Creating medical and drug code lists to identify cases in primary care databases
This paper demonstrates how compilation of medical and drug code lists for outcomes or exposures of interest for studies using primary care databases can be carried out efficiently using Stata. Use of Stata do-files to record and execute the commands provides good documentation and ease of replication of the procedure.
Available from: journals.plos.org
- "In UK primary care, diagnoses are recorded using Read codes, a hierarchical classification system that includes terms relating to signs and symptoms, diagnosis, procedures and investigations. Clinical diagnoses made by specialists and results from diagnostic tests are entered retrospectively in general practice. "
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Small GTPase Rap1 has been implicated in a number of basic cellular functions, including cell-cell and cell-matrix adhesion, proliferation and regulation of polarity. Evolutionarily conserved, Rap1 has been studied in model organisms: yeast, Drosophila and mice. Mouse in vivo studies implicate Rap1 in the control of multiple stem cell, leukocyte and vascular cell functions. In vitro, several Rap1 effectors and regulatory mechanisms have been proposed. In particular, Rap1 has been implicated in maintaining epithelial and endothelial cell junction integrity and linked with cerebral cavernous malformations.
How Rap1 signaling network controls mammalian development is not clear. As a first step in addressing this question, we present phenotypes of murine total and vascular-specific Rap1a, Rap1b and double Rap1a and Rap1b (Rap1) knockout (KO) mice.
Results and conclusions:
The majority of total Rap1 KO mice die before E10.5, consistent with the critical role of Rap1 in epithelial morphogenesis. At that time point, about 50% of Tie2-double Rap1 KOs appear grossly normal and develop normal vasculature, while the remaining 50% suffer tissue degeneration and show vascular abnormalities, including hemorrhages and engorgement of perineural vessels, albeit with normal branchial arches. However, no Tie2-double Rap1 KO embryos are present at E15.5, with hemorrhages a likely cause of death. Therefore, at least one Rap1 allele is required for development prior to the formation of the vascular system; and in endothelium-for the life-supporting function of the vasculature.
Available from: Marc De Hert
- "Data search was performed with the permission of Egton Medical Information Systems clinical database (EMISWeb®; EMIS Group, Leeds, UK), the provider of the GP operating system in this area. All individuals included in the initial search were on the SMI Register, defined based on READ codes (Davé and Peterson, 2009). Records were anonymised at the time they were obtained and contained demographic information, medical history (diagnoses), test results and additional health-related data, such as smoking status and drug treatments. "
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ABSTRACT: Background: Diabetes, obesity and metabolic syndrome are highly prevalent in patients with Severe Mental Illness (SMI) and can impose a major physical health burden.
Objective: To determine how anthropometric and metabolic features changed over time in a retrospective cohort of people with SMI living in Cheshire, UK.
Methods: 1,307 individuals on the SMI Register were followed up between 2002 and 2012 in UK general practice (GP). Subjects were identified through a pseudanonymised search of GP registers.
Results: Baseline body mass index (BMI) was 28.6 kg/m2 increasing to 31.0 at 10-year follow up, (r2=0.84; p=0.0002). There was a significant increase in fasting blood glucose (FBG) from 5.72 mmol/L to 6.79 mmol/L (r2=0.48; p=0.026). Correspondingly, there was a strong positive univariate relation between increase in BMI and FBG (r2=0.54; p<0.0001) taking into account all measurements. FBG also increased slightly with age (p=0.028). With increasing use of statins, total cholesterol fell from 4.5 mmol/L to 3.9 mmol/L (r2=0.88; p=0.0001), as did low-density lipoprotein-cholesterol from 3.43 mmol/L to 2.35 mmol/L (r2=0.94; p=0.0001). In multivariate models, adjusting for age, gender, smoking and blood pressure, each unit increase in BMI (OR=1.07 (1.01, 1.13); p=0.031) and triglycerides (OR=1.28 (1.06, 1.55); p=0.009) were independently associated with an increased risk of having type 2 diabetes.
Conclusions: Increasing BMI relates to increasing rates of dysglycaemia over time. Measures to encourage weight reduction should be key strategies to reduce dysglycaemia rates in SMI. Prescribing of statins may have been effective in improving the lipid profile in this group.
Available from: Geri Keane
- "All patients over the age of 18 with a Read code diagnosis for PDAC or BTC during the study period were included in the study. Read code lists of diagnostic terms for PDAC and BTC were developed using previously described methodology . Data from the first 6 months of registration were excluded to prevent the accidental inclusion of retrospective incident cases of PDAC or BTC. "
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The UK incidence of pancreatic ductal adenocarcinoma (PDAC) is approximately 9/100,000 population compared with 1–2/100,000 for biliary tract cancer (BTC). This study explores the incidence of these cancers over time and the influence of socio-demographic and geographic factors in a UK primary care cohort.
This study uses data from a large UK primary care database, The Health Improvement Network (THIN). All adult patients contributing data to THIN between January 2000 and December 2010 were included. Annual incidence rates were calculated, adjusted for age, gender, time period, deprivation score (Townsend quintile) and strategic health authority.
From 2000–2010, the annual incidence of PDAC increased by an average of 3% per year (95% CI 1.00–4.00%) and BTC by 4% (95% CI 2.00–6.00%). Incidence of both cancers increased steeply with age and was higher in men. BTC was associated with increasing deprivation (most deprived versus least deprived quintile (OR: 1.45 [95% CI: 1.17, 1.79.]).
The overall incidence of both cancers is low but increasing. Variations in incidence may reflect changes in coding practice or increased exposure to associated risk factors.
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