Evolution of primary care databases in UK: a scientometric analysis of research output

Pooling of primary care electronic health record (EHR) data on Huntington's disease (HD) and cancer: establishing comparability of two large UK databases

OBJECTIVES

To explore whether UK primary care databases arising from two different software systems can be feasibly combined, by comparing rates of Huntington's disease (HD, which is rare) and 14 common cancers in the two databases, as well as characteristics of people with these conditions.

DESIGN

Descriptive study.

SETTING

Primary care electronic health records from Clinical Practice Research Datalink (CPRD) GOLD and CPRD Aurum databases, with linked hospital admission and death registration data.

PARTICIPANTS

4986 patients with HD and 1 294 819 with an incident cancer between 1990 and 2019.

PRIMARY AND SECONDARY OUTCOME MEASURES

Incidence and prevalence of HD by calendar period, age group and region, and annual age-standardised incidence of 14 common cancers in each database, and in a subset of 'overlapping' practices which contributed to both databases. Characteristics of patients with HD or incident cancer: medical history, recent prescribing, healthcare contacts and database follow-up.

RESULTS

Incidence and prevalence of HD were slightly higher in CPRD GOLD than CPRD Aurum, but with similar trends over time. Cancer incidence in the two databases differed between 1990 and 2000, but converged and was very similar thereafter. Participants in each database were most similar in terms of medical history (median standardised difference, MSD 0.03 (IQR 0.01-0.03)), recent prescribing (MSD 0.06 (0.03-0.10)) and demographics and general health variables (MSD 0.05 (0.01-0.09)). Larger differences were seen for healthcare contacts (MSD 0.27 (0.10-0.41)), and database follow-up (MSD 0.39 (0.19-0.56)).

CONCLUSIONS

Differences in cancer incidence trends between 1990 and 2000 may relate to use of a practice-level data quality filter (the 'up-to-standard' date) in CPRD GOLD only. As well as the impact of data curation methods, differences in underlying data models can make it more challenging to define exactly equivalent clinical concepts in each database. Researchers should be aware of these potential sources of variability when planning combined database studies and interpreting results.

Sodium-based paracetamol: impact on blood pressure, cardiovascular events, and all-cause mortality

BACKGROUND AND AIMS

Effervescent formulations of paracetamol containing sodium bicarbonate have been reported to associate with increased blood pressure and a higher risk of cardiovascular diseases and all-cause mortality. Given the major implications of these findings, the reported associations were re-examined.

METHODS

Using linked electronic health records data, a cohort of 475 442 UK individuals with at least one prescription of paracetamol, aged between 60 and 90 years, was identified. Outcomes in patients taking sodium-based paracetamol were compared with those taking non-sodium-based formulations of the same. Using a deep learning approach, associations with systolic blood pressure (SBP), major cardiovascular events (myocardial infarction, heart failure, and stroke), and all-cause mortality within 1 year after baseline were investigated.

RESULTS

A total of 460 980 and 14 462 patients were identified for the non-sodium-based and sodium-based paracetamol exposure groups, respectively (mean age: 74 years; 64% women). Analysis revealed no difference in SBP [mean difference -0.04 mmHg (95% confidence interval -0.51, 0.43)] and no association with major cardiovascular events [relative risk (RR) 1.03 (0.91, 1.16)]. Sodium-based paracetamol showed a positive association with all-cause mortality [RR 1.46 (1.40, 1.52)]. However, after further accounting of other sources of residual confounding, the observed association attenuated towards the null [RR 1.08 (1.01, 1.16)]. Exploratory analyses revealed dysphagia and related conditions as major sources of uncontrolled confounding by indication for this association.

CONCLUSIONS

This study does not support previous suggestions of increased SBP and an elevated risk of cardiovascular events from short-term use of sodium bicarbonate paracetamol in routine clinical practice.

Risk of COVID-19 among unvaccinated and vaccinated patients with systemic lupus erythematosus: a general population study

OBJECTIVE

To compare the risk of SARS-CoV-2 infection and its related severe sequelae between patients with systemic lupus erythematosus (SLE) and the general population according to COVID-19 vaccination status.

METHODS

We performed cohort studies using data from The Health Improvement Network to compare the risks of SARS-CoV-2 infection and severe sequelae between patients with SLE and the general population. Individuals aged 18-90 years with no previously documented SARS-CoV-2 infection were included. We estimated the incidence rates and HRs of SARS-CoV-2 infection and severe sequelae between patients with SLE and the general population according to COVID-19 vaccination status using exposure score overlap weighted Cox proportional hazards model.

RESULTS

We identified 3245 patients with SLE and 1 755 034 non-SLE individuals from the unvaccinated cohort. The rates of SARS-CoV-2 infection, COVID-19 hospitalisation, COVID-19 death and combined severe outcomes per 1000 person-months were 10.95, 3.21, 1.16 and 3.86 among patients with SLE, and 8.50, 1.77, 0.53 and 2.18 among general population, respectively. The corresponding adjusted HRs were 1.28 (95% CI: 1.03 to 1.59), 1.82 (95% CI: 1.21 to 2.74), 2.16 (95% CI: 1.00 to 4.79) and 1.78 (95% CI: 1.21 to 2.61). However, no statistically significant differences were observed between vaccinated patients with SLE and vaccinated general population over 9 months of follow-up.

CONCLUSION

While unvaccinated patients with SLE were at higher risk of SARS-CoV-2 infection and its severe sequelae than the general population, no such difference was observed among vaccinated population. The findings indicate that COVID-19 vaccination provides an adequate protection to most patients with SLE from COVID-19 breakthrough infection and its severe sequelae.

