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Tomlinson OW, Mitchelmore P, Williams CA. Comparison of Reporting Quality in National Cystic Fibrosis Patient Registries: Implications for Identifying Use of Novel CFTR Modulators. Pulm Ther 2024:10.1007/s41030-024-00274-y. [PMID: 39333383 DOI: 10.1007/s41030-024-00274-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2024] [Accepted: 09/16/2024] [Indexed: 09/29/2024] Open
Abstract
INTRODUCTION Advances in development of cystic fibrosis transmembrane conductance regulator modulator (CFTRm) therapies mean that now people who are heterozygous (instead of having to be homozygous) for the common F508del variant can benefit from these therapies. Recent economic estimates suggest only approximately 15% of the global population have CFTRm access, yet it is unknown how prevalence of F508del and economic factors may affect this availability. METHODS Data related to prevalence of cystic fibrosis (CF), CFTRm usage, and prevalence of F508del in 10 countries were extracted from publicly accessible registry reports from 2021. National gross domestic product (GDP) was obtained via open access World Bank data. Descriptive statistics and correlation coefficients assessed relationships. RESULTS Notable discrepancies were noted in the equity of availability of data between national registries-only four countries reported number of patients eligible for CFTRm. Registry data represented 70,694 patients, with 42,858 found to be using CFTRm (60.6%). Prevalence of CFTRm usage ranged from 1.8% to 76.7% and prevalence of F508del ranged from 35.2% to 94.4%. The correlation between prevalence of CFTRm usage and F508del is positive (r = 0.56, p = 0.10), and the correlation between CFTRm usage and GDP (per capita) was also positive, and significant (r = 0.72, p = 0.02). CONCLUSION Both F508del prevalence and GDP are associated with variable CFTRm usage rates, although a predominant reason is unclear as a result of poor consistency in registry reporting. Urgent action is needed to create uniform reporting of registry data and increase availability of novel CFTRm therapies to the global CF population.
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Affiliation(s)
- Owen W Tomlinson
- Department of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Heavitree Road, Exeter, EX1 2LU, UK.
- Academic Department of Respiratory Medicine, Royal Devon University Healthcare NHS Foundation Trust, Exeter, EX2 5DW, UK.
| | - Philip Mitchelmore
- Academic Department of Respiratory Medicine, Royal Devon University Healthcare NHS Foundation Trust, Exeter, EX2 5DW, UK
| | - Craig A Williams
- Academic Department of Respiratory Medicine, Royal Devon University Healthcare NHS Foundation Trust, Exeter, EX2 5DW, UK
- Department of Public Health and Sport Science, University of Exeter Medical School, University of Exeter, Exeter, EX1 2LU, UK
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Tanner KT, Diaz-Ordaz K, Keogh RH. Implementation of a dynamic model updating pipeline provides a systematic process for maintaining performance of prediction models. J Clin Epidemiol 2024; 175:111531. [PMID: 39277059 DOI: 10.1016/j.jclinepi.2024.111531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 08/28/2024] [Accepted: 09/04/2024] [Indexed: 09/17/2024]
Abstract
OBJECTIVES We describe the steps for implementing a dynamic updating pipeline for clinical prediction models and illustrate the proposed methods in an application of 5-year survival prediction in cystic fibrosis. STUDY DESIGN AND SETTING Dynamic model updating refers to the process of repeated updating of a clinical prediction model with new information to counter performance degradation. We describe 2 types of updating pipeline: "proactive updating" where candidate model updates are tested any time new data are available, and "reactive updating" where updates are only made when performance of the current model declines or the model structure changes. Methods for selecting the best candidate updating model are based on measures of predictive performance under the 2 pipelines. The methods are illustrated in our motivating example of a 5-year survival prediction model in cystic fibrosis. Over a dynamic updating period of 10 years, we report the updating decisions made and the performance of the prediction models selected under each pipeline. RESULTS Both the proactive and reactive updating pipelines produced survival prediction models that overall had better performance in terms of calibration and discrimination than a model that was not updated. Further, use of the dynamic updating pipelines ensured that the prediction model's performance was consistently and frequently reviewed in new data. CONCLUSION Implementing a dynamic updating pipeline will help guard against model performance degradation while ensuring that the updating process is principled and data-driven.
