and 47.6% female respectively).


Defining disease phenotypes using national linked electronic health records: a case study of atrial fibrillation.

Morley KI, Wallace J, Denaxas SC, Hunter RJ, Patel RS, Perel P, Shah AD, Timmis AD, Schilling RJ, Hemingway H - PLoS ONE (2014)

Proportion of incident atrial fibrillation cases identified in each source by age at diagnosis.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4219705&req=5

pone-0110900-g004: Proportion of incident atrial fibrillation cases identified in each source by age at diagnosis.
Mentions: The proportion of cases contributed by each source differed by age at diagnosis; individuals identified by inferred diagnosis criteria made up a greater proportion of cases diagnosed at younger ages (≤60 years), while cases diagnosed at older ages (≥80 years) were mostly identified from secondary care data (see Figure 4). The proportion of cases identified in primary care was highest for ages 60–80 years, but for all age groups primary care contributed fewer cases than secondary care. For patients diagnosed in secondary care, AF was more likely to be the main diagnosis for the hospital episode when individuals were younger (≤50 years), whereas amongst those diagnosed at older ages AF was much more likely to be a secondary diagnosis made during admission for another condition. Patients with diagnoses recorded only in secondary care were slightly more likely to be female compared to those with diagnoses in both data sources, primary care only, or inferred diagnoses (51.3%, 48.2%, 48.8% and 47.6% female respectively).

Bottom Line: The proportion of cases identified from each source differed by diagnosis age; inferred diagnoses contributed a greater proportion of younger cases (≤ 60 years), while older patients (≥ 80 years) were mainly diagnosed in SC.Associations of risk factors (hypertension, myocardial infarction, heart failure) with incident AF defined using different EHR sources were comparable in magnitude to those from traditional consented cohorts.A single EHR source is not sufficient to identify all patients, nor will it provide a representative sample.

View Article: PubMed Central - PubMed

Affiliation: Farr Institute of Health Informatics Research, University College London, London, United Kingdom, and Clinical Epidemiology, Department of Epidemiology and Public Health, University College London, London, United Kingdom; Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, United Kingdom; Melbourne School of Global and Population Health, The University of Melbourne, Melbourne, Australia.

ABSTRACT

Background: National electronic health records (EHR) are increasingly used for research but identifying disease cases is challenging due to differences in information captured between sources (e.g. primary and secondary care). Our objective was to provide a transparent, reproducible model for integrating these data using atrial fibrillation (AF), a chronic condition diagnosed and managed in multiple ways in different healthcare settings, as a case study.

Methods: Potentially relevant codes for AF screening, diagnosis, and management were identified in four coding systems: Read (primary care diagnoses and procedures), British National Formulary (BNF; primary care prescriptions), ICD-10 (secondary care diagnoses) and OPCS-4 (secondary care procedures). From these we developed a phenotype algorithm via expert review and analysis of linked EHR data from 1998 to 2010 for a cohort of 2.14 million UK patients aged ≥ 30 years. The cohort was also used to evaluate the phenotype by examining associations between incident AF and known risk factors.

Results: The phenotype algorithm incorporated 286 codes: 201 Read, 63 BNF, 18 ICD-10, and four OPCS-4. Incident AF diagnoses were recorded for 72,793 patients, but only 39.6% (N = 28,795) were recorded in primary care and secondary care. An additional 7,468 potential cases were inferred from data on treatment and pre-existing conditions. The proportion of cases identified from each source differed by diagnosis age; inferred diagnoses contributed a greater proportion of younger cases (≤ 60 years), while older patients (≥ 80 years) were mainly diagnosed in SC. Associations of risk factors (hypertension, myocardial infarction, heart failure) with incident AF defined using different EHR sources were comparable in magnitude to those from traditional consented cohorts.

Conclusions: A single EHR source is not sufficient to identify all patients, nor will it provide a representative sample. Combining multiple data sources and integrating information on treatment and comorbid conditions can substantially improve case identification.

Show MeSH
Related in: MedlinePlus