Using primary care databases for addiction research: An introduction and overview of strengths and weaknesses

Primary care databases extract and combine routine data from the electronic patient records of various participating practices on a regular basis. These databases can be used for innovative and relevant addiction research, but such use requires a thorough understanding of how data were originally collected and how they need to be processed and statistically analysed to produce sound scientific evidence. The aims of this paper are therefore to (1) make a case for why primary care databases should be considered more frequently for addiction research; (2) provide an overview of how primary care databases are constructed; (3) highlight important methodological and statistical strengths and weaknesses of using primary care databases for research; and (4) give practical advice about how a researcher can get access to databases. Three major primary care databases from the UK serve as examples: Clinical Practice Research Datalink (CPRD), The Health Improvement Network (THIN), and QResearch.

Concept Libraries for Repeatable and Reusable Research: Qualitative Study Exploring the Needs of Users

Background

Big data research in the field of health sciences is hindered by a lack of agreement on how to identify and define different conditions and their medications. This means that researchers and health professionals often have different phenotype definitions for the same condition. This lack of agreement makes it difficult to compare different study findings and hinders the ability to conduct repeatable and reusable research.

Objective

This study aims to examine the requirements of various users, such as researchers, clinicians, machine learning experts, and managers, in the development of a data portal for phenotypes (a concept library).

Methods

This was a qualitative study using interviews and focus group discussion. One-to-one interviews were conducted with researchers, clinicians, machine learning experts, and senior research managers in health data science (N=6) to explore their specific needs in the development of a concept library. In addition, a focus group discussion with researchers (N=14) working with the Secured Anonymized Information Linkage databank, a national eHealth data linkage infrastructure, was held to perform a SWOT (strengths, weaknesses, opportunities, and threats) analysis for the phenotyping system and the proposed concept library. The interviews and focus group discussion were transcribed verbatim, and 2 thematic analyses were performed.

Results

Most of the participants thought that the prototype concept library would be a very helpful resource for conducting repeatable research, but they specified that many requirements are needed before its development. Although all the participants stated that they were aware of some existing concept libraries, most of them expressed negative perceptions about them. The participants mentioned several facilitators that would stimulate them to share their work and reuse the work of others, and they pointed out several barriers that could inhibit them from sharing their work and reusing the work of others. The participants suggested some developments that they would like to see to improve reproducible research output using routine data.

Conclusions

The study indicated that most interviewees valued a concept library for phenotypes. However, only half of the participants felt that they would contribute by providing definitions for the concept library, and they reported many barriers regarding sharing their work on a publicly accessible platform. Analysis of interviews and the focus group discussion revealed that different stakeholders have different requirements, facilitators, barriers, and concerns about a prototype concept library.

Findability of UK health datasets available for research: a mixed methods study

OBJECTIVE

How health researchers find secondary data to analyse is unclear. We sought to describe the approaches that UK organisations take to help researchers find data and to assess the findability of health data that are available for research.

METHODS

We surveyed established organisations about how they make data findable. We derived measures of findability based on the first element of the FAIR principles (Findable, Accessible, Interoperable, Reproducible). We applied these to 13 UK health datasets and measured their findability via two major internet search engines in 2018 and repeated in 2021.

RESULTS

Among 12 survey respondents, 11 indicated that they made metadata publicly available. Respondents said internet presence was important for findability, but that this needed improvement. In 2018, 8 out of 13 datasets were listed in the top 100 search results of 10 searches repeated on both search engines, while the remaining 5 were found one click away from those search results. In 2021, this had reduced to seven datasets directly listed and one dataset one click away. In 2021, Google Dataset Search had become available, which listed 3 of the 13 datasets within the top 100 search results.

DISCUSSION

Measuring findability via online search engines is one method for evaluating efforts to improve findability. Findability could perhaps be improved with catalogues that have greater inclusion of datasets, field-level metadata and persistent identifiers.

CONCLUSION

UK organisations recognised the importance of the internet for finding data for research. However, health datasets available for research were no more findable in 2021 than in 2018.

Internationalisation of general practice journals: a bibliometric analysis of the Science Citation Index database

Research plays a crucial role in the development of primary health care. Researchers in other specialities have studied the internationalisation of their journals, but no such study has been conducted for general practice. The aim of this study was to analyse the volume of publication and internationalisation of general practice journals indexed in the Science Citation Index (SCI) database in 2019. Of the total 1573 articles and reviews in 19 journals indexed under the subject category of 'primary health care' in the SCI database, 86.4% (n = 1359) were published in four English-speaking countries (32.8% in seven US journals, 34.8% in five UK journals, 12.5% in two Australian journals and 6.4% in one Canadian journal) and 40.6% (n = 639) were authored or coauthored by authors from a country other than that in which the journal was published. There was a significant (P < 0.05) relationship between the country of publication and the degree of internationalisation of the journal. The degree of internationalisation of general practice journals varied from 94.2% for family practice to 2.0% for primary care. There are wide disparities in internationalisation among different countries and general practice journals. There is much room for improvement in the internationalisation of general practice journals in the SCI database.