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Affiliation(s)
- Kamaryn T Tanner
- Dept of Medical Statistics, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK.
| | - Karla Diaz-Ordaz
- Dept of Statistical Science, University College London, London, WC1E 6BT, UK
| | - Ruth H Keogh
- Dept of Medical Statistics, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
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Palma M, Keogh RH, Carr SB, Szczesniak R, Taylor-Robinson D, Wood AM, Muniz-Terrera G, Barrett JK. Demographic factors associated with within-individual variability of lung function for adults with cystic fibrosis: A UK registry study. J Cyst Fibros 2024; 23:936-942. [PMID: 38969604 PMCID: PMC11409769 DOI: 10.1016/j.jcf.2024.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 05/21/2024] [Accepted: 05/23/2024] [Indexed: 07/07/2024]
Abstract
BACKGROUND Lung function is a key outcome used in the evaluation of disease progression in cystic fibrosis. The variability of individual lung function measurements over time (within-individual variability) has been shown to predict subsequent lung function changes. Nevertheless, the association between within-individual lung function variability and demographic and genetic covariates has not been quantified. METHODS We performed a longitudinal analysis of data from a cohort of 7099 adults with cystic fibrosis (between 18 and 49 years old) from the UK cystic fibrosis registry, containing annual review data between 1996 and 2020. A mixed-effects location-scale model is used to quantify mean FEV1 (forced expiratory volume in 1 s) trajectories and FEV1 within-individual variability as a function of sex, age at annual review, diagnosis after first year of life, homozygous F508 genotype and birth cohort. RESULTS Mean FEV1 decreased with age and lung function variability showed a near-quadratic trend by age. Males showed higher FEV1 mean and variability than females across the whole age range. Earlier diagnosis and homozygous F508 genotype were also associated with higher FEV1 mean and variability. Individuals who died during follow-up showed on average higher lung function variability than those who survived. CONCLUSIONS Key variables known to be linked with mean lung function in cystic fibrosis are also associated with an individual's lung function variability. This work opens new avenues to understand the role played by lung function variability in disease progression and its utility in predicting key outcomes such as mortality.
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Affiliation(s)
- Marco Palma
- MRC Biostatistics Unit, University of Cambridge, United Kingdom.
| | - Ruth H Keogh
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, United Kingdom
| | - Siobhán B Carr
- Royal Brompton Hospital, part of Guy's and St Thomas' NHS Foundation Trust, United Kingdom; National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Rhonda Szczesniak
- Divisions of Biostatistics and Epidemiology and Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, United States; Department of Pediatrics, University of Cincinnati, United States
| | - David Taylor-Robinson
- Department of Public Health, Policy and Systems, University of Liverpool, United Kingdom
| | - Angela M Wood
- Cardiovascular Epidemiology Unit, University of Cambridge, United Kingdom
| | - Graciela Muniz-Terrera
- Ohio University Heritage College of Osteopathic Medicine, United States; University of Edinburgh, United Kingdom
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Calthorpe R, Rosenfeld M, Goss CH, Green N, Derleth M, Carr SB, Smyth A, Stewart I. Pancreatic enzyme prescription following ivacaftor licensing: A retrospective analysis of the US and UK cystic fibrosis registries. J Cyst Fibros 2024; 23:746-753. [PMID: 38342635 PMCID: PMC11315808 DOI: 10.1016/j.jcf.2024.01.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/20/2023] [Accepted: 01/29/2024] [Indexed: 02/13/2024]
Abstract
BACKGROUND Relieving gastrointestinal symptoms is a research priority in cystic fibrosis. Emerging evidence highlights effects of cystic fibrosis transmembrane conductance regulator (CFTR) modulators on gastrointestinal function, including pancreatic sufficiency. This study explores ivacaftor licensing and treatment on recorded pancreatic enzyme replacement therapy (PERT) prescription in the US and UK CF registries. METHODS Retrospective longitudinal registry study of recorded pancreatic PERT use between 2008 and 2017. Interrupted time series analysis in propensity-matched cohorts estimated annual change and step change according to ivacaftor eligibility before and after licensing year, 2012. Generalised estimating equations assessed adjusted risk of PERT use in individuals treated with ivacaftor after 2012 compared to untreated individuals. RESULTS In the US CF registry, the difference in annual change in prevalence of PERT use post-2012 between eligible cases and ineligible controls was -5.0 per 1000 people/year (95 %CI -7.6; -2.3, p = 0.001). The step change and annual change in prevalence of PERT use in eligible cases was not significantly different to controls in the UK CF registry. Relative to the relationship in 2013, ivacaftor treatment in the US CF registry was associated with a lower adjusted risk ratio of PERT use compared to untreated individuals by 2016 (0.97, 95 %CI 0.96; 0.99), which was not observed in the UK CF registry. CONCLUSIONS Licensing of ivacaftor was followed by a lower prevalence of PERT use in the eligible US population compared to pre-licensing period, as well as lower risk of PERT use in those who received treatment. Inconsistencies in US and UK CF registries were observed.
