scholarly journals Transforming and evaluating electronic health record disease phenotyping algorithms using the OMOP common data model: a case study in heart failure

JAMIA Open ◽  
2021 ◽  
Author(s):  
Vaclav Papez ◽  
Maxim Moinat ◽  
Stefan Payralbe ◽  
Folkert W Asselbergs ◽  
R Thomas Lumbers ◽  
...  
Keyword(s):  
Heart Failure ◽  
Primary Care ◽  
Data Model ◽  
Observational Research ◽  
Practice Research ◽  
Chronic Obstructive ◽  
Common Data Model ◽  
Clinical Practice Research Datalink ◽  
Clinical Biomarkers ◽  
Electronic Health

Abstract Objective The aim of the study was to transform a resource of linked electronic health records (EHR) to the OMOP common data model (CDM) and evaluate the process in terms of syntactic and semantic consistency and quality when implementing disease and risk factor phenotyping algorithms. Materials and Methods Using heart failure (HF) as an exemplar, we represented three national EHR sources (Clinical Practice Research Datalink, Hospital Episode Statistics Admitted Patient Care, Office for National Statistics) into the OMOP CDM 5.2. We compared the original and CDM HF patient population by calculating and presenting descriptive statistics of demographics, related comorbidities, and relevant clinical biomarkers. Results We identified a cohort of 502 536 patients with the incident and prevalent HF and converted 1 099 195 384 rows of data from 216 581 914 encounters across three EHR sources to the OMOP CDM. The largest percentage (65%) of unmapped events was related to medication prescriptions in primary care. The average coverage of source vocabularies was >98% with the exception of laboratory tests recorded in primary care. The raw and transformed data were similar in terms of demographics and comorbidities with the largest difference observed being 3.78% in the prevalence of chronic obstructive pulmonary disease (COPD). Conclusion Our study demonstrated that the OMOP CDM can successfully be applied to convert EHR linked across multiple healthcare settings and represent phenotyping algorithms spanning multiple sources. Similar to previous research, challenges mapping primary care prescriptions and laboratory measurements still persist and require further work. The use of OMOP CDM in national UK EHR is a valuable research tool that can enable large-scale reproducible observational research.

Preliminary results from the COPE study using primary-care electronic health records and environmental modelling to examine COPD exacerbations

2018 ◽  
Vol 68 (suppl 1) ◽  
pp. bjgp18X696749 ◽  
Author(s):  
Maimoona Hashmi ◽  
Mark Wright ◽  
Kirin Sultana ◽  
Benjamin Barratt ◽  
Lia Chatzidiakou ◽  
...  
Keyword(s):  
Primary Care ◽  
Electronic Health Records ◽  
Health Management ◽  
Practice Research ◽  
Chronic Obstructive ◽  
Clinical Practice Research Datalink ◽  
Health Records ◽  
Preliminary Results ◽  
Copd Exacerbations ◽  
Electronic Health

BackgroundChronic Obstructive Airway Disease (COPD) is marked by often severely debilitating exacerbations. Efficient patient-centric research approaches are needed to better inform health management primary-care.AimThe ‘COPE study’ aims to develop a method of predicting COPD exacerbations utilising personal air quality sensors, environmental exposure modelling and electronic health records through the recruitment of patients from consenting GPs contributing to the Clinical Practice Research Datalink (CPRD).MethodThe study made use of Electronic Healthcare Records (EHR) from CPRD, an anonymised GP records database to screen and locate patients within GP practices in Central London. Personal air monitors were used to capture data on individual activities and environmental exposures. Output from the monitors were then linked with the EHR data to obtain information on COPD management, severity, comorbidities and exacerbations. Symptom changes not equating to full exacerbations were captured on diary cards. Linear regression was used to investigate the relationship between subject peak flow, symptoms, exacerbation events and exposure data.ResultsPreliminary results on the first 80 patients who have completed the study indicate variable susceptibility to environmental stressors in COPD patients. Some individuals appear highly susceptible to environmental stress and others appear to have unrelated triggers.ConclusionRecruiting patients through EHR for a study is feasible and allows easy collection of data for long term follow up. Portable environmental sensors could now be used to develop personalised models to predict risk of COPD exacerbations in susceptible individuals. Identification of direct links between participant health and activities would allow improved health management thus cost savings.