E-Infrastructures and the divergent assetization of public health data: Expectations, uncertainties, and asymmetries

In this article, we examine some of the expectations, frictions and uncertainties involved with the assetization of de-identified NHS patient data by (primary care) research services in UK. Pledges to Electronic Health Record (EHR) data-driven research attempt to reconfigure public health data as an asset for realizing multiple values across healthcare, research and finance. We introduce the concept of 'asymmetrical divergence' in public health data assetization to study the various practices of configuring and using this data, both as a continuously generated resource to be extracted and as an asset to be circulated in the knowledge economy. As data assetization and exploitations grow bigger and more diverse, the capitalization of these datasets may constitute EHR data-driven research in healthcare as an attractive technoscientific activity, but one limited to those actors with specific sociotechnical resources in place to fully exploit them at the required scale.

Therapeutic inertia in the management of dyslipidaemia and hypertension in incident type 2 diabetes and the resulting risk factor burden: Real-world evidence from primary care

OBJECTIVE

To investigate trends in the prevalence of hypertension and dyslipidaemia in incident type 2 diabetes (T2DM), time to antihypertensive (AHT) and lipid-lowering therapy (LLT), and the association with systolic blood pressure (SBP) and lipid control.

RESEARCH DESIGN AND METHODS

Using The Health Improvement Network UK primary care database, 254 925 people with incident T2DM and existing dyslipidaemia or hypertension were identified. Among those without atherosclerotic cardiovascular disease (ASCVD) history and not on AHT or LLT at diagnosis, the adjusted median months to initiating an AHT or an LLT, and the probabilities of high SBP or lipid levels over 2 years in people initiating therapy within or after 1 year were evaluated according to high and low ASCVD risk status.

RESULTS

At diabetes diagnosis, 66% and 66% had dyslipidaemia and hypertension, respectively. During 2005 to 2016, dyslipidaemia prevalence increased by 10% in people aged <60 years, while hypertension prevalence remained stable in all age groups. Among those with high ASCVD risk status in the age groups 18 to 39, 40 to 49, and 50 to 59 years, the median number of months to initiation of therapy were 20.4 (95% confidence interval [CI] 20.3-20.5), 10.9 (95% CI 10.8-11.0), and 9.5 (95% CI 9.4-9.6) in the dyslipidaemia subcohort, and 28.1 (95% CI 28.0-28.2), 19.2 (95% CI 19.1-19.3), and 19.9 (95% CI 19.8-20.0) in the hypertension subcohort. Among people with high and low ASCVD risk status, respectively, compared to early LLT initiators, those who initiated LLT after 1 year had a 65.3% to 85.3% and a 65.0% to 85.3% significantly higher probability of failing lipid control at 2 years of follow-up, while late AHT initiators had a 46.5% to 57.9% and a 40.0% to 58.7% significantly higher probability of failing SBP control.

CONCLUSIONS

Significant delay in initiating cardioprotective therapies was observed, and time to first prescription was similar in the primary prevention setting, irrespective of ASCVD risk status across all T2DM diagnosis age groups, resulting in poor risk factor control at 2 years of follow-up.

Concept libraries for automatic electronic health record based phenotyping: A review

Introduction

Electronic health records (EHR) are linked together to examine disease history and to undertake research into the causes and outcomes of disease. However, the process of constructing algorithms for phenotyping (e.g., identifying disease characteristics) or health characteristics (e.g., smoker) is very time consuming and resource costly. In addition, results can vary greatly between researchers. Reusing or building on algorithms that others have created is a compelling solution to these problems. However, sharing algorithms is not a common practice and many published studies do not detail the clinical code lists used by the researchers in the disease/characteristic definition. To address these challenges, a number of centres across the world have developed health data portals which contain concept libraries (e.g., algorithms for defining concepts such as disease and characteristics) in order to facilitate disease phenotyping and health studies.

Objectives

This study aims to review the literature of existing concept libraries, examine their utilities, identify the current gaps, and suggest future developments.

Methods

The five-stage framework of Arksey and O'Malley was used for the literature search. This approach included defining the research questions, identifying relevant studies through literature review, selecting eligible studies, charting and extracting data, and summarising and reporting the findings.

Results

This review identified seven publicly accessible Electronic Health data concept libraries which were developed in different countries including UK, USA, and Canada. The concept libraries (n = 7) investigated were either general libraries that hold phenotypes of multiple specialties (n = 4) or specialized libraries that manage only certain specialities such as rare diseases (n = 3). There were some clear differences between the general libraries such as archiving data from different electronic sources, and using a range of different types of coding systems. However, they share some clear similarities such as enabling users to upload their own code lists, and allowing users to use/download the publicly accessible code. In addition, there were some differences between the specialized libraries such as difference in ability to search, and if it was possible to use different searching queries such as simple or complex searches. Conversely, there were some similarities between the specialized libraries such as enabling users to upload their own concepts into the libraries and to show where they were published, which facilitates assessing the validity of the concepts. All the specialized libraries aimed to encourage the reuse of research methods such as lists of clinical code and/or metadata.

Conclusion

The seven libraries identified have been developed independently and appear to replicate similar concepts but in different ways. Collaboration between similar libraries would greatly facilitate the use of these libraries for the user. The process of building code lists takes time and effort. Access to existing code lists increases consistency and accuracy of definitions across studies. Concept library developers should collaborate with each other to raise awareness of their existence and of their various functions, which could increase users’ contributions to those libraries and promote their wide-ranging adoption.