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Affiliation(s)
- Rebecca Calthorpe
- School of Medicine, University of Nottingham, Nottingham, UK; NIHR Nottingham Biomedical Research Centre, Nottingham, UK
| | - Margaret Rosenfeld
- Seattle Children's Research Institute and Department of Pediatrics, University of Washington School of Medicine, US
| | - Christopher H Goss
- Seattle Children's Research Institute and Department of Pediatrics, University of Washington School of Medicine, US; Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington School of Medicine, US
| | - Nicole Green
- Seattle Children's Research Institute and Department of Pediatrics, University of Washington School of Medicine, US; Division of Gastroenterology, University of Washington School of Medicine, US
| | - Mark Derleth
- Division of Gastroenterology, University of Washington School of Medicine, US
| | - Siobhán B Carr
- National Heart and Lung Institute, NIHR Imperial Biomedical Research Centre, Imperial College, London, UK; Department of Paediatric Respiratory Medicine, Royal Brompton Hospital, part of GSTT NHS Foundation Trust, London, UK
| | - Alan Smyth
- School of Medicine, University of Nottingham, Nottingham, UK; NIHR Nottingham Biomedical Research Centre, Nottingham, UK; School of Medicine, Dentistry and Biomedical Sciences, Queens University Belfast, Belfast
| | - Iain Stewart
- National Heart and Lung Institute, NIHR Imperial Biomedical Research Centre, Imperial College, London, UK.
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Bényei ÉB, Nazeer RR, Askenasy I, Mancini L, Ho PM, Sivarajan GAC, Swain JEV, Welch M. The past, present and future of polymicrobial infection research: Modelling, eavesdropping, terraforming and other stories. Adv Microb Physiol 2024; 85:259-323. [PMID: 39059822 DOI: 10.1016/bs.ampbs.2024.04.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2024]
Abstract
Over the last two centuries, great advances have been made in microbiology as a discipline. Much of this progress has come about as a consequence of studying the growth and physiology of individual microbial species in well-defined laboratory media; so-called "axenic growth". However, in the real world, microbes rarely live in such "splendid isolation" (to paraphrase Foster) and more often-than-not, share the niche with a plethora of co-habitants. The resulting interactions between species (and even between kingdoms) are only very poorly understood, both on a theoretical and experimental level. Nevertheless, the last few years have seen significant progress, and in this review, we assess the importance of polymicrobial infections, and show how improved experimental traction is advancing our understanding of these. A particular focus is on developments that are allowing us to capture the key features of polymicrobial infection scenarios, especially as those associated with the human airways (both healthy and diseased).
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Affiliation(s)
| | | | - Isabel Askenasy
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Leonardo Mancini
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Pok-Man Ho
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | | | - Jemima E V Swain
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom
| | - Martin Welch
- Department of Biochemistry, Tennis Court Road, Cambridge, United Kingdom.
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Griffiths SL, Murray GK, Logeswaran Y, Ainsworth J, Allan SM, Campbell N, Drake RJ, Katshu MZUH, Machin M, Pope MA, Sullivan SA, Waring J, Bogatsu T, Kane J, Weetman T, Johnson S, Kirkbride JB, Upthegrove R. Implementing and Evaluating a National Integrated Digital Registry and Clinical Decision Support System in Early Intervention in Psychosis Services (Early Psychosis Informatics Into Care): Co-Designed Protocol. JMIR Res Protoc 2024; 13:e50177. [PMID: 38502175 PMCID: PMC10988369 DOI: 10.2196/50177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 01/21/2024] [Accepted: 02/21/2024] [Indexed: 03/20/2024] Open
Abstract
BACKGROUND Early intervention in psychosis (EIP) services are nationally mandated in England to provide multidisciplinary care to people experiencing first-episode psychosis, which disproportionately affects deprived and ethnic minority youth. Quality of service provision varies by region, and people from historically underserved populations have unequal access. In other disease areas, including stroke and dementia, national digital registries coupled with clinical decision support systems (CDSSs) have revolutionized the delivery of equitable, evidence-based interventions to transform patient outcomes and reduce population-level disparities in care. Given psychosis is ranked the third most burdensome mental health condition by the World Health Organization, it is essential that we achieve the same parity of health improvements. OBJECTIVE This paper reports the protocol for the program development phase of this study, in which we aimed to co-design and produce an evidence-based, stakeholder-informed framework for the building, implementation, piloting, and evaluation of a national integrated digital registry and CDSS for psychosis, known as EPICare (Early Psychosis Informatics into Care). METHODS We conducted 3 concurrent work packages, with reciprocal knowledge exchange between each. In work package 1, using a participatory co-design framework, key stakeholders (clinicians, academics, policy makers, and patient and public contributors) engaged in 4 workshops to review, refine, and identify a core set of essential and desirable measures and features of the EPICare registry and CDSS. Using a modified Delphi approach, we then developed a consensus of data priorities. In work package 2, we collaborated with National Health Service (NHS) informatics teams to identify relevant data currently captured in electronic health records, understand data retrieval methods, and design the software architecture and data model to inform future implementation. In work package 3, observations of stakeholder workshops and individual interviews with representative stakeholders (n=10) were subject to interpretative qualitative analysis, guided by normalization process theory, to identify factors likely to influence the adoption and implementation of EPICare into routine practice. RESULTS Stage 1 of the EPICare study took place between December 2021 and September 2022. The next steps include stage 2 building, piloting, implementation, and evaluation of EPICare in 5 demonstrator NHS Trusts serving underserved and diverse populations with substantial need for EIP care in England. If successful, this will be followed by stage 3, in which we will seek NHS adoption of EPICare for rollout to all EIP services in England. CONCLUSIONS By establishing a multistakeholder network and engaging them in an iterative co-design process, we have identified essential and desirable elements of the EPICare registry and CDSS; proactively identified and minimized potential challenges and barriers to uptake and implementation; and addressed key questions related to informatics architecture, infrastructure, governance, and integration in diverse NHS Trusts, enabling us to proceed with the building, piloting, implementation, and evaluation of EPICare. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/50177.