scholarly journals Antibiotic Prescribing Before and After the Diagnosis of Comorbidity: A Cohort Study Using Primary Care Electronic Health Records

2019 ◽  
Vol 71 (7) ◽  
pp. e50-e57 ◽  
Author(s):  
Patrick Rockenschaub ◽  
Andrew Hayward ◽  
Laura Shallcross
Keyword(s):  
Heart Failure ◽  
Primary Care ◽  
Respiratory Symptoms ◽  
Antibiotic Use ◽  
Arterial Disease ◽  
Practice Research ◽  
Chronic Obstructive ◽  
Clinical Practice Research Datalink ◽  
Antibiotic Prescribing ◽  
Before And After

Abstract Background Comorbidities such as diabetes and chronic obstructive pulmonary disease (COPD) increase patients’ susceptibility to infections, but it is unclear how the onset of comorbidity impacts antibiotic use. We estimated rates of antibiotic use before and after diagnosis of comorbidity in primary care to identify opportunities for antibiotic stewardship. Methods We analyzed UK primary care records from the Clinical Practice Research Datalink. Adults registered between 2008–2015 without prior comorbidity diagnoses were eligible for inclusion. Monthly adjusted rates of antibiotic prescribing were estimated for patients with new-onset stroke, coronary heart disease, heart failure, peripheral arterial disease, asthma, chronic kidney disease, diabetes, or COPD in the 12 months before and after diagnosis and for controls without comorbidity. Results 106 540/1 071 943 (9.9%) eligible patients were diagnosed with comorbidity. Antibiotic prescribing rates increased 1.9- to 2.3-fold in the 4–9 months preceding diagnosis of asthma, heart failure, and COPD before declining to stable levels within 2 months after diagnosis. A less marked trend was seen for diabetes (rate ratio, 1.55; 95% confidence interval, 1.48–1.61). Prescribing rates for patients with vascular conditions increased immediately before diagnosis and remained 30%–39% higher than baseline afterwards. Rates of prescribing to controls increased by 17%–28% in the months just before and after consultation. Conclusions Antibiotic prescribing increased rapidly before diagnosis of conditions that present with respiratory symptoms (COPD, heart failure, asthma) and declined afterward. Onset of respiratory symptoms may be misdiagnosed as infection. Earlier diagnosis of these comorbidities could reduce avoidable antibiotic prescribing.

scholarly journals Real-world presentation with heart failure in primary care: do patients selected to follow diagnostic and management guidelines have better outcomes?

Open Heart ◽  
2018 ◽  
Vol 5 (2) ◽  
pp. e000935
Author(s):  
Alex Bottle ◽  
Dani Kim ◽  
Paul P Aylin ◽  
F Azeem Majeed ◽  
Martin R Cowie ◽  
...  
Keyword(s):  
Heart Failure ◽  
Primary Care ◽  
Practice Research ◽  
Clinical Practice Research Datalink ◽  
Initial Management ◽  
Risk Of Death ◽  
Specialist Referral ◽  
Partial Completion ◽  
General Practices ◽  
Using Data

