204 Idiopathic intracranial hypertension in Wales: population characterisation, epidemiological trends and healthcare utilisation

Objective

To characterise the Welsh idiopathic intracranial hypertension (IIH) population, epidemiologi- cal trends and healthcare outcomes using routinely collected healthcare data.

Methods

We used primary and secondary care healthcare diagnostic codes within the Secure Anonymised Information Linkage databank to ascertain IIH cases and controls in a retrospective cohort study between 2003–2017. We validated IIH diagnosis codes using anonymised secondary care lists of IIH cases.

Results

We analysed 35 million patient years of data (2003–2017). There were 1765 cases of IIH in 2017 (85% female). The prevalence and incidence of IIH in 2017 was 76/100,000 and 7.8/100,000, significantly increased from 2003 (prevalence=12/100,000, incidence=2.3/100,000). IIH prevalence is associated with socio-economic deprivation and increasing body mass index (BMI). 9% of people with IIH had CSF shunts with less than 0.2% having bariatric surgery. Unscheduled hospital admissions were significantly higher in the IIH cohort compared to controls; and also in IIH patients with CSF shunts compared to those without.

Conclusions

IIH incidence and prevalence is increasing significantly, corresponding to population increases in BMI. This has important implications for healthcare professionals and policy makers given the comor- bidities, complications and increased healthcare utilisation and economic burden associated with IIH.

lotif_miah@hotmail.com

Achievement of European Society of Cardiology/European Atherosclerosis Society lipid targets in very high-risk patients: Influence of depression and sex

AIMS

To explore differences in the use of lipid lowering therapy and/or achievement of lipid guideline targets in patients with and without prior depression and influence of sex in very high-risk coronary patients.

METHODS & FINDINGS

A retrospective observational cohort study was conducted using individual-level linked electronic health record data in patients who underwent percutaneous coronary intervention (2012-2017) in Wales. The cohort comprised of 13,781 patients (27.4% female), with 26.1% having prior depression. Lipid levels were recorded in 10,050 patients of whom 25% had depression. History of depression was independently associated with not having lipids checked (OR 0.79 95%CI 0.72-0.87 p<0.001). Patients with prior depression were less likely to achieve targets for low density lipoprotein cholesterol (LDL-C <1.8mmol/l), non-high density lipoprotein cholesterol (non-HDL-C <2.6mmol/l) and triglycerides (<2.3mmol/l) than patients without depression (OR 0.86 95%CI 0.78-0.96 p = 0.007, OR 0.80 95%CI 0.69-0.92 p = 0.003 & OR 0.69 95CI% 0.61-0.79 p<0.001 respectively). Females were less likely to achieve targets for LDL-C and non-HDL-C than males (OR 0.55 95%CI 0.50-0.61 p<0.001 & OR 0.63 95%CI 0.55-0.73 p<0.001). There was an additive effect of depression and sex; females with depression were not only least likely to be tested (OR 0.74 95%CI 0.65-0.84 p<0.001) but also (where levels were known) less likely to achieve LDL-C (OR 0.47 95%CI 0.41-0.55 p<0.001) and non-HDL-C targets (OR 0.50 95%CI 0.41-0.60 p<0.001). It was not possible to look at the influence of medication adherence on achievement of lipid targets due to limitations of the use of anonymised routinely-held clinical care data.

CONCLUSION

Patients with prior depression were less likely to have their lipids monitored and achieve guideline targets within 1-year. Females with depression are the least likely to be tested and achieve lipid targets, suggesting not only a greater risk of future events, but also an opportunity to improve care.

Markup: A Web-Based Annotation Tool Powered by Active Learning

Across various domains, such as health and social care, law, news, and social media, there are increasing quantities of unstructured texts being produced. These potential data sources often contain rich information that could be used for domain-specific and research purposes. However, the unstructured nature of free-text data poses a significant challenge for its utilisation due to the necessity of substantial manual intervention from domain-experts to label embedded information. Annotation tools can assist with this process by providing functionality that enables the accurate capture and transformation of unstructured texts into structured annotations, which can be used individually, or as part of larger Natural Language Processing (NLP) pipelines. We present Markup (https://www.getmarkup.com/) an open-source, web-based annotation tool that is undergoing continued development for use across all domains. Markup incorporates NLP and Active Learning (AL) technologies to enable rapid and accurate annotation using custom user configurations, predictive annotation suggestions, and automated mapping suggestions to both domain-specific ontologies, such as the Unified Medical Language System (UMLS), and custom, user-defined ontologies. We demonstrate a real-world use case of how Markup has been used in a healthcare setting to annotate structured information from unstructured clinic letters, where captured annotations were used to build and test NLP applications.

Epilepsy, antiepileptic drugs, and the risk of major cardiovascular events

OBJECTIVE

This study was undertaken to determine whether epilepsy and antiepileptic drugs (including enzyme-inducing and non-enzyme-inducing drugs) are associated with major cardiovascular events using population-level, routinely collected data.