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Affiliation(s)
- Siân Lowri Griffiths
- Institute for Mental Health, University of Birmingham, Birmingham, United Kingdom
| | - Graham K Murray
- Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom
- CAMEO, Cambridgeshire and Peterborough NHS Foundation Trust, Cambridge, United Kingdom
| | - Yanakan Logeswaran
- Division of Psychiatry, University College London, London, United Kingdom
| | - John Ainsworth
- The University of Manchester, Manchester, United Kingdom
- NIHR Manchester Biomedical Research Centre, Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Sophie M Allan
- Department of Clinical Psychology and Psychotherapies, Medical School, University of East Anglia, Norwich, United Kingdom
- School of Health Sciences, University of East Anglia, Norwich, United Kingdom
| | - Niyah Campbell
- Institute for Mental Health, University of Birmingham, Birmingham, United Kingdom
| | - Richard J Drake
- The University of Manchester, Manchester, United Kingdom
- Greater Manchester Mental Health NHS Foundation Trust, Manchester, United Kingdom
| | - Mohammad Zia Ul Haq Katshu
- Institute of Mental Health, School of Medicine, University of Nottingham, Nottingham, United Kingdom
- Nottinghamshire Healthcare NHS Foundation Trust, Nottingham, United Kingdom
| | - Matthew Machin
- The University of Manchester, Manchester, United Kingdom
| | - Megan A Pope
- Institute for Mental Health, University of Birmingham, Birmingham, United Kingdom
| | - Sarah A Sullivan
- Centre for Academic Mental Health, University of Bristol, Bristol, United Kingdom
- Biomedical Research Centre, University of Bristol, Bristol, United Kingdom
| | - Justin Waring
- School of Social Policy, University of Birmingham, Birmingham, United Kingdom
| | - Tumelo Bogatsu
- Institute for Mental Health, University of Birmingham, Birmingham, United Kingdom
| | - Julie Kane
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | - Tyler Weetman
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
| | - Sonia Johnson
- Division of Psychiatry, University College London, London, United Kingdom
- Camden and Islington NHS Foundation Trust, London, United Kingdom
| | - James B Kirkbride
- Division of Psychiatry, University College London, London, United Kingdom
| | - Rachel Upthegrove
- Institute for Mental Health, University of Birmingham, Birmingham, United Kingdom
- Birmingham Women's and Children's NHS Foundation Trust, Birmingham, United Kingdom
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Granger E, Davies G, Keogh RH. Emulated trial investigating effects of multiple treatments: estimating combined effects of mucoactive nebulisers in cystic fibrosis using registry data. Thorax 2023; 78:1011-1018. [PMID: 37451864 PMCID: PMC10511967 DOI: 10.1136/thorax-2023-220031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/14/2023] [Indexed: 07/18/2023]
Abstract
INTRODUCTION People with cystic fibrosis (CF) are often on multiple long-term treatments, including mucoactive nebulisers. In the UK, the most common mucoactive nebuliser is dornase alfa (DNase). A common therapeutic approach for people already on DNase is to add hypertonic saline (HS). The effects of DNase and HS used alone have been studied in randomised trials, but their effects in combination have not. This study investigates whether, for people already prescribed DNase, adding HS has additional benefit for lung function or use of intravenous antibiotics. METHODS Using UK CF Registry data from 2007 to 2018, we emulated a target trial. We included people aged 6 years and over who were prescribed DNase without HS for 2 years. We investigated the effects of combinations of DNase and HS over 5 years of follow-up. Inverse-probability-of-treatment weighting was used to control confounding. The period predated triple combination CF transmembrane conductance regulator modulators in routine care. RESULTS 4498 individuals were included. At baseline, average age and forced expiratory volume in 1 s (FEV1%) predicted were 21.1 years and 69.7 respectively. During first year of follow-up, 3799 individuals were prescribed DNase alone; 426 added HS; 57 switched to HS alone and 216 were prescribed neither. We found no evidence that adding HS improved FEV1% at 1-5 years, or use of intravenous antibiotics at 1-4 years, compared with DNase alone. CONCLUSION For individuals with CF prescribed DNase, we found no evidence that adding HS had an effect on FEV1% or prescription of intravenous antibiotics. Our study illustrates the emulated target trial approach using CF Registry data.