ObjectiveTo describe associations between initial management of people presenting with heart failure (HF) symptoms in primary care, including compliance with the recommendations of the National Institute for Health and Care Excellence (NICE), and subsequent unplanned hospitalisation for HF and death.MethodsThis is a retrospective cohort study using data from general practices submitting records to the Clinical Practice Research Datalink. The cohort comprised patients diagnosed with HF during 2010–2013 and presenting to their general practitioners with breathlessness, fatigue or ankle swelling.Results13 897 patients were included in the study. Within the first 6 months, only 7% had completed the NICE-recommended pathway; another 18.6% had followed part of it (B-type natriuretic peptide testing and/or echocardiography, or specialist referral). Significant differences in hazards were seen in unadjusted analysis in favour of full or partial completion of the NICE-recommended pathway. Covariate adjustment attenuated the relations with death much more than those for HF admission. Compared with patients placed on the NICE pathway, treatment with HF medications had an HR of 1.16 (95% CI 1.05 to 1.28, p=0.003) for HF admission and 1.03 (95% CI 0.90 to 1.17, p= 0.674) for death. Patients who partially followed the NICE pathway had similar hazards to those who completed it. Patients on no pathway had the highest hazard for HF admission at 1.30 (95% 1.18 to 1.43, p<0.001) but similar hazard for death.ConclusionsPatients not put on at least some elements of the NICE-recommended pathway had significantly higher risk of HF admission but non-significant higher risk of death than other patients had.

scholarly journals Childhood obesity trends from primary care electronic health records in England between 1994 and 2013: population-based cohort study

2015 ◽  
Vol 100 (3) ◽  
pp. 214-219 ◽  
Author(s):  
Cornelia H M van Jaarsveld ◽  
Martin C Gulliford
Keyword(s):  
Primary Care ◽  
Cohort Study ◽  
Electronic Health Records ◽  
Age Groups ◽  
Overweight And Obesity ◽  
Practice Research ◽  
Clinical Practice Research Datalink ◽  
Health Records ◽  
Obesity Trends ◽  
Electronic Health

ObjectiveThis study aimed to use primary care electronic health records to evaluate the prevalence of overweight and obesity in 2–15-year-old children in England and compare trends over the last two decades.DesignCohort study of primary care electronic health records.Setting375 general practices in England that contribute to the UK Clinical Practice Research Datalink.PatientsIndividual participants were sampled if they were aged between 2 and 15 years during the period 1994–2013 and had one or more records of body mass index (BMI).Main outcome measurePrevalence of overweight (including obesity) was defined as a BMI equal to or greater than the 85th centile of the 1990 UK reference population.ResultsData were analysed for 370 544 children with 507 483 BMI records. From 1994 to 2003, the odds of overweight and obesity increased by 8.1% per year (95% CI 7.2% to 8.9%) compared with 0.4% (−0.2% to 1.1%) from 2004 to 2013. Trends were similar for boys and girls, but differed by age groups, with prevalence stabilising in 2004 to 2013 in the younger (2–10 year) but not older (11–15 year) age group, where rates continued to increase.ConclusionsPrimary care electronic health records in England may provide a valuable resource for monitoring obesity trends. More than a third of UK children are overweight or obese, but the prevalence of overweight and obesity may have stabilised between 2004 and 2013.

Routes to diagnosis of heart failure: observational study using linked data in England

Heart ◽  
2017 ◽  
Vol 104 (7) ◽  
pp. 600-605 ◽  
Author(s):  
Alex Bottle ◽  
Dani Kim ◽  
Paul Aylin ◽  
Martin R Cowie ◽  
Azeem Majeed ◽  
...  
Keyword(s):  
Heart Failure ◽  
Primary Care ◽  
Natriuretic Peptide ◽  
Hospital Admissions ◽  
Practice Research ◽  
Clinical Practice Research Datalink ◽  
Missed Opportunities ◽  
Specialist Referral ◽  
Care Consultation ◽  
Primary Care Practices

ObjectiveTimely diagnosis and management of heart failure (HF) is critical, but identification of patients with suspected HF can be challenging, especially in primary care. We describe the journey of people with HF in primary care from presentation through to diagnosis and initial management.MethodsWe used the Clinical Practice Research Datalink (primary care consultations linked to hospital admissions data and national death registrations for patients registered with participating primary care practices in England) to describe investigation and referral pathways followed by patients from first presentation with relevant symptoms to HF diagnosis, particularly alignment with recommendations of the National Institute for Health and Care Excellence guideline for HF diagnosis.Results36 748 patients had a diagnosis of HF recorded that met the inclusion criteria between 1 January 2010 and 31 March 2013. For 29 113 (79.2%) patients, this was first recorded in hospital. In the 5 years prior to diagnosis, 15 057 patients (41.0%) had a primary care consultation with one of three key HF symptoms recorded, 17 724 (48.2%) attended for another reason and 3967 (10.8%) did not see their general practitioner. Only 24% of those with recorded HF symptoms followed a pathway aligned with guidelines (echocardiogram and/or serum natriuretic peptide test and specialist referral), while 44% had no echocardiogram, natriuretic peptide test or referral.ConclusionsPatients follow various pathways to the diagnosis of HF. However, few appear to follow a pathway supported by guidelines for investigation and referral. There are likely to be missed opportunities for earlier HF diagnosis in primary care.