METHODS

Using anonymized, routinely collected, health care data in Wales, UK, we performed a retrospective matched cohort study (2003-2017) of adults with epilepsy prescribed an antiepileptic drug. Controls were matched with replacement on age, gender, deprivation quintile, and year of entry into the study. Participants were followed to the end of the study for the occurrence of a major cardiovascular event, and survival models were constructed to compare the time to a major cardiovascular event (cardiac arrest, myocardial infarction, stroke, ischemic heart disease, clinically significant arrhythmia, thromboembolism, onset of heart failure, or a cardiovascular death) for individuals in the case group versus the control group.

RESULTS

There were 10 241 cases (mean age = 49.6 years, 52.2% male, mean follow-up = 6.1 years) matched to 35 145 controls. A total of 3180 (31.1%) cases received enzyme-inducing antiepileptic drugs, and 7061 (68.9%) received non-enzyme-inducing antiepileptic drugs. Cases had an increased risk of experiencing a major cardiovascular event compared to controls (adjusted hazard ratio = 1.58, 95% confidence interval [CI] = 1.51-1.63, p < .001). There was no notable difference in major cardiovascular events between those treated with enzyme-inducing antiepileptic drugs and those treated with non-enzyme-inducing antiepileptic drugs (adjusted hazard ratio = .95, 95% CI = .86-1.05, p = .300).

SIGNIFICANCE

Individuals with epilepsy prescribed antiepileptic drugs are at an increased risk of major cardiovascular events compared with population controls. Being prescribed an enzyme-inducing antiepileptic drug is not associated with a greater risk of a major cardiovascular event compared to treatment with other antiepileptic drugs. Our data emphasize the importance of cardiovascular risk management in the clinical care of people with epilepsy.

Making the Most of Big Data in Plastic Surgery: Improving Outcomes, Protecting Patients, Informing Service Providers

ABSTRACT

In medicine, "big data" refers to the interdisciplinary analysis of high-volume, diverse clinical and lifestyle information on large patient populations. Recent advancements in data storage and electronic record keeping have enabled the expansion of research in this field. In the United Kingdom, Big data has been highlighted as one of the government's "8 Great Technologies," and the Medical Research Council has invested more than £100 million since 2012 in developing the Health Data Research UK infrastructure. The recent Royal College of Surgeons Commission of the Future of Surgery concluded that analysis of big data is one of the 4 most likely avenues to bring some of the most innovative changes to surgical practice in the 21st century.In this article, we provide an overview of the nascent field of big data analytics in plastic and highlight how it has the potential to improve outcomes, increase safety, and aid service planning.We outline the current resources available, the emerging role of big data within the subspecialties of burns, microsurgery, skin and breast cancer, and how these data can be used. We critically review the limitations and considerations raised with big data, offer suggestions regarding database optimization, and suggest future directions for research in this exciting field.

Incidence, Prevalence, and Health Care Outcomes in Idiopathic Intracranial Hypertension: A Population Study

OBJECTIVE

To characterize trends in incidence, prevalence, and health care outcomes in the idiopathic intracranial hypertension (IIH) population in Wales using routinely collected health care data.

METHODS

We used and validated primary and secondary care IIH diagnosis codes within the Secure Anonymised Information Linkage databank to ascertain IIH cases and controls in a retrospective cohort study between 2003 and 2017. We recorded body mass index (BMI), deprivation quintile, CSF diversion surgery, and unscheduled hospital admissions in case and control cohorts.

RESULTS

We analyzed 35 million patient-years of data. There were 1,765 cases of IIH in 2017 (85% female). The prevalence and incidence of IIH in 2017 was 76/100,000 and 7.8/100,000/y, a significant increase from 2003 (corresponding figures = 12/100,000 and 2.3/100,000/y) (p < 0.001). IIH prevalence is associated with increasing BMI and increasing deprivation. The odds ratio for developing IIH in the least deprived quintile compared to the most deprived quintile, adjusted for sex and BMI, was 0.65 (95% confidence interval 0.55 to 0.76). Nine percent of IIH cases had CSF shunts with less than 0.2% having bariatric surgery. Unscheduled hospital admissions were higher in the IIH cohort compared to controls (rate ratio 5.28, p < 0.001) and in individuals with IIH and CSF shunts compared to those without shunts (rate ratio 2.02, p < 0.01).

CONCLUSIONS

IIH incidence and prevalence is increasing considerably, corresponding to population increases in BMI, and is associated with increased deprivation. This has important implications for health care professionals and policy makers given the comorbidities, complications, and increased health care utilization associated with IIH.

Idiopathic Intracranial Hypertension in Wales

IntroductionIdiopathic Intracranial Hypertension (IIH) is a condition of unknown aetiology that is strongly associated with obesity. IIH predominantly affects women of childbearing age and causes chronic disabling headaches, visual disturbance and, in a minority of patients, permanent visual loss. Objectives and ApproachWe characterised the IIH population, epidemiological trends and healthcare outcomes in Wales using routinely collected healthcare data. We used primary and secondary care healthcare diagnosis codes within the Secure Anonymised Information Linkage databank to ascertain IIH cases and controls in a retrospective cohort study between 2003 and 2017. We validated IIH diagnosis codes using anonymised secondary care lists of IIH cases. ResultsWe analysed 35 million patient years of data (2003–2017). There were 1765 cases of IIH in 2017 (85% female). The prevalence and incidence of IIH in 2017 was 76/100,000 and 7.8/100,000/year, a significant increase from 2003 (corresponding figures=12/100,000 and 2.3/100,000/year). The odds ratio for developing IIH in the least deprived quintile compared to the most deprived quintile, adjusted for gender and Body Mass Index (BMI), was 0.65 (95% CI=0.55–0.76). 9% of people with IIH had CSF shunts with less than 0.2% having bariatric surgery. Unscheduled hospital admissions were significantly higher in the IIH cohort compared to controls (rate ratio=5.28, p<0.001) and in the people with IIH with CSF shunts compared to those without (rate ratio=2.02, p<0.01). Conclusion / ImplicationsIIH incidence and prevalence is increasing significantly, corresponding to population increases in BMI, and is associated with increased deprivation. This has important implications for healthcare professionals and policy makers given the comorbidities, complications and increased healthcare utilisation associated with IIH.