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Affiliation(s)
- Emily Granger
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK
| | - Gwyneth Davies
- UCL Great Ormond Street Institute of Child Health, UCL, London, UK
- Respiratory Medicine, Great Ormond Street Hospital For Children NHS Foundation Trust, London, UK
| | - Ruth H Keogh
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK
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Keogh RH, Gran JM, Seaman SR, Davies G, Vansteelandt S. Causal inference in survival analysis using longitudinal observational data: Sequential trials and marginal structural models. Stat Med 2023; 42:2191-2225. [PMID: 37086186 PMCID: PMC7614580 DOI: 10.1002/sim.9718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Revised: 01/26/2023] [Accepted: 03/14/2023] [Indexed: 04/23/2023]
Abstract
Longitudinal observational data on patients can be used to investigate causal effects of time-varying treatments on time-to-event outcomes. Several methods have been developed for estimating such effects by controlling for the time-dependent confounding that typically occurs. The most commonly used is marginal structural models (MSM) estimated using inverse probability of treatment weights (IPTW) (MSM-IPTW). An alternative, the sequential trials approach, is increasingly popular, and involves creating a sequence of "trials" from new time origins and comparing treatment initiators and non-initiators. Individuals are censored when they deviate from their treatment assignment at the start of each "trial" (initiator or noninitiator), which is accounted for using inverse probability of censoring weights. The analysis uses data combined across trials. We show that the sequential trials approach can estimate the parameters of a particular MSM. The causal estimand that we focus on is the marginal risk difference between the sustained treatment strategies of "always treat" vs "never treat." We compare how the sequential trials approach and MSM-IPTW estimate this estimand, and discuss their assumptions and how data are used differently. The performance of the two approaches is compared in a simulation study. The sequential trials approach, which tends to involve less extreme weights than MSM-IPTW, results in greater efficiency for estimating the marginal risk difference at most follow-up times, but this can, in certain scenarios, be reversed at later time points and relies on modelling assumptions. We apply the methods to longitudinal observational data from the UK Cystic Fibrosis Registry to estimate the effect of dornase alfa on survival.
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Affiliation(s)
- Ruth H. Keogh
- Department of Medical Statistics and Centre for Statistical MethodologyLondon School of Hygiene and Tropical MedicineKeppel StreetLondonWC1E 7HTUK
| | - Jon Michael Gran
- Oslo Centre for Biostatistics and Epidemiology, Department of Biostatistics, Institute of Basic Medical SciencesUniversity of OsloP.O. Box 1122 BlindernOslo0317Norway
| | - Shaun R. Seaman
- MRC Biostatistics UnitUniversity of CambridgeEast Forvie Building, Forvie Site, Robinson WayCambridgeCB2 0SRUK
| | - Gwyneth Davies
- Population, Policy and Practice Research and Teaching Department, UCL Great Ormond Street Institute of Child HealthUniversity College LondonWC1N 1EHLondonUK
| | - Stijn Vansteelandt
- Department of Medical Statistics and Centre for Statistical MethodologyLondon School of Hygiene and Tropical MedicineKeppel StreetLondonWC1E 7HTUK
- Department of Applied Mathematics, Computer Science and StatisticsGhent University9000GhentBelgium
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Ho PM, Nazeer RR, Welch M. Therapeutic interventions alter ecological interactions among cystic fibrosis airway microbiota. Front Microbiol 2023; 14:1178131. [PMID: 37323900 PMCID: PMC10265647 DOI: 10.3389/fmicb.2023.1178131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/28/2023] [Indexed: 06/17/2023] Open
Abstract
The airways of people with cystic fibrosis (CF) often harbor a diverse microbiota and in recent years, much effort has been invested in cataloguing these. In spite of providing a wealth of insight, this cataloguing tells us little about how the organisms interact with one another in the CF airways. However, such relationships can be inferred using the theoretical framework of the Lotka-Volterra (LV) model. In the current work, we use a generalized Lotka-Volterra model to interrogate the nationwide data collected and curated by the UK CF Registry. This longitudinal dataset (covering the period 2008-2020) contains annual depositions that record the presence/absence of microbial taxa in each patient, their medication, and their CF genotype. Specifically, we wanted to identify trends in ecological relationships between the CF microbiota at a nationwide level, and whether these are potentially affected by medication. Our results show that some medications have a distinct influence on the microbial interactome, especially those that potentially influence the "gut-lung axis" or mucus viscosity. In particular, we found that patients treated with a combination of antimicrobial agents (targeting the airway microbiota), digestive enzymes (assisting in the assimilation of dietary fats and carbohydrates), and DNase (to reduce mucus viscosity) displayed a distinctly different airway interactome compared with patients treated separately with these medications.