scholarly journals Adherence to guidelines in management of symptoms suggestive of heart failure in primary care

Heart ◽  
2018 ◽  
Vol 105 (9) ◽  
pp. 678-685 ◽  
Author(s):  
Benedict Hayhoe ◽  
Dani Kim ◽  
Paul P Aylin ◽  
F Azeem Majeed ◽  
Martin R Cowie ◽  
...  
Keyword(s):  
Heart Failure ◽  
Primary Care ◽  
Median Time ◽  
Practice Research ◽  
Clinical Practice Research Datalink ◽  
Presenting Symptoms ◽  
Specialist Referral ◽  
General Practices ◽  
Treatment And Diagnosis ◽  
Symptom Type

ObjectiveClinical guidelines on heart failure (HF) suggest timings for investigation and referral in primary care. We calculated the time for patients to achieve key elements in the recommended pathway to diagnosis of HF.MethodsIn this observational study, we used linked primary and secondary care data (Clinical Practice Research Datalink, a database of anonymised electronic records from UK general practices) between 2010 and 2013. Records were examined for presenting symptoms (breathlessness, fatigue, ankle swelling) and key elements of the National Institute for Health and Care Excellence-recommended pathway to diagnosis (serum natriuretic peptide (NP) test, echocardiography, specialist referral).Results42 403 patients were diagnosed with HF, of whom 16 597 presented in primary care with suggestive symptoms. 6464 (39%) had recorded NP or echocardiography, and 6043 (36%) specialist referral. Median time from recorded symptom(s) to investigation (NP or echocardiography) was 292 days (IQR 34–844) and to referral 236 days (IQR 42–721). Median time from symptom(s) to diagnosis was 972 days (IQR 337–1468) and to treatment with HF-relevant medication 803 days (IQR 230–1364). Factors significantly affecting timing of referral, treatment and diagnosis included patients’ sex (p=0.001), age (p<0.001), deprivation score (p=0.001), comorbidities (p<0.001) and presenting symptom type (p<0.001).ConclusionsMedian times to investigation or referral of patients presenting in primary care with symptoms suggestive of HF considerably exceeded recommendations. There is a need to support clinicians in the diagnosis of HF in primary care, with improved access to investigation and specialist assessment to support timely management.

scholarly journals Concomitant diagnosis of asthma and COPD: a quantitative study in UK primary care

2018 ◽  
Vol 68 (676) ◽  
pp. e775-e782 ◽  
Author(s):  
Francis Nissen ◽  
Daniel R Morales ◽  
Hana Mullerova ◽  
Liam Smeeth ◽  
Ian J Douglas ◽  
...  
Keyword(s):  
Primary Care ◽  
Practice Research ◽  
Chronic Obstructive ◽  
Clinical Practice Research Datalink ◽  
Read Code ◽  
Care Environment ◽  
Missed Opportunities ◽  
Obstructive Pulmonary Disease ◽  
Additional Information ◽  
The Uk