Markup: A Web-Based Clinical Annotation Tool with Enhanced Ontology Mapping

IntroductionUnstructured free-text clinical notes often contain valuable information relating to patient symptoms, prescriptions and diagnoses. These can assist with better care for patients and novel healthcare research if transformed into accessible, structured clinical text. In particular, Natural Language Processing (NLP) algorithms can produce such structured outputs, but require gold standard data to train and validate their accuracy. While existing tools such as Brat and Webanno provide interfaces to manually annotate text, there is a lack of capability to efficiently annotate complex clinical information. Objectives and ApproachWe present Markup, an open-source, web-based annotation tool developed for use within clinical contexts by domain experts to produce gold standard annotations for NLP development. Markup incorporates NLP and Active Learning technologies to enable rapid and accurate annotation of unstructured documents. Markup supports custom user configurations, automated annotation suggestions, and automated mapping to existing clinical ontologies such as the Unified Medical Language System (UMLS), the Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT), or custom, user-defined ontologies. ResultsMarkup has been tested on Epilepsy clinic letters, where captured annotations were used to build and test NLP applications. Markup allowed for inter-annotator statistics to be calculated in the case of multiple annotators. Re-annotation, following iterations of annotation definitions, was incorporated for flexibility. UMLS codes, certainty context, and multiple components from complex phrases were all able to be captured and exported in a structured format. Conclusions / ImplicationsMarkup allows gold standard annotations to be collected efficiently across unstructured text and is optimized to capture health-specific information. These annotations are important to develop and validate NLP algorithms that automate the capture of important information from clinic letters at scale.

A National Level Case-Control Study for Determining Risk of Major Cardiovascular Events in People with Epilepsy

IntroductionThe risk of cardiovascular events amongst people with epilepsy who are receiving enzyme-inducing anti-epileptic drugs (EIAEDs) seems to be higher than those on other medications and the general population. National-level record linkage enables development of case-control studies at a wider scope accounting for multiple factors. Objectives and ApproachPeople with epilepsy were identified between 2003-01-01 and 2017-12-31 and were matched to a control group on: age, gender, deprivation quintile and year of diagnosis, accounting for any changes in clinical therapeutic guidelines. Primary and secondary care population records were linked to capture relevant comorbidities and major cardiovascular events. Annual district birth and death extract were used in combination with the Welsh Demographic Service (WDS) dataset to capture demographic and cardiovascular related death records. The WDS dataset was used to identify eligible control groups for each case and a linkage approach between the control and case database was developed for matching cases and controls with replacement and randomization. Survival analysis was conducted to evaluate the difference in time to first major cardiovascular event in patients receiving EIAED versus Non-EIAEDs and controls. Results10,241 cases (mean age 49.6 years, 52.2% male) with diagnosis of epilepsy were matched to 35,145 controls. 3,180 (31.1%) cases received EIAEDs and 7,061 (68.9%) received non-EIAEDs. The risk of experiencing a major cardiovascular event was higher in cases compared to controls (adjusted hazard ratio 1.52,95%CI[1.50–1.55];p<0.001). There was no significant difference in cardiovascular events between those treated with non-EIAEDs and EIAEDs (adjusted hazard ratio 1.04,95%CI[0.95-1.12];p=0.407). Conclusion / ImplicationsData linkage provides a unique opportunity and insight into studying disease risk factors. We have shown that individuals with epilepsy prescribed antiepileptic drugs, re at an increased risk of a major cardiovascular events regardless of treatment type (EIAED,NEIAED) compared with a matched control population.

Toward a Risk-Utility Data Governance Framework for Research Using Genomic and Phenotypic Data in Safe Havens: Multifaceted Review

BACKGROUND

Research using genomic data opens up new insights into health and disease. Being able to use the data in association with health and administrative record data held in safe havens can multiply the benefits. However, there is much discussion about the use of genomic data with perceptions of particular challenges in doing so safely and effectively.

OBJECTIVE

This study aimed to work toward a risk-utility data governance framework for research using genomic and phenotypic data in an anonymized form for research in safe havens.

METHODS

We carried out a multifaceted review drawing upon data governance arrangements in published research, case studies of organizations working with genomic and phenotypic data, public views and expectations, and example studies using genomic and phenotypic data in combination. The findings were contextualized against a backdrop of legislative and regulatory requirements and used to create recommendations.