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Affiliation(s)
| | | | - Martin Welch
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
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Khan MS, Douglas P, Hansell AL, Simmonds NJ, Piel FB. Assessing the health risk of living near composting facilities on lung health, fungal and bacterial disease in cystic fibrosis: a UK CF Registry study. Environ Health 2022; 21:130. [PMID: 36517903 PMCID: PMC9753251 DOI: 10.1186/s12940-022-00932-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 10/27/2022] [Indexed: 06/17/2023]
Abstract
AIM To explore the health risk of living near permitted composting sites (PCSs) on disease severity in children and adults with cystic fibrosis (CF) across the UK. METHODS: A semi-individual cross-sectional study was used to examine the risk of disease severity in people with CF (pwCF) within and beyond 4 km of PCSs in the UK in 2016. All pwCF registered in the UK CF Registry were eligible for this study. Linear and Poisson regressions, adjusted for age, gender, genotype, BMI, Pseudomonas aeruginosa and deprivation, were used to quantify associations between distance to a PCS and percent predicted forced expiratory volume in one second (ppFEV1), pulmonary exacerbations (#IVdays), and fungal and bacterial infections. RESULTS The mean age of the 9,361 pwCF (3,931 children and 5,430 adults) studied was 20.1 (SD = 14.1) years; 53.3% were male; and 49.2% were homozygous F508del. Over 10% of pwCF (n = 1,015) lived within 4 km of a PCS. We found no statistically significant difference in ppFEV1 and #IVdays/year in children. However, in adults, ppFEV1 was -1.07% lower (95% confidence interval (CI): -2.29%, 0.16%) and #IVdays/year were 1.02 day higher (95%CI: 1.01, 1.04) within 4 km of a PCS. Furthermore, there were statistically significant differences in mean ppFEV1 in CF adults with Aspergillus fumigatus (58.2.% vs 62.0%, p = 0.005) and Candida spp. (56.9% vs 59.9%, p = 0.029) residing within 4 km of a PCS. No associations were identified for allergic bronchopulmonary aspergillosis, P. aeruginosa or Staphylococcus aureus. CONCLUSIONS This novel national study provides evidence that adults with CF living near a PCS may experience small reductions in lung function, an increased risk of pulmonary exacerbations, and more frequent fungal infections. If confirmed by studies using refined exposure assessment methods accounting for bioaerosol dispersion, these results could have important implications for the living environment of pwCF.
