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Denaxas, S.

Publications and source records attributed to Denaxas, S..

6 recordsLinked to original sources

Genome-wide association study provides new insights into the genetic architecture and pathogenesis of heart failure

Heart failure (HF) is a leading cause of morbidity and mortality worldwide1. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained2-4. We report the largest GWAS meta-analysis of HF to-date, comprising 47,309 cases and 930,014 controls. We identify 12 independent variant associations with HF at 11 genomic loci, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function suggesting shared genetic aetiology. Expression quantitative trait analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homeostasis (BAG3), and cellular senescence (CDKN1A). Using Mendelian randomisation analysis we provide new evidence supporting previously equivocal causal roles for several HF risk factors identified in observational studies, and demonstrate CAD-independent effects for atrial fibrillation, body mass index, hypertension and triglycerides. These findings extend our knowledge of the genes and pathways underlying HF and may inform the development of new therapeutic approaches.

genetics↗

Analyzing the heterogeneity of rule-based EHR phenotyping algorithms in CALIBER and the UK Biobank

Electronic Health Records (EHR) are data generated during routine interactions across healthcare settings and contain rich, longitudinal information on diagnoses, symptoms, medications, investigations and tests. A primary use-case for EHR is the creation of phenotyping algorithms used to identify disease status, onset and progression or extraction of information on risk factors or biomarkers. Phenotyping however is challenging since EHR are collected for different purposes, have variable data quality and often require significant harmonization. While considerable effort goes into the phenotyping process, no consistent methodology for representing algorithms exists in the UK. Creating a national repository of curated algorithms can potentially enable algorithm dissemination and reuse by the wider community. A critical first step is the creation of a robust minimum information standard for phenotyping algorithm components (metadata, implementation logic, validation evidence) which involves identifying and reviewing the complexity and heterogeneity of current UK EHR algorithms. In this study, we analyzed all available EHR phenotyping algorithms (n=70) from two large-scale contemporary EHR resources in the UK (CALIBER and UK Biobank). We documented EHR sources, controlled clinical terminologies, evidence of algorithm validation, representation and implementation logic patterns. Understanding the heterogeneity of UK EHR algorithms and identifying common implementation patterns will facilitate the design of a minimum information standard for representing and curating algorithms nationally and internationally.

bioinformatics↗

UK phenomics platform for developing and validating EHR phenotypes: CALIBER

ObjectiveElectronic health records 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 Electronic Health Records (EHR) in the UK with applications for translational research. Materials and MethodsWe implemented a rule-based phenotyping framework, with up to six 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 such as blood pressure, medication information and coded diagnoses, symptoms, procedures and referrals, recorded using five controlled clinical terminologies: a) Read (primary care, subset of SNOMED-CT), b) ICD-9, ICD-10 (secondary care diagnoses and cause of mortality), c) OPCS-4 (hospital surgical procedures) and d) Gemscript Drug Codes. ResultsThe open-access CALIBER Portal (https://www.caliberresearch.org/portal) demonstrates phenotyping algorithms for 50 diseases, syndromes, biomarkers and lifestyle risk factors and provides up to six validation layers. These phenotyping algorithms have been used by 40 national/international research groups in 60 peer-reviewed publications. ConclusionHerein, we describe the UK EHR phenomics approach, CALIBER, with initial evidence of validity and use, as an important step towards international use of UK EHR data for health research.

epidemiology↗

Bleeding in cardiac patients prescribed antithrombotic drugs: Electronic health record phenotyping algorithms, incidence, trends and prognosis