RESULTS

We proposed recommendations toward a risk-utility model with a flexible suite of controls to safeguard privacy and retain data utility for research. These were presented as overarching principles aligned to the core elements in the data sharing framework produced by the Global Alliance for Genomics and Health and as practical control measures distilled from published literature and case studies of operational safe havens to be applied as required at a project-specific level.

CONCLUSIONS

The recommendations presented can be used to contribute toward a proportionate data governance framework to promote the safe, socially acceptable use of genomic and phenotypic data in safe havens. They do not purport to eradicate risk but propose case-by-case assessment with transparency and accountability. If the risks are adequately understood and mitigated, there should be no reason that linked genomic and phenotypic data should not be used in an anonymized form for research in safe havens.

Achievement of European guideline-recommended lipid levels post-percutaneous coronary intervention: A population-level observational cohort study

AIMS

European Society of Cardiology/European Atherosclerosis Society 2019 guidelines recommend more aggressive lipid targets in high- and very high-risk patients and the addition of adjuvant treatments to statins in uncontrolled patients. We aimed to assess (a) achievement of prior and new European Society of Cardiology/European Atherosclerosis Society lipid targets and (b) lipid-lowering therapy prescribing in a nationwide cohort of very high-risk patients.

METHODS

We conducted a retrospective observational population study using linked health data in patients undergoing percutaneous coronary intervention (2012-2017). Follow-up was for one-year post-discharge.

RESULTS

Altogether, 10,071 patients had a documented LDL-C level, of whom 48% had low-density lipoprotein cholesterol (LDL-C)<1.8 mmol/l (2016 target) and (23%) <1.4 mmol/l (2019 target). Five thousand three hundred and forty patients had non-high-density lipoprotein cholesterol (non-HDL-C) documented with 57% <2.6 mmol/l (2016) and 37% <2.2 mmol/l (2019). In patients with recurrent vascular events, fewer than 6% of the patients achieved the 2019 LDL-C target of <1.0 mmol/l. A total of 10,592 patients had triglyceride (TG) levels documented, of whom 14% were ≥2.3 mmol/l and 41% ≥1.5 mmol/l (2019). High-intensity statins were prescribed in 56.4% of the cohort, only 3% were prescribed ezetimibe, fibrates or prescription-grade N-3 fatty acids. Prescribing of these agents was lower amongst patients above target LDL-C, non-HDL-C and triglyceride levels. Females were more likely to have LDL-C, non-HDL-C and triglyceride levels above target.

CONCLUSION

There was a low rate of achievement of the new European Society of Cardiology/European Atherosclerosis Society lipid targets in this large post-percutaneous coronary intervention population and relatively low rates of intensive lipid-lowering therapy prescribing in those with uncontrolled lipids. There is considerable potential to optimise lipid-lowering therapy further through statin intensification and appropriate use of novel lipid-lowering therapy, especially in women.

Epilepsy Mortality in Wales: 2005-2017

BackgroundEpilepsy is a common, chronic neurological condition that affects 50 million people worldwide. The risk of premature death in people with epilepsy is up to three times higher than for the general population making this disease a significant public health concern. In England, there are around 3,100 deaths associated with epilepsy each year; 49 per cent of these deaths are premature. The mortality of epilepsy in Wales in recent years is currently unknown. Main Aim To ascertain mortality figures for deaths associated with epilepsy in Wales. MethodWe anonymously linked the Annual District Death Extract and the Welsh Demographics Service datasets within the Secure Anonymised Information Linkage Databank. Using ICD-10 codes for epilepsy, we identified all people who died with a mention of epilepsy on their death certificate, date of their death, and age at death between 2005 and 2017. Number of deaths per year were summed for each year. We also calculated the proportion of premature deaths and mean age at death for each year. All-cause mortality figures were collated as comparators. ResultsDuring the study period, there were around 173 deaths associated with epilepsy in Wales each year. The proportion of epilepsy-associated deaths compared with all-cause deaths increased almost two-fold during this time. 54% of all deaths associated with epilepsy occurred under the age of 75 years, compared with 33 per cent of all-cause deaths. The mean age at death for people with epilepsy is 67 years; 11 years younger than all-cause deaths (78 years). ConclusionThe number of deaths associated with epilepsy is increasing every year in Wales. These figures also show that having epilepsy reduces life expectancy. More research is needed into the causes of epilepsy-associated deaths to inform policy and improve outcomes for this patient group.

Association between levodopa and ischemic heart disease

Background Several studies linked the use of levodopa to an increase in homocysteine level, which can lead eventually to ischemic heart disease (IHD) in Parkinson’s disease (PD) patients. There is a lack of large population studies that have investigated the cardiovascular safety of levodopa. Objectives The main objective of the study is to investigate the one-year risk of IHD hospitalisation, all-cardiovascular hospital hospitalisation, and all-cause mortality among users of L-dopa compared with users of Monoamine oxidase B (MAO-B) inhibitors (as a reference). Methods A population-based study evaluated data obtained from the Secure Anonymised Information Linkage (SAIL) Databank of residents in Wales, aged 40 years or older, newly treated with PD medications between 2000 and 2016. The General Practice (GP) database was used to identify the PD diagnostic codes, PD medications, and other medications used by PD patients. Hospital data were used to identify the first hospitalisation event (IHD and other cardiovascular events). A fully adjusted propensity score multivariate Cox regression analysis was used to examine associations between levodopa and the study outcomes. The index date was set at the date of the first PD prescription in the newly diagnosed PD patients. Other variables included gender, comorbidities, social deprivation score and previous medications history were controlled for. Findings There were 5,140 participants on levodopa and 494 on MAO-B inhibitors. L-dopa was not associated with IHD (p=0.561), other cardiovascular events (p=0.233), or all-cause mortality (p=0.334). For IHD, the lack of difference was seen also in the unadjusted model and in the age-only adjusted model. Conclusion This study has shown that L-dopa does not increase the risk of IHD, cardiovascular risk, or all-cause mortality in the newly diagnosed PD patient within one year after the therapy initiation. This could contribute to the safety profile of L-dopa therapy. Future research with a longer follow up period is warranted.