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Affiliation(s)
- Muhammad Saleem Khan
- UK Small Area Health Statistics Unit, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
- National Institute for Health Research Health Protection Research Units in Environmental Exposures and Health, Imperial College London, London, UK
| | - Philippa Douglas
- National Institute for Health Research Health Protection Research Units in Environmental Exposures and Health, Imperial College London, London, UK
- Centre for Radiation, Chemical and Environmental Hazards, UK Health Security Agency (UKHSA), Harwell Science Campus, Didcot, UK
- Centre for Environmental Health and Sustainability, University of Leicester, Leicester, UK
- National Institute for Health Research Health Protection Research Units in Environmental Exposures and Health, University of Leicester, Leicester, UK
| | - Anna L. Hansell
- Centre for Environmental Health and Sustainability, University of Leicester, Leicester, UK
- National Institute for Health Research Health Protection Research Units in Environmental Exposures and Health, University of Leicester, Leicester, UK
| | - Nicholas J. Simmonds
- Adult Cystic Fibrosis Centre, Royal Brompton Hospital, London, UK
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Frédéric B. Piel
- UK Small Area Health Statistics Unit, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
- National Institute for Health Research Health Protection Research Units in Environmental Exposures and Health, Imperial College London, London, UK
- MRC Centre for Environment and Health, School of Public Health, Faculty of Medicine, Imperial College London, London, UK
- Protection Research Unit in Chemical and Radiation Threats and Hazards, Imperial College London, London, UK
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Tanner KT, Daniel RM, Bilton D, Simmonds NJ, Sharples LD, Keogh RH. Mediation of the total effect of cystic fibrosis-related diabetes on mortality: A UK Cystic Fibrosis Registry cohort study. Diabet Med 2022; 39:e14958. [PMID: 36075586 PMCID: PMC9826418 DOI: 10.1111/dme.14958] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/12/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
AIM To investigate whether the effect of cystic fibrosis-related diabetes (CFRD) on the composite outcome of mortality or transplant could act through lung function, pulmonary exacerbations and/or nutritional status. METHODS A retrospective cohort of adult cystic fibrosis (CF) patients who had not been diagnosed with CFRD were identified from the UK Cystic Fibrosis Registry (n = 2750). Rate of death or transplant was compared between patients who did and did not develop CFRD (with insulin use) during follow-up using Poisson regression, separately by sex. Causal mediation methods were used to investigate whether lung function, pulmonary exacerbations and nutritional status lie on the causal pathway between insulin-treated CFRD and mortality/transplant. RESULTS At all ages, the mortality/transplant rate was higher in both men and women diagnosed with CFRD. Pulmonary exacerbations were the strongest mediator of the effect of CFRD on mortality/transplant, with an estimated 15% [95% CI: 7%, 28%] of the effect at 2 years post-CFRD diagnosis attributed to exacerbations, growing to 24% [95% CI: 9%, 46%] at 4 years post-diagnosis. Neither lung function nor nutritional status were found to be significant mediators of this effect. Estimates were similar but with wider confidence intervals in a cohort that additionally included people with CFRD but not using insulin. CONCLUSION There is evidence that pulmonary exacerbations mediate the effect of CFRD on mortality but, as they are estimated to mediate less than one-quarter of the total effect, the mechanism through which CFRD influences survival may involve other factors.
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Affiliation(s)
- Kamaryn T. Tanner
- Department of Medical StatisticsThe London School of Hygiene and Tropical MedicineLondonUK
| | | | - Diana Bilton
- Imperial College London, Faculty of MedicineNational Heart and Lung InstituteLondonUK
- Royal Brompton HospitalLondonUK
| | - Nicholas J. Simmonds
- Imperial College London, Faculty of MedicineNational Heart and Lung InstituteLondonUK
- Royal Brompton HospitalLondonUK
| | - Linda D. Sharples
- Department of Medical StatisticsThe London School of Hygiene and Tropical MedicineLondonUK
| | - Ruth H. Keogh
- Department of Medical StatisticsThe London School of Hygiene and Tropical MedicineLondonUK
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Granger E, Keogh RH, Frost F. The long-term effects of insulin use in incident cystic fibrosis-related diabetes: a target trial emulated using longitudinal national registry data. ERJ Open Res 2022; 8:00170-2022. [PMID: 36382232 PMCID: PMC9638829 DOI: 10.1183/23120541.00170-2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
Introduction Cystic fibrosis-related diabetes (CFRD) is a common complication of cystic fibrosis and is associated with deleterious clinical outcomes. Insulin is recommended as a treatment by international guidelines. However, there are scarce clinical trial data to support the use of insulin, and little is known about the long-term outcomes of treatment. The aim of this study was to compare the long-term impacts of insulin use versus non-use in CFRD. Methods We used data from the national UK Cystic Fibrosis Registry and adopted a target trial framework. Eligible individuals included those 12 years and older with a new diagnosis of CFRD. Outcomes were change in % predicted forced expiratory volume in 1 s (FEV1 %) and body mass index z-scores (BMI) over a 5-year follow-up period. Treatment strategies were to receive insulin or not for the duration of follow-up. Treatment effect estimates were obtained using two methods to control for confounding: inverse-probability-of-treatment weighted estimation of marginal structural models and the G-formula. Results We identified 1613 individuals diagnosed with CFRD between 2008 and 2016 and included 1196 and 1192 in the FEV1 % and BMI outcome analyses respectively. We found no evidence of an effect of insulin on FEV1 % over the 5-year study period. Similarly, we found no overall effect of insulin on BMI; however, there was some evidence for a positive treatment effect in patients with lower baseline BMI. Conclusion Using well-established national registry data, we found no evidence of long-term treatment effects for insulin on FEV1 % or BMI in people with incident CFRD. This target trial using registry data to estimate the effects of insulin use on clinical outcomes in incident cystic fibrosis-related diabetes found no evidence of a long-term benefit (up to 5 years) of insulin use on lung function or BMIhttps://bit.ly/3B8azKz