Corporate Social Responsibility and Corporate Tax Aggressiveness: A Scientometric Analysis of the Existing Literature to Map the Future

Using data from 2003 to 2020, this study uses a scientometric approach to investigate the nexus between Corporate Social Responsibility (CSR) and corporate tax aggressiveness research. The objective is to identify under-explored regions, variables, citation patterns, theories, and unexplored topics in the body of knowledge to establish trends in publications on issues about corporate social responsibility and corporate tax aggressiveness. In addition, the study also considers publication journal areas of focus. Research linking CSR and tax avoidance using VOSviewer and triangulating with CiteSpace, by way of approach, is not found in the literature. The findings suggest that CSR and corporate tax aggressiveness researchers do not use far-reaching relevant theories and applicable findings from studies beyond their clusters. Another finding is that African countries remain under-explored due to the absence of institutional representation and an adequate number of investigators regarding CSR and corporate tax aggressiveness research. Finally, the study reveals a number of research topics to be explored. Governments, particularly in developing economies, should create policies that define taxes as part of an entity’s CSR narrative to enhance transparency and legitimacy. In addition, the study is of immense significance to master and PhD students since it provides an agenda for future research.

Data extraction for epidemiological research (DExtER): a novel tool for automated clinical epidemiology studies

The use of primary care electronic health records for research is abundant. The benefits gained from utilising such records lies in their size, longitudinal data collection and data quality. However, the use of such data to undertake high quality epidemiological studies, can lead to significant challenges particularly in dealing with misclassification, variation in coding and the significant effort required to pre-process the data in a meaningful format for statistical analysis. In this paper, we describe a methodology to aid with the extraction and processing of such databases, delivered by a novel software programme; the "Data extraction for epidemiological research" (DExtER). The basis of DExtER relies on principles of extract, transform and load processes. The tool initially provides the ability for the healthcare dataset to be extracted, then transformed in a format whereby data is normalised, converted and reformatted. DExtER has a user interface designed to obtain data extracts specific to each research question and observational study design. There are facilities to input the requirements for; eligible study period, definition of exposed and unexposed groups, outcome measures and important baseline covariates. To date the tool has been utilised and validated in a multitude of settings. There have been over 35 peer-reviewed publications using the tool, and DExtER has been implemented as a validated public health surveillance tool for obtaining accurate statistics on epidemiology of key morbidities. Future direction of this work will be the application of the framework to linked as well as international datasets and the development of standardised methods for conducting electronic pre-processing and extraction from datasets for research purposes.

Linkage of the CHHiP randomised controlled trial with primary care data: a study investigating ways of supplementing cancer trials and improving evidence-based practice

BACKGROUND

Randomised controlled trials (RCTs) are the gold standard for evidence-based practice. However, RCTs can have limitations. For example, translation of findings into practice can be limited by design features, such as inclusion criteria, not accurately reflecting clinical populations. In addition, it is expensive to recruit and follow-up participants in RCTs. Linkage with routinely collected data could offer a cost-effective way to enhance the conduct and generalisability of RCTs. The aim of this study is to investigate how primary care data can support RCTs.

METHODS

Secondary analysis following linkage of two datasets: 1) multicentre CHHiP radiotherapy trial (ISRCTN97182923) and 2) primary care database from the Royal College of General Practitioners Research and Surveillance Centre. Comorbidities and medications recorded in CHHiP at baseline, and radiotherapy-related toxicity recorded in CHHiP over time were compared with primary care records. The association of comorbidities and medications with toxicity was analysed with mixed-effects logistic regression.

RESULTS

Primary care records were extracted for 106 out of 2811 CHHiP participants recruited from sites in England (median age 70, range 44 to 82). Complementary information included longitudinal body mass index, blood pressure and cholesterol, as well as baseline smoking and alcohol usage but was limited by the considerable missing data. In the linked sample, 9 (8%) participants were recorded in CHHiP as having a history of diabetes and 38 (36%) hypertension, whereas primary care records indicated incidence prior to trial entry of 11 (10%) and 40 (38%) respectively. Concomitant medications were not collected in CHHiP but available in primary care records. This indicated that 44 (41.5%) men took aspirin, 65 (61.3%) statins, 14 (13.2%) metformin and 46 (43.4%) phosphodiesterase-5-inhibitors at some point before or after trial entry.

CONCLUSIONS

We provide a set of recommendations on linkage and supplementation of trials. Data recorded in primary care are a rich resource and linkage could provide near real-time information to supplement trials and an efficient and cost-effective mechanism for long-term follow-up. In addition, standardised primary care data extracts could form part of RCT recruitment and conduct. However, this is at present limited by the variable quality and fragmentation of primary care data.

Incidence and prevalence of primary care antidepressant prescribing in children and young people in England, 1998-2017: A population-based cohort study

BACKGROUND

The use of antidepressants in children and adolescents remains controversial. We examined trends over time and variation in antidepressant prescribing in children and young people in England and whether the drugs prescribed reflected UK licensing and guidelines.