Early Discontinuation of P2Y12 Antagonists and Adverse Clinical Events Post-Percutaneous Coronary Intervention: A Hospital and Primary Care Linked Cohort

Background

Early discontinuation of P2Y₁₂ antagonists post–percutaneous coronary intervention may increase risk of stent thrombosis or nonstent recurrent myocardial infarction. Our aims were to (1) analyze the early discontinuation rate of P2Y₁₂ antagonists post–percutaneous coronary intervention, (2) explore factors associated with early discontinuation, and (3) analyze the risk of major adverse cardiovascular events (death, acute coronary syndrome, revascularization, or stroke) associated with discontinuation from a prespecified prescribing instruction of 1 year.

Method and Results

We studied 2090 patients (2011–2015) who were recommended for clopidogrel for 12 months (+aspirin) post–percutaneous coronary intervention within a retrospective observational population cohort. Relationships between clopidogrel discontinuation and major adverse cardiac events were evaluated over 18‐month follow‐up. Discontinuation of clopidogrel in the first 4 quarters was low at 1.1%, 2.6%, 3.7%, and 6.1%, respectively. Previous revascularization, previous ischemic stroke, and age >80 years were independent predictors of early discontinuation. In a time‐dependent multiple regression model, clopidogrel discontinuation and bleeding (hazard ratio=1.82 [1.01–3.30] and hazard ratio=5.30 [3.14–8.94], respectively) were independent predictors of major adverse cardiac events as were age <49 and ≥70 years (versus those aged 50–59 years), hypertension, chronic kidney disease stage 4+, previous revascularization, ischemic stroke, and thromboembolism. Furthermore, in those with both bleeding and clopidogrel discontinuation, hazard ratio for major adverse cardiac events was 9.34 (3.39–25.70).

Conclusions

Discontinuation of clopidogrel is low in the first year post–percutaneous coronary intervention, where a clear discharge instruction to treat for 1 year is provided. Whereas this is reassuring from the population level, at an individual level discontinuation earlier than the intended duration is associated with an increased rate of adverse events, most notably in those with both bleeding and discontinuation.

Validating epilepsy diagnoses in routinely collected data

IntroductionPrimary healthcare records are used for studies within large data repositories. One of the limitations of using these routinely collected data for epilepsy research is the possibility of including incorrectly recorded diagnoses. To our knowledge, the accuracy of UK GP diagnosis codes for epilepsy has only partially been validated. Objectives and ApproachWe aimed to validate the accuracy of case ascertainment algorithms in identifying people with epilepsy in routinely collected Welsh healthcare data. A reference population of 150 people with definite epilepsy and 150 people without epilepsy was ascertained from hospital records and linked to records held within the Secure Anonymised Information Linkage (SAIL) databank in Wales. We used three different algorithms to identify the reference population: a) individuals with an epilepsy diagnosis code and two consecutive AED prescription codes; b) individuals with an epilepsy diagnosis code only; c) individuals with two consecutive AED prescription codes only. ResultsWe applied the algorithms to all patients and to adults and children separately. For all patients, combining diagnosis and AED prescription codes had a sensitivity of 84% (95% ci 77–90) and specificity of 98% (95–100) in identifying people with epilepsy; diagnosis codes alone had a sensitivity of 86% (80–91) and a specificity of 97% (92–99); and AED prescription codes alone achieved a sensitivity of 92% (70–83) and a specificity of 73% (65–80). Using AED codes only was more accurate in children, achieving a sensitivity of 88% (75–95) and specificity of 98% (88–100). This can be explained by the widespread use of AEDs for indications other than epilepsy in adults, which is not the case for children. Conclusion/ImplicationsGP epilepsy diagnosis and AED prescription codes can be used to identify people with epilepsy using anonymised healthcare records in Wales. In children using AED prescription codes alone is an accurate way to identify epilepsy cases. These results are generalizable to other studies that use UK primary care records.