BackgroundClinical guidelines and public health authorities lack recommendations on scalable approaches to defining and monitoring the occurrence and severity of bleeding in populations prescribed antithrombotic therapy. We aimed to develop electronic health record algorithms for different bleeding phenotypes, and to determine the incidence, time trends and prognosis of bleeding in patients with incident cardiac disorders indicated for antiplatelet and/or vitamin K antagonist (VKA) therapy. MethodsWe examined linked primary care, hospital admission and death registry electronic health records (CALIBER 1998-2010, England) of patients with newly diagnosed atrial fibrillation, acute myocardial infarction, unstable angina or stable angina to develop algorithms for bleeding events. Kaplan-Meier plots were used to estimate the incidence of bleeding events and we used Cox regression models to assess prognosis for all-cause mortality, atherothrombotic events and further bleeding following bleeding events. ResultsWe present electronic health record phenotyping algorithms for bleeding based on bleeding diagnosis in primary or hospital care, symptoms, transfusion, surgical procedures, and haemoglobin values. In validation of the phenotype we estimated a positive predictive value of 0.88 (95% Cl: 0.64, 0.99) for hospitalised bleeding. Amongst 128,815 patients, 27259 (21.2%) had at least one bleeding event, with 5 year risks of bleeding of 29.1%, 21.9%, 25.3% and 23.4% following diagnoses of atrial fibrillation, acute myocardial infarction, unstable angina and stable angina respectively. Rates of hospitalised bleeding per 1000 patients more than doubled from 1.02 (95% Cl: 0.83, 1.22) in January 1998 to 2.68 (95% Cl: 2.49, 2.88) in December 2009 coinciding with increased rates of antiplatelet and VKA prescribing. Patients with hospitalised bleeding and primary care bleeding, with or without markers of severity, were at increased risk of all-cause mortality and atherothrombotic events compared to those with no bleeding. For example the hazard ratio for all-cause mortality was 1.98 (95% Cl: 1.86, 2.11) for primary care bleeding with markers of severity, and 1.99 (95% Cl: 1.92, 2.05) for hospitalised bleeding without markers of severity, compared to patients with no bleeding. ConclusionsElectronic health record bleeding phenotyping algorithms offer a scalable approach to monitoring bleeding in the population. Incidence of bleeding has doubled in incidence since 1998, affects 1 in 4 cardiac patients, and is associated with poor prognosis. Efforts are required to tackle this iatrogenic epidemic. O_LSTWhat is already known?C_LSTO_LIClinical guidelines and public health authorities lack recommendations on how to define or monitor the occurrence and severity of bleeding in populations. C_LIO_LIThis is particularly important because clinical guidelines increasingly recommend the use of one, two or three antiplatelet and vitamin K antagonist drugs to lower the risk of subsequent atherothrombotic events in common heart diseases including atrial fibrillation, acute coronary syndromes and chronic stable angina. C_LIO_LIClinical guidelines lack consistent recommendations of how to reduce the main side effect of bleeding. C_LIO_LIFor acute myocardial infarction it has been shown that combining primary care electronic health records (which include information from hospital discharge summaries) and hospital admission data can generate valid EHR disease phenotypes and provide real-world estimates of disease occurrence. C_LI O_LSTWhat is not known?C_LSTO_LIIt is not known how to define bleeding occurrence and severity in large scale, unselected populations by combining available information on bleeding diagnosis in primary or hospital care, symptoms, transfusion, surgical procedures, and haemoglobin values. C_LIO_LIThe population-based incidence, time trends and long-term prognosis of bleeding have not been evaluated in people with common cardiac disorders. C_LIO_LIComparisons of the population burden of bleeding across common cardiac disorders, such as atrial fibrillation, acute coronary syndromes and stable angina, are lacking. C_LI O_LSTWhat this study adds?C_LSTO_LIPhenotype: We developed standardised replicable EHR phenotyping algorithms defining bleeding and severity measures based on available clinical information across structured primary and hospital care EHR sources. C_LIO_LIIncidence: At 5 years of follow-up, one in five patients with cardiac disease had a bleeding event and 6.5% had fatal or severe bleeding. C_LIO_LITrends: There was approximately a two-fold increase in incidence of primary care and hospitalised bleeding between 1998 and 2010. The rate of fatal bleeding remained stable. C_LIO_LIPrognosis: Patients with bleeding recorded in primary care or in hospital admissions are at increased bleeding between 1998 and 2010. The rate of fatal bleeding remained stable, risk of all-cause death and atherothrombotic events. C_LI

epidemiology↗

Phenome-wide association analysis of LDL-cholesterol lowering genetic variants in PCSK9

BackgroundWe characterised the phenotypic consequence of genetic variation at the PCSK9 locus and compared findings with recent trials of pharmacological inhibitors of PCSK9.\n\nMethodsPublished and individual participant level data (300,000+ participants) were combined to construct a weighted PCSK9 gene-centric score (GS). Fourteen randomized placebo controlled PCSK9 inhibitor trials were included, providing data on 79,578 participants. Results were scaled to a one mmol/L lower LDL-C concentration\n\nResultsThe PCSK9 GS (comprising 4 SNPs) associations with plasma lipid and apolipoprotein levels were consistent in direction with treatment effects. The GS odds ratio (OR) for myocardial infarction (MI) was 0.53 (95%CI 0.42; 0.68), compared to a PCSK9 inhibitor effect of 0.90 (95%CI 0.86; 0.93). For ischemic stroke ORs were 0.84 (95%CI 0.57; 1.22) for the GS, compared to 0.85 (95%CI 0.78; 0.93) in the drug trials. ORs with type 2 diabetes mellitus (T2DM) were 1.29 (95% CI 1.11; 1.50) for the GS, as compared to 1.00 (95%CI 0.96; 1.04) for incident T2DM in PCSK9 inhibitor trials. No genetic associations were observed for cancer, heart failure, atrial fibrillation, chronic obstructive pulmonary disease, or Alzheimers disease - outcomes for which large-scale trial data were unavailable.\n\nConclusionsGenetic variation at the PCSK9 locus recapitulates the effects of therapeutic inhibition of PCSK9 on major blood lipid fractions and MI. Apparent discordance between genetic associations and trial outcome for T2DM might be explained lack by a of statistical precision, or differences in the nature and duration of genetic versus pharmacological perturbation of PCSK9.\n\nFundingThis research was funded by the British Heart Foundation (SP/13/6/30554, RG/10/12/28456, FS/18/23/33512), UCL Hospitals NIHR Biomedical Research Centre, by the Rosetrees and Stoneygate Trusts.\n\nCondensed abstractEvidence on the long-term efficacy and safety of therapeutic inhibition of PCSK9 is lacking. To explore potential long-term effects of PCSK9 inhibition, we characterised the phenotypic consequence of LDL-cholesterol lowering variants at the PCSK9 locus. A PCSK9 gene score comprising 4 SNPs recapitulated the effects of therapeutic inhibition of PCSK9 on major blood lipid fractions and risk of myocardial infarction, and was associated with an increased risk of type 2 diabetes. No associations with safety outcomes such as cancer, COPD, Alzheimers disease or atrial fibrillation were identified. Our findings suggest PCSK9 inhibition may be safe and effective during prolonged use.

genetics↗

Flipping the odds of drug development success through human genomics

Drug development depends on accurately identifying molecular targets that both play a causal role in a disease and are amenable to pharmacological action by small molecule drugs or bio-therapeutics, such as monoclonal antibodies.\n\nErrors in drug target specification contribute to the extremely high rates of drug development failure.\n\nIntegrating knowledge of genes that encode druggable targets with those that influence susceptibility to common disease has the potential to radically improve the probability of drug development success.

genomics↗