METHODS AND FINDINGS

QResearch is a primary care database containing anonymised healthcare records of over 32 million patients from more than 1,500 general practices across the UK. All eligible children and young people aged 5-17 years in 1998-2017 from QResearch were included. Incidence and prevalence rates of antidepressant prescriptions in each year were calculated overall, for 4 antidepressant classes (selective serotonin reuptake inhibitors [SSRIs], tricyclic and related antidepressants [TCAs], serotonin and norepinephrine reuptake inhibitors [SNRIs], and other antidepressants), and for individual drugs. Adjusted trends over time and differences by social deprivation, region, and ethnicity were examined using Poisson regression, taking clustering within general practitioner (GP) practices into account using multilevel modelling. Of the 4.3 million children and young people in the cohort, 49,434 (1.1%) were prescribed antidepressants for the first time during 20 million years of follow-up. Males made up 52.0% of the cohorts, but only 34.1% of those who were first prescribed an antidepressant in the study period. The largest proportion of the cohort was from London (24.4%), and whilst ethnicity information was missing for 39.5% of the cohort, of those with known ethnicity, 75.3% were White. Overall, SSRIs (62.6%) were the most commonly prescribed first antidepressant, followed by TCAs (35.7%). Incident antidepressant prescribing decreased in 5- to 11-year-olds from a peak of 0.9 in females and 1.6 in males in 1999 to less than 0.2 per 1,000 for both sexes in 2017, but incidence rates more than doubled in 12- to 17-year-olds between 2005 and 2017 to 9.7 (females) and 4.2 (males) per 1,000 person-years. The lowest prescription incidence rates were in London, and the highest were in the South East of England (excluding London) for all sex and age groups. Those living in more deprived areas were more likely to be prescribed antidepressants after adjusting for region. The strongest trend was seen in 12- to 17-year-old females (adjusted incidence rate ratio [aIRR] 1.12, 95% confidence interval [95% CI] 1.11-1.13, p < 0.001, per deprivation quintile increase). Prescribing rates were highest in White and lowest in Black adolescents (aIRR 0.32, 95% CI 0.29-0.36, p < 0.001 [females]; aIRR 0.32, 95% CI 0.27-0.38, p < 0.001 [males]). The 5 most commonly prescribed antidepressants were either licensed in the UK for use in children and young people (CYP) or included in national guidelines. Limitations of the study are that, because we did not have access to secondary care prescribing information, we may be underestimating the prevalence and misidentifying the first antidepressant prescription. We could not assess whether antidepressants were dispensed or taken.

CONCLUSIONS

Our analysis provides evidence of a continuing rise of antidepressant prescribing in adolescents aged 12-17 years since 2005, driven by SSRI prescriptions, but a decrease in children aged 5-11 years. The variation in prescribing by deprivation, region, and ethnicity could represent inequities. Future research should examine whether prescribing trends and variation are due to true differences in need and risk factors, access to diagnosis or treatment, prescribing behaviour, or young people's help-seeking behaviour.

Implementing learning health systems in the UK NHS: Policy actions to improve collaboration and transparency and support innovation and better use of analytics

Learning health systems (LHS) use digital health and care data to improve care, shorten the timeframe of improvement projects, and ensure these are based on real-world data. In the United Kingdom, policymakers are depending on digital innovation, driven by better use of data about current health service performance, to enable service transformation and a more sustainable health system. This paper examines what would be needed to develop LHS in the United Kingdom, considering national policy implications and actions, which local organisations and health systems could take. The paper draws on a seminar attended by academics, policymakers, and practitioners, a brief literature review, and feedback from policy experts and National Health Service (NHS) stakeholders. Although there are examples of some aspects of LHS in the UK NHS, it is hard to find examples where there is a continuous cycle of improvement driven by information and where analysis of data and implementing improvements is part of usual ways of working. The seminar and literature identified a number of barriers. Incentives and capacity to develop LHS are limited, and requires a shift in analytic capacity from regulation and performance, to quality improvement and transformation. The balance in priority given to research compared with implementation also needs to change. Policy initiatives are underway which address some barriers, including building analytical capacity, developing infrastructure, and data standards. The NHS and research partners are investing in infrastructure which could support LHS, although clinical buy in is needed to bring about improvement or address operational challenges. We identify a number of opportunities for local NHS organisations and systems to make better use of health data, and for ways that national policy could promote the collaboration and greater use of analytics which underpin the LHS concept.

UK phenomics platform for developing and validating electronic health record phenotypes: CALIBER

OBJECTIVE

Electronic health records (EHRs) are a rich source of information on human diseases, but the information is variably structured, fragmented, curated using different coding systems, and collected for purposes other than medical research. We describe an approach for developing, validating, and sharing reproducible phenotypes from national structured EHR in the United Kingdom with applications for translational research.

MATERIALS AND METHODS

We implemented a rule-based phenotyping framework, with up to 6 approaches of validation. We applied our framework to a sample of 15 million individuals in a national EHR data source (population-based primary care, all ages) linked to hospitalization and death records in England. Data comprised continuous measurements (for example, blood pressure; medication information; coded diagnoses, symptoms, procedures, and referrals), recorded using 5 controlled clinical terminologies: (1) read (primary care, subset of SNOMED-CT [Systematized Nomenclature of Medicine Clinical Terms]), (2) International Classification of Diseases-Ninth Revision and Tenth Revision (secondary care diagnoses and cause of mortality), (3) Office of Population Censuses and Surveys Classification of Surgical Operations and Procedures, Fourth Revision (hospital surgical procedures), and (4) DM+D prescription codes.

RESULTS

Using the CALIBER phenotyping framework, we created algorithms for 51 diseases, syndromes, biomarkers, and lifestyle risk factors and provide up to 6 validation approaches. The EHR phenotypes are curated in the open-access CALIBER Portal (https://www.caliberresearch.org/portal) and have been used by 40 national and international research groups in 60 peer-reviewed publications.

CONCLUSIONS

We describe a UK EHR phenomics approach within the CALIBER EHR data platform with initial evidence of validity and use, as an important step toward international use of UK EHR data for health research.

Use of real-world evidence in postmarketing medicines regulation in the European Union: a systematic assessment of European Medicines Agency referrals 2013-2017

OBJECTIVES

To assess the use, and evaluate the usefulness, of non-interventional studies and routinely collected healthcare data in postmarketing assessments conducted by the European Medicines Agency (EMA).