Using natural language processing to extract structured epilepsy data from unstructured clinic letters

IntroductionElectronic health records (EHR) are a powerful resource in enabling large-scale healthcare research. EHRs often lack detailed disease-specific information that is collected in free text within clinical settings. This challenge can be addressed by using Natural Language Processing (NLP) to derive and extract detailed clinical information from free text. Objectives and ApproachUsing a training sample of 40 letters, we used the General Architecture for Text Engineering (GATE) framework to build custom rule sets for nine categories of epilepsy information as well as clinic date and date of birth. We used a validation set of 200 clinic letters to compare the results of our algorithm to a separate manual review by a clinician, where we evaluated a “per item” and a “per letter” approach for each category. ResultsThe “per letter” approach identified 1,939 items of information with overall precision, recall and F1-score of 92.7%, 77.7% and 85.6%. Precision and recall for epilepsy specific categories were: diagnosis (85.3%,92.4%),  type (93.7%,83.2%), focal seizure (99.0%,68.3%), generalised seizure (92.5%,57.0%), seizure frequency (92.0%,52.3%), medication (96.1%,94.0%), CT (66.7%,47.1%), MRI (96.6%,51.4%) and EEG (95.8%,40.6%). By combining all items per category, per letter we were able to achieve higher precision, recall and F1-scores of 94.6%, 84.2% and 89.0% across all categories. Conclusion/ImplicationsOur results demonstrate that NLP techniques can be used to accurately extract rich phenotypic details from clinic letters that is often missing from routinely-collected data. Capturing these new data types provides a platform for conducting novel precision neurology research, in addition to potential applicability to other disease areas.

Socioeconomic inequality in medication persistence in primary and secondary prevention of coronary heart disease - A population-wide electronic cohort study

Background

Coronary heart disease (CHD) mortality in England fell by 36% between 2000 and 2007 and it is estimated that approximately 50% of the fall was due to improved treatment uptake. Marked socio-economic inequalities in CHD mortality in the United Kingdom (UK) remain, with higher age-adjusted rates in more deprived groups. Inequalities in the persistence of medication for primary and secondary prevention of CHD may contribute to the observed social gradient and we investigated this possibility in the population of Wales (UK).

Methods and findings

An electronic cohort of individuals aged over 20 (n = 1,199,342) in Wales (UK) was formed using linked data from primary and secondary care and followed for six years (2004–2010). We identified indications for medication (statins, aspirin, ACE inhibitors, clopidogrel) recommended in UK National Institute for Clinical Excellence (NICE) guidance for CHD (high risk, stable angina, stable angina plus diabetes, unstable angina, and myocardial infarction) and measured the persistence of indicated medication (time from initiation to discontinuation) across quintiles of the Welsh Index of Multiple Deprivation, an area-based measure of socio-economic inequality, using Cox regression frailty models. In models adjusted for demographic factors, CHD risk and comorbidities across 15 comparisons for persistence of the medications, none favoured the least deprived quintile, two favoured the most deprived quintile and 13 showed no significant differences.

Conclusions

During our study period (2004–2010) we found no significant evidence of socio-economic inequality in the persistence of recommended medication for primary and secondary prevention of CHD.

Codifying unstructured data: A Natural Language Processing approach to extract rich data from clinical letters

ABSTRACT ObjectivesElectronic healthcare records (EHR) are the main data sources that facilitate epidemiology research. Routinely collected data such as primary and secondary care are now easily linked to produce novel and high impact research. There are, however, rich data locked in the free text of clinical letters that are not otherwise translated into EHRs. It is highly desirable to be able to extract this information to strengthen the body of information in existing EHRs. The Swansea Collaborative in Analysis of NLP Research (SCANR) group at Swansea University has been established to evaluate the usage of Natural Language Processing platforms for obtaining new clinical data. To use Clix Enrich to extract SNOMED concepts from a variety of clinical free texts and produce EHRs from the extraction process. Approach SNOMED concepts contain common items of interest such as diagnosis, medication and symptoms, as well as contextual concepts such as historical reference and negation. Clix Enrich uses the SNOMED dictionary to encode clinical free text (pre-co-ordinated) and find contextually correct SNOMED concepts (post co-ordinated). We used Clix Enrich to extract meaningful clinical terms from MS and Epilepsy consultant letters, as well as presenting complaint fields from a Welsh Emergency Department (ED). ResultsWe tailored Clix Enrich to extract a wide variety of clinical terms from each source (fourty texts per source) and validated the extraction accuracy with clinical experts in each domain. Clix Enrich was able to accurately extract the correct diagnosis for MS, Epilepsy and ED attendance (100%, 95% and 80%), dosage and frequency of anti-epileptic medication and MS modifying therapy (90%, 100%) and EDDS score (94%). We note a probable source of discrepancy in extraction accuracy between letter sources in the frequency of abbreviated terms, particularly within the presenting complaint field of the ED sample. ConclusionClix Enrich can be used to accurately extract SNOMED concepts from clinical letters. The resulting datasets are readily available to link to existing EHRs, and can be linked to EHRs that adopt the SNOMED coding structure, or backward compatible hierarchies. Clix Enrich comes with out-of-the-box extraction methods but the optimum way to extract the correct information would be to build in custom queries, thus requiring clinical expertise to validate extraction.

Equity in healthcare for coronary heart disease, Wales (UK) 2004-2010: A population-based electronic cohort study

BACKGROUND

Despite substantial falls in coronary heart disease (CHD) mortality in the United Kingdom (UK), marked socioeconomic inequalities in CHD risk factors and CHD mortality persist. We investigated whether inequity in CHD healthcare in Wales (UK) could contribute to the observed social gradient in CHD mortality.