BackgroundAsthma and chronic obstructive pulmonary disease (COPD) share many characteristics and symptoms, and the differential diagnosis between the two diseases can be difficult in primary care. This study explored potential overlap between both diseases in a primary care environment.AimTo quantify how commonly patients with COPD have a concomitant diagnosis of asthma, and how commonly patients with asthma have a concomitant diagnosis of COPD in UK primary care. Additionally, the study aimed to determine the extent of possible misdiagnosis and missed opportunities for diagnosis.Design and settingPatients with validated asthma and patients with validated COPD in primary care were identified from the UK Clinical Practice Research Datalink (CPRD) in separate validation studies, and the diseases were confirmed by review of GP questionnaires.MethodThe prevalence of concurrent asthma and COPD in validated cases of either disease was examined based on CPRD coding, GP questionnaires, and requested additional information.ResultsIn total, 400 patients with COPD and 351 patients with asthma in primary care were identified. Of the patients with validated asthma, 15% (n = 52) had previously received a diagnostic COPD Read code, although COPD was only likely in 14.8% (95% confidence interval [CI] = 11.3 to 19.0) of patients with validated asthma. More than half (52.5%, n = 210) of patients with validated COPD had previously received a diagnostic asthma Read code. However, when considering additional evidence to support a diagnosis of asthma, concurrent asthma was only likely in 14.5% (95% CI = 11.2 to 18.3) of patients with validated COPD.ConclusionA concurrent asthma and COPD diagnosis appears to affect a relative minority of patients with COPD (14.5%) or asthma (14.8%). Asthma diagnosis may be over-recorded in people with COPD.

scholarly journals Validation of asthma recording in the Clinical Practice Research Datalink (CPRD)

BMJ Open ◽  
2017 ◽  
Vol 7 (8) ◽  
pp. e017474 ◽  
Author(s):  
Francis Nissen ◽  
Daniel R Morales ◽  
Hana Mullerova ◽  
Liam Smeeth ◽  
Ian J Douglas ◽  
...  
Keyword(s):  
Primary Care ◽  
Clinical Practice ◽  
Observational Research ◽  
Practice Research ◽  
Clinical Practice Research Datalink ◽  
Prescription Data ◽  
Read Code ◽  
Asthma Diagnosis ◽  
Optimal Method ◽  
Additional Information

ObjectivesThe optimal method of identifying people with asthma from electronic health records in primary care is not known. The aim of this study is to determine the positive predictive value (PPV) of different algorithms using clinical codes and prescription data to identify people with asthma in the United Kingdom Clinical Practice Research Datalink (CPRD).Methods684 participants registered with a general practitioner (GP) practice contributing to CPRD between 1 December 2013 and 30 November 2015 were selected according to one of eight predefined potential asthma identification algorithms. A questionnaire was sent to the GPs to confirm asthma status and provide additional information to support an asthma diagnosis. Two study physicians independently reviewed and adjudicated the questionnaires and additional information to form a gold standard for asthma diagnosis. The PPV was calculated for each algorithm.Results684 questionnaires were sent, of which 494 (72%) were returned and 475 (69%) were complete and analysed. All five algorithms including a specific Read code indicating asthma or non-specific Read code accompanied by additional conditions performed well. The PPV for asthma diagnosis using only a specific asthma code was 86.4% (95% CI 77.4% to 95.4%). Extra information on asthma medication prescription (PPV 83.3%), evidence of reversibility testing (PPV 86.0%) or a combination of all three selection criteria (PPV 86.4%) did not result in a higher PPV. The algorithm using non-specific asthma codes, information on reversibility testing and respiratory medication use scored highest (PPV 90.7%, 95% CI (82.8% to 98.7%), but had a much lower identifiable population. Algorithms based on asthma symptom codes had low PPVs (43.1% to 57.8%)%).ConclusionsPeople with asthma can be accurately identified from UK primary care records using specific Read codes. The inclusion of spirometry or asthma medications in the algorithm did not clearly improve accuracy.Ethics and disseminationThe protocol for this research was approved by the Independent Scientific Advisory Committee (ISAC) for MHRA Database Research (protocol number15_257) and the approved protocol was made available to the journal and reviewers during peer review. Generic ethical approval for observational research using the CPRD with approval from ISAC has been granted by a Health Research Authority Research Ethics Committee (East Midlands—Derby, REC reference number 05/MRE04/87).The results will be submitted for publication and will be disseminated through research conferences and peer-reviewed journals.

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