DESIGN

We reviewed and systematically assessed all referrals to the EMA made due to safety or efficacy concerns that were evaluated between 1 January 2013 and 30 June 2017. We extracted information from the assessment report and the referral notification. Two reviewers independently assessed the contribution of non-interventional evidence to decision-making.

RESULTS

The preliminary evidence leading to the assessment in 52 eligible referrals was mostly from spontaneous reports (cited in 26 of 52 referrals) and randomised trials (22/52). In contrast, many evidence types were used for the full assessment. Non-interventional studies were frequently used in the full assessment for the evaluation of product safety (31/52) and product efficacy (18/52). In particular, non-interventional studies were relied on for the evaluation of safety and efficacy in subgroups, the evaluation of safety relating to a rare adverse event, understanding product usage and misuse and for evaluation of the effectiveness of risk minimisation measures. The most common recommendations were changes to product information (43/52) and marketing authorisation withdrawal or suspension (12/52). In the majority of referrals, non-interventional evidence was judged to contribute to the decision made (30/52) and in three referrals it was the primary source of evidence.

CONCLUSIONS

European regulatory decision-making relies on multiple evidence types, particularly randomised trials, spontaneous reports and non-interventional studies. Non-interventional studies had an important role particularly for the characterisation and quantification of adverse events, the evaluation of product usage and for evaluating the effectiveness of regulatory action to minimise risk.

Willingness of general dental practices in South East London to engage with research

This study assessed the willingness of general dental practices (GDPs) to participate in research. All 263 GDPs in South East London that provide dental care under National Health Service (NHS) contracts were invited. The survey instrument was adapted from previous studies and piloted before administration. Geographical factors and practice characteristics associated with willingness to participate in research were explored in logistic regression models. A total of 77 responses were received (response rate: 29%). Of them, 40 (53%) expressed interest in being involved in primary care research. They saw their main role as collecting data and facilitating access to patients. Time, bureaucracy and lack of energy were the main reasons behind a decision not to engage with research. Those spending more time in NHS services were more likely to be willing to participate in research. Other possible indicators were single-handed GDPs, participation in the dental foundation training programme and location in more affluent areas.

A bibliometric analysis on waste electrical and electronic equipment research

Waste electrical and electronic equipment (WEEE) contains both toxic and valuable materials. Due to rapid development of information and communication technologies (ICT), a large amount of WEEE have been produced, leading to increasing academic efforts in this field. This study aims to depict the trends and features of WEEE-related studies through a bibliometric analysis. The results show that the total number of WEEE-related publications had sharply increased, with China as the leading country. University of Chinese Academy of Sciences is the most productive WEEE-related research institution, while Mai BX is the most productive author. As such, Waste Management, Journal of Cleaner Production, and Environmental Science & Technology are the most influential journals. The research hotspots of WEEE mainly focus on the recycling and treatment technologies, environmental impacts, and relevant policies of WEEE. By tracing the evolutionary pathway of WEEE research, it is clear that the research frontiers have switched from electronic equipment, extended producer responsibility, sediment, environment and design, risk assessment to life cycle assessment, mobile phone, and behaviors. This study provides valuable insights to those WEEE-related scholars so that they can identify their own research topics and partners. This paper is one of the first studies in WEEE research field that offers critical discussions and suggestions related to research development and future trends, and used visualized tools to present the holistic picture of this field.

Characteristics and trends of oral leukoplakia research: A bibliometric study of the 100 most cited articles

BACKGROUND

Bibliometric analysis highlights the key topics and studies which have shaped the understanding and management of a disease of interest. Here the top-cited articles on oral leukoplakia (OL) were characterized, and research patterns and trends were analyzed.

METHODS

A comprehensive search was performed and identified in the Scopus database up to 22 February 2019 for the 100 most-cited articles on OL.

RESULTS

The number of citations of the 100 selected articles varied from 116 to 1418, with a mean of 226.7 citations per article. Both Journal of Oral Pathology and Medicine and Oral Surgery Oral Medicine Oral Pathology Oral Radiology were journals with the most articles published (n = 10). Both Hong W.K. and Lippman S. were the most frequently contributing authors (n = 9). United States (n = 43) and M.D. Anderson Cancer Center (n = 12) was most contributing country and institution, respectively. Systematic reviews/meta-analysis (n = 3) and randomized controlled trial (n = 7) were study designs with high evidence level. It is noteworthy that the majority of high-quality articles were the research of chemopreventive drugs (n = 21) and molecular markers/targets (n = 10), which may indicate a trend of key topics.

CONCLUSIONS

The results of this first citation analysis of the most-cited articles on OL provide a historical perspective on scientific evolution, and suggest further research trends and clinical practice in the field of OL.

Challenges in IBD Research: Pragmatic Clinical Research

Pragmatic clinical research is part of five focus areas of the Challenges in IBD research document, which also includes preclinical human IBD mechanisms, environmental triggers, novel technologies, and precision medicine. The Challenges in IBD research document provides a comprehensive overview of current gaps in inflammatory bowel diseases (IBD) research and delivers actionable approaches to address them. It is the result of multidisciplinary input from scientists, clinicians, patients, and funders, and represents a valuable resource for patient centric research prioritization. In particular, the pragmatic clinical research section is focused on highlighting gaps that need to be addressed in order to optimize and standardize IBD care. Identified gaps include: 1) understanding the incidence and prevalence of IBD; 2) evaluating medication positioning to increase therapeutic effectiveness; 3) understanding the utility of therapeutic drug monitoring (TDM); 4) studying pain management; and 5) understanding healthcare economics and resources utilization. To address these gaps, there is a need to emphasize the use of emerging data sources and real-world evidence to better understand epidemiologic and therapeutic trends in IBD, expanding on existing data to better understand how and where we should improve care. Proposed approaches include epidemiological studies in ethnically and geographically diverse cohorts to estimate incidence and prevalence of IBD and impact of diversity on treatment patterns and outcomes. The implementation of new clinical trial design and methodologies will be essential to evaluate optimal medication positioning, appropriate use of TDM in adults and children, and multidisciplinary approaches to IBD pain management and its impact on healthcare resources.