METHODS AND FINDINGS

Linking data from primary and secondary care we constructed an electronic cohort of individuals (n = 1199342) with six year follow-up, 2004-2010. We identified indications for recommended CHD interventions, measured time to their delivery, and estimated risk of receiving the interventions for each of five ordered deprivation groups using a time-to-event approach with Cox regression frailty models. Interventions in primary and secondary prevention included risk-factor measurement, smoking management, statins and antihypertensive therapy, and in established CHD included medication and revascularization. For primary prevention, five of the 11 models favoured the more deprived and one favoured the less deprived. For medication in secondary prevention and established CHD, one of the 15 models favoured the more deprived and one the less deprived. In relation to revascularization, six of the 12 models favoured the less deprived and none favoured the more deprived-this evidence of inequity exemplified by a hazard ratio for revascularization in stable angina of 0.79 (95% confidence interval 0.68, 0.92). The main study limitation is the possibility of under-ascertainment or misclassification of clinical indications and treatment from variability in coding.

CONCLUSIONS

Primary care components of CHD healthcare were equitably delivered. Evidence of inequity was found for revascularization procedures, although this inequity is likely to have only a modest effect on social gradients in CHD mortality. Policymakers should focus on reducing inequalities in CHD risk factors, particularly smoking, as these, rather than inequity in healthcare, are likely to be key drivers of inequalities in CHD mortality.

Statins for secondary prevention: clinical use in patients with acute coronary syndrome in Wales

AIM

Statins have a proven role for the secondary prevention of cardiovascular disease. Despite this, typical patient use in real life is variable. Our aim was to investigate the typical clinical use, including adherence, for statins in a sample population in South Wales (UK).

METHODS

We identified 2248 patients admitted to hospitals in South Wales with acute coronary syndrome using a retrospective 3-year-long longitudinal study. We performed data linkage using the Secure Anonymized Information Linkage databank.

RESULTS & CONCLUSION

In total, 1806 (80.3%) of patients were initiated on statins at discharge, with simvastatin being most common. Only 38% of patients were on high-intensity dosage. There was minimal change in cholesterol levels, with discontinuation rates of 53.7 and 84.3% at 1- and 3-year follow-up, respectively.

Increased morbidity, mortality and length of in-hospital stay for patients with acute coronary syndrome with pre-morbid psychiatric diagnoses

BACKGROUND

Psychiatric and cardiac comorbidities form the top two budget categories for health systems in high-income countries with evidence that psychiatric pre-morbidities lead to worse outcomes in patients with acute coronary syndrome (ACS). There are no studies examining this relationship in a national multicentre population level study in the UK, and no studies examining their impact on length of in-hospital stay (LoS) in ACS. Recognizing at-risk populations and reducing LoS in ACS is an essential part of improving patient care and cost-effectiveness.

METHODS

We investigated the impact of psychiatric diagnoses on morbidity, all-cause mortality and LoS amongst 57,668 ACS patients between Jan-2004 and Dec-2014 using the Secure-Anonymized-Information-Linkage (SAIL) databank. Demographics, admissions, cardiac and psychiatric comorbidities were identified using coded data.

RESULTS

There were a total of 3857 out of 57,668 patients who had a pre-morbid psychiatric diagnosis. The mean LoS in patients without psychiatric comorbidities was 9.78days (95% CI: 9.66-9.91). This was higher (p<0.01) in the presence of any psychiatric diagnosis (14.72), dementia (20.87), schizophrenia (15.67), and mood disorders (13.41). Patients with psychiatric comorbidities had worse net adverse cardiac events (HR 1.18, 95% CI: 1.16-1.21) and mortality rates (HR 1.26, 95% CI: 1.23-1.30).

CONCLUSIONS

Our results demonstrate that psychiatric comorbidities have a significant and clinically important impact on morbidity, mortality and LoS in ACS patients in Wales, UK. Clinicians' awareness and active management of psychiatric conditions amongst ACS patients is needed to reduce poor outcomes and LoS and ultimately the risk for patients and financial burden for the health-service.

Severe symptomatic aortic stenosis: medical therapy and transcatheter aortic valve implantation (TAVI)-a real-world retrospective cohort analysis of outcomes and cost-effectiveness using national data

Objectives

Determine the real-world difference between 2 groups of patients with severe aortic stenosis and similar baseline comorbidities: surgical turn down (STD) patients, who were managed medically prior to the availability of transcatheter aortic valve implantation (TAVI) following formal surgical outpatient assessment, and patients managed with a TAVI implant.

Design

Retrospective cohort study from real-world data.

Setting

Electronic patient letters were searched for patients with a diagnosis of severe aortic stenosis and a formal outpatient STD prior to the availability of TAVI (1999–2009). The second group comprised the first 90 cases of TAVI in South Wales (2009 onwards). 2 years prior to and 5 years following TAVI/STD were assessed. Patient data were pseudoanonymised, using the Secure Anonymized Information Linkage (SAIL) databank, and extracted from Office National Statistics (ONS), Patient-Episode Database for Wales (PEDW) and general practitioner databases.

Population

90 patients who had undergone TAVI in South Wales, and 65 STD patients who were medically managed.

Main outcome measures

Survival, hospital admission frequency and length of stay, primary care visits, and cost-effectiveness.