Limitations for health research with restricted data collection from UK primary care

Purpose

UK primary care provides a rich data source for research. The impact of proposed data collection restrictions is unknown. This study aimed to assess the impact of restricting the scope of electronic health record (EHR) data collection on the ability to conduct research. The study estimated the consequences of restricted data collection on published Clinical Practice Research Datalink studies from high impact journals or referenced in clinical guidelines.

Methods

A structured form was used to systematically analyse the extent to which individual studies would have been possible using a database with data collection restrictions in place: (1) retrospective collection of specified diseases only; (2) retrospective collection restricted to a 6‐ or 12‐year period; (3) prospective and retrospective collection restricted to non‐sensitive data. Outcomes were categorised as unfeasible (not reproducible without major bias); compromised (feasible with design modification); or unaffected.

Results

Overall, 91% studies were compromised with all restrictions in place; 56% studies were unfeasible even with design modification. With restrictions on diseases alone, 74% studies were compromised; 51% were unfeasible. Restricting collection to 6/12 years had a major impact, with 67 and 22% of studies compromised, respectively. Restricting collection of sensitive data had a lesser but marked impact with 10% studies compromised.

Conclusion

EHR data collection restrictions can profoundly reduce the capacity for public health research that underpins evidence‐based medicine and clinical guidance. National initiatives seeking to collect EHRs should consider the implications of restricting data collection on the ability to address vital public health questions.

Individual, programmatic and systemic indicators of the quality of mental health care using a large health administrative database: an avenue for preventing suicide mortality

Suicide is a major public health issue in Canada. The quality of health care services, in addition to other individual and population factors, has been shown to affect suicide rates. In publicly managed care systems, such as systems in Canada and the United Kingdom, the quality of health care is manifested at the individual, program and system levels. Suicide audits are used to assess health care services in relation to the deaths by suicide at individual level and when aggregated at the program and system levels. Large health administrative databases comprise another data source used to inform population-based decisions at the system, program and individual levels regarding mental health services that may affect the risk of suicide. This status report paper describes a project we are conducting at the Institut national de santé publique du Québec (INSPQ) with the Quebec Integrated Chronic Disease Surveillance System (QICDSS) in collaboration with colleagues from Wales (United Kingdom) and the Norwegian Institute of Public Health. This study describes the development of quality of care indicators at three levels and the corresponding statistical analysis strategies designed. We propose 13 quality of care indicators, including system-level and several population-level determinants, primary care treatment, specialist care, the balance between care sectors, emergency room utilization, and mental health and addiction budgets, that may be drawn from a chronic disease surveillance system.

Under-recording of hospital bleeding events in UK primary care: a linked Clinical Practice Research Datalink and Hospital Episode Statistics study

BACKGROUND

Primary care databases represent a rich source of data for health care research; however, the quality of recording of secondary care events in these databases is uncertain. This study sought to investigate the completeness of recording of hospital admissions for bleeds in primary care records and explore the impact of incomplete recording on estimates of bleeding risk associated with antithrombotic treatment.

METHODS

The study population consisted of adults with non-valvular atrial fibrillation who had at least one bleed recorded in either the Clinical Practice Research Datalink (CPRD) or Hospital Episode Statistics (HES) while receiving prescriptions for an oral anticoagulant. The proportion of bleeds recorded in HES that had a corresponding bleed recorded in the subsequent 12 weeks in CPRD was calculated, and factors associated with having a corresponding record were identified. Cox proportional hazards analyses investigating the hazard of subsequent bleeding associated with antithrombotic treatment were carried out using linked CPRD-HES data and using CPRD only data, and the results were compared.

RESULTS

Less than 20% of the 14,361 bleeds recorded in the HES data had a corresponding bleed coded in the CPRD in the subsequent 12 weeks. This proportion varied by bleed characteristics, calendar time, day of week of admission (weekday vs weekend) and oral anticoagulant treatment at the time of the bleed. The hazard of subsequent bleeding associated with vitamin K antagonists (VKAs) and antiplatelet agents (APAs) relative to no antithrombotic treatment were similar using the linked primary and secondary care dataset (VKA HRadj 1.06 CI95 0.96-1.16; APA HRadj 1.08 CI95 0.96-1.21) and the unlinked primary care data (VKA HRadj 1.12 CI95 1.01-1.24; APA HRadj 1.06 CI95 0.95-1.20).

CONCLUSION

Secondary care bleeding events are not completely recorded in primary care records and under-recording may be differential with respect to a variety of factors, including antithrombotic treatment. While the impact of under-recording on estimates of the comparative safety of antithrombotic drugs was limited, the extent of the under-recording suggests its potential impact should be considered, and ideally evaluated in future studies utilizing standalone primary care data.

Spatial distribution of clinical computer systems in primary care in England in 2016 and implications for primary care electronic medical record databases: a cross-sectional population study

OBJECTIVES

UK primary care databases (PCDs) are used by researchers worldwide to inform clinical practice. These databases have been primarily tied to single clinical computer systems, but little is known about the adoption of these systems by primary care practices or their geographical representativeness. We explore the spatial distribution of clinical computing systems and discuss the implications for the longevity and regional representativeness of these resources.