Results

TAVI patients were significantly older (81.8 vs 79.2), more likely to be male (59.1% vs 49.3%), baseline comorbidities were balanced. Mortality in TAVI versus STD was 28% vs 70% at 1000 days follow-up. There were significantly more hospital admissions per year in the TAVI group prior to TAVI/STD (1.5 (IQR 1.0–2.4) vs 1.0 IQR (0.5–1.5)). Post TAVI/STD, the TAVI group had significantly lower hospital admissions (0.3 (IQR 0.0–1.0) vs 1.2 (IQR 0.7–3.0)) and lengths of stay (0.4 (IQR 0.0–13.8) vs 11.0 (IQR 2.5–28.5), p<0.05). The incremental cost-effectiveness ratio (ICER) for TAVI was £10 533 per quality-adjusted life year (QALY).

Conclusions

TAVI patients were more likely to survive and avoid hospital admissions compared with the medically managed STD group. The ICER for TAVI was £10 533 per QALY, making it a cost-effective procedure.

Cohort profile: the housing regeneration and health study

A cohort comprising residents of a housing regeneration and health programme was created from routinely collected data using a system which allows us to anonymously link housing data to individuals and their health. The regeneration programme incorporating four rolling work packages runs from 2009 to 2014. The main intervention cohort we describe here contains the 18 312 residents of 9051 residences at baseline. The cohort will be followed continuously through routine health data (demographics, mortality, hospital admissions and general practitioner records including prescriptions) with periodic updates of housing regeneration intervention data. Here, we describe the baseline data for the primary health outcomes of emergency hospital admissions for cardiovascular and respiratory conditions and injuries for those aged ≥60 years. We will compare the health of residents within the homes before and after the housing regeneration work has taken place, and we will calculate the change in health service costs with use of hospital and General Practitioners (GP) services. We will also use a difference in differences approach to assess changes in comparison with comparator cohorts. These data will be accessible at the end of the study period in 2016. Further information about this study can be obtained from Ronan Lyons; r.a.lyons@swansea.ac.uk.

Barriers to uptake of services for coronary heart disease: qualitative study

OBJECTIVES

To identify factors within the South Yorkshire coalfields that influence use of health services by people with angina.

DESIGN

Qualitative study using semistructured individual and group interviews.

SETTING

General practice and community settings in Barnsley and Rotherham health authorities.

PARTICIPANTS

14 patients with stable angina and nine primary care staff had individual interviews plus five community groups and one group of general practitioners.

MAIN OUTCOME MEASURES

Barriers to accessing health services.

RESULTS

A complex web of factors was identified that prevented, delayed, or facilitated referral to secondary care. Delay, denial, and self management by patients meant that the full extent of symptoms often remained hidden from general practitioners, resulting in a delayed or missed referral. Barriers identified fell into six categories: structural, personal, social and cultural, past experience and expectations, diagnostic confusion, and knowledge and awareness.

CONCLUSIONS

Many of the factors influencing referral operate before general practitioners become involved. Community development could be one way of tackling inequalities and promoting sustainable change. Structural changes are needed to improve access and increase the acceptability of general practice services. Primary care staff should be educated to detect underreporting of symptoms and promote appropriate referral.

Sensitivity of the cervical transformation zone to estrogen-induced squamous carcinogenesis

Regions where one type of epithelium replaces another (metaplasia) have a predilection for cancer formation. Environmental factors are closely linked to metaplastic carcinogenesis. In particular, cervical cancers associated with human papillomavirus (HPV) infection develop primarily at the transformation zone, a region where metaplastic squamous cells are detected in otherwise columnar epithelial-lined endocervical glands. Previously, we reported estrogen-induced multistage vaginal and cervical carcinogenesis in transgenic mice expressing HPV16 oncogenes in basal squamous epithelial cells. In the present study to investigate the threshold neoplastic response to exogenous estrogen, we treated groups of transgenic mice with lower hormone doses. A 5-fold reduction in estrogen dose induced squamous carcinogenesis solely at the cervical transformation zone compared with other reproductive tract sites. Further study delineated stages of transformation zone carcinogenesis, including formation of hyperplastic lower uterine glands and emergence of multiple foci of squamous metaplasia from individual stem-like glandular reserve cells, followed by neoplastic progression of metaplasia to dysplasia and squamous cancer. We propose that a combination of low-dose estrogen and low-level HPV oncogene expression biases transformation zone glandular reserve cells toward squamous rather than columnar epithelial fate decisions. Synergistic activation of proliferation by viral oncoprotein cell cycle dysregulation and estrogen receptor signaling, together with altered paracrine stromal-epithelial interactions, may conspire to support and promote neoplastic progression and cancer formation.

Post-partum rubella immunisation: a controlled trial of two vaccines

The effectiveness of two rubella vaccines (RA 27/3 and Cendehill) in women vaccinated post partum was compared. Significantly more women who received RA 27/3 gave satisfactory seroconversion responses than women who received Cendehill (97.6% vs 82.2%). This difference was reflected in the geometric mean titres (43.6 vs 17.0). More women who received RA 27/3 had minor side-effects, but the difference was not significant. The serological response to both vaccines was not affected by the concurrent administration of anti-D immunoglobulin. In view of these findings, the replacement of Cendehill vaccine with RA 27/3 vaccine for women vaccinated post partum should be considered.