DESIGN

Cross-sectional study.

SETTING

English primary care clinical computer systems.

PARTICIPANTS

7526 general practices in August 2016.

METHODS

Spatial mapping of family practices in England in 2016 by clinical computer system at two geographical levels, the lower Clinical Commissioning Group (CCG, 209 units) and the higher National Health Service regions (14 units). Data for practices included numbers of doctors, nurses and patients, and area deprivation.

RESULTS

Of 7526 practices, Egton Medical Information Systems (EMIS) was used in 4199 (56%), SystmOne in 2552 (34%) and Vision in 636 (9%). Great regional variability was observed for all systems, with EMIS having a stronger presence in the West of England, London and the South; SystmOne in the East and some regions in the South; and Vision in London, the South, Greater Manchester and Birmingham.

CONCLUSIONS

PCDs based on single clinical computer systems are geographically clustered in England. For example, Clinical Practice Research Datalink and The Health Improvement Network, the most popular primary care databases in terms of research outputs, are based on the Vision clinical computer system, used by <10% of practices and heavily concentrated in three major conurbations and the South. Researchers need to be aware of the analytical challenges posed by clustering, and barriers to accessing alternative PCDs need to be removed.

Future Roadmaps for Precision Medicine Applied to Diabetes: Rising to the Challenge of Heterogeneity

Precision medicine, the concept that specific treatments can be targeted to groups of individuals with specific genetic, cellular, or molecular features, is a key aspect of modern healthcare, and its use is rapidly expanding. In diabetes, the application of precision medicine has been demonstrated in monogenic disease, where sulphonylureas are used to treat patients with neonatal diabetes due to mutations in ATP-dependent potassium (K_ATP) channel genes. However, diabetes is highly heterogeneous, both between and within polygenic and monogenic subtypes. Making the correct diagnosis and using the correct treatment from diagnosis can be challenging for clinicians, but it is crucial to prevent long-term morbidity and mortality. To facilitate precision medicine in diabetes, research is needed to develop a better understanding of disease heterogeneity and its impact on potential treatments for specific subtypes. Animal models have been used in diabetes research, but they are not translatable to humans in the majority of cases. Advances in molecular genetics and functional laboratory techniques and availability and sharing of large population data provide exciting opportunities for human studies. This review will map the key elements of future diabetes research in humans and its potential for clinical translation to promote precision medicine in all diabetes subtypes.

Global cocaine intoxication research trends during 1975-2015: a bibliometric analysis of Web of Science publications

BACKGROUND

Cocaine is subject to recreational abuse as a stimulant and psychoactive agent, which poses a major worldwide health problem. The aim of the present study was to perform a bibliometric analysis of publication related to cocaine intoxication an insight of the research trends at a global level to enable recommendations for future research strategies in this field.

METHODS

Publications about cocaine intoxication were retrieved from the Web of Science (WoS) Core Collection database on December 28, 2016, and analysed regarding the following bibliometric indicators: research trends, document types, languages, countries/territories with their h-index, collaboration patterns, journals with their impact factors (IF), and institutions.

RESULTS

In total, 2,902 scientific publications from 1975 to 2015 were retrieved from the WoS database. The annual number of publications related to cocaine toxicity increased slightly after 1990 and reached a peak of 148 in 1992, with an average of 103 publications per year. The USA outranked other countries/territories with 2,089 publications, of which 1,927 arose exclusively from the USA and 162 involved international collaborations. The h-index for all publications related to cocaine was 212, and the h-index for all publications related to cocaine intoxication was 99. Moreover, the USA had the highest h-index of 95, followed by Spain with h-index of 24, and Canada with h-index of 24. The main research topics were consistently reproductive toxicity, clinical management of acute cocaine exposure, laboratory methods for detection of exposure to cocaine, cocaine metabolism, and cocaine toxicity in animals.

CONCLUSIONS

This is the first bibliometric approach to examining research related to cocaine toxicity and shows that research activity has become more global and extensive since 1990. The USA remains the leading country regarding published literature, the highest h-index, and greatest role in international collaborations.

Methods for enhancing the reproducibility of biomedical research findings using electronic health records

BACKGROUND

The ability of external investigators to reproduce published scientific findings is critical for the evaluation and validation of biomedical research by the wider community. However, a substantial proportion of health research using electronic health records (EHR), data collected and generated during clinical care, is potentially not reproducible mainly due to the fact that the implementation details of most data preprocessing, cleaning, phenotyping and analysis approaches are not systematically made available or shared. With the complexity, volume and variety of electronic health record data sources made available for research steadily increasing, it is critical to ensure that scientific findings from EHR data are reproducible and replicable by researchers. Reporting guidelines, such as RECORD and STROBE, have set a solid foundation by recommending a series of items for researchers to include in their research outputs. Researchers however often lack the technical tools and methodological approaches to actuate such recommendations in an efficient and sustainable manner.

RESULTS

In this paper, we review and propose a series of methods and tools utilized in adjunct scientific disciplines that can be used to enhance the reproducibility of research using electronic health records and enable researchers to report analytical approaches in a transparent manner. Specifically, we discuss the adoption of scientific software engineering principles and best-practices such as test-driven development, source code revision control systems, literate programming and the standardization and re-use of common data management and analytical approaches.

CONCLUSION

The adoption of such approaches will enable scientists to systematically document and share EHR analytical workflows and increase the reproducibility of biomedical research using such complex data sources.