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Macdougall A, Jarvis D, Keogh RH, Bowerman C, Bilton D, Davies G, Carr SB, Stanojevic S. Trajectories of early growth and subsequent lung function in cystic fibrosis: An observational study using UK and Canadian registry data. J Cyst Fibros 2022:S1569-1993(22)00658-0. [PMID: 36088206 DOI: 10.1016/j.jcf.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 08/18/2022] [Accepted: 09/01/2022] [Indexed: 10/14/2022]
Abstract
BACKGROUND Understanding the pulmonary impact of changes in early life nutritional status over time in a paediatric CF population may help inform how to use nutritional assessment to guide clinical care. National registry data provides an opportunity to study patterns of weight gain over time at the level of the individual, and thus to gain detailed understanding of the relationship between early weight trajectories and later lung function in children with Cystic Fibrosis (CF). METHODS Using data from the United Kingdom (UK) and Canadian CF Registries, a mixed effects linear regression model was used to describe children's weight and BMI z-score trajectories from age 1 to 5 years. The intercept (weight-for-age at age 1) and slope (weight-for-age trajectory) from this model were then used as covariates in a linear regression of first lung function measurement at age 6 years. RESULTS In both the UK and Canadian data, greater weight-for-age z-score at age 1 year and greater change in weight-for-age over time were associated with higher FEV1% predicted. A greater weight-for-age z-score at age 1 year was associated with a higher FEV1% predicted (UK: 3.78% (95% CI: 1.76; 4.70); Canada: 3.20% (95%CI: 1.76, 4.70)). These associations were reproduced for BMI z-scores and FVC% predicted. CONCLUSIONS Early weight-for-age, specifically at age 1 year, and weight-for-age trajectories across early childhood are associated with later lung function. This relationship persists after adjustment for potential confounders. Current guidelines may need to be updated to place less emphasis on a specific cut-off (such as the 10th percentile) and encourage tracking of weight-for-age over time.
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Affiliation(s)
- Amy Macdougall
- National Heart and Lung Institute, Imperial College London, London, United Kingdom.
| | - Deborah Jarvis
- National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Ruth H Keogh
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom
| | - Cole Bowerman
- Department of Community Health & Epidemiology, Dalhousie University, Halifax, Canada
| | - Diana Bilton
- Royal Brompton and Harefield NHS Foundation Trust, National Heart and Lung Institute, Imperial College, Sydney Street, London, United Kingdom
| | - Gwyneth Davies
- UCL Great Ormond Street Institute of Child Health, London, UK, Great Ormond Street Hospital for Children and GOSH NIHR BRC, London, United Kingdom
| | - Siobhán B Carr
- Royal Brompton Hospital and Imperial College London, United Kingdom
| | - Sanja Stanojevic
- Department of Community Health & Epidemiology, Dalhousie University, Halifax, Canada
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14
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Keogh RH, Cosgriff R, Andrinopoulou ER, Brownlee KG, Carr SB, Diaz-Ordaz K, Granger E, Jewell NP, Lewin A, Leyrat C, Schlüter DK, van Smeden M, Szczesniak RD, Connett GJ. Projecting the impact of triple CFTR modulator therapy on intravenous antibiotic requirements in cystic fibrosis using patient registry data combined with treatment effects from randomised trials. Thorax 2022; 77:873-881. [PMID: 34556554 PMCID: PMC8940731 DOI: 10.1136/thoraxjnl-2020-216265] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 08/12/2021] [Indexed: 11/19/2022]
Abstract
BACKGROUND Cystic fibrosis (CF) is a life-threatening genetic disease, affecting around 10 500 people in the UK. Precision medicines have been developed to treat specific CF-gene mutations. The newest, elexacaftor/tezacaftor/ivacaftor (ELEX/TEZ/IVA), has been found to be highly effective in randomised controlled trials (RCTs) and became available to a large proportion of UK CF patients in 2020. Understanding the potential health economic impacts of ELEX/TEZ/IVA is vital to planning service provision. METHODS We combined observational UK CF Registry data with RCT results to project the impact of ELEX/TEZ/IVA on total days of intravenous (IV) antibiotic treatment at a population level. Registry data from 2015 to 2017 were used to develop prediction models for IV days over a 1-year period using several predictors, and to estimate 1-year population total IV days based on standards of care pre-ELEX/TEZ/IVA. We considered two approaches to imposing the impact of ELEX/TEZ/IVA on projected outcomes using effect estimates from RCTs: approach 1 based on effect estimates on FEV1% and approach 2 based on effect estimates on exacerbation rate. RESULTS ELEX/TEZ/IVA is expected to result in significant reductions in population-level requirements for IV antibiotics of 16.1% (~17 800 days) using approach 1 and 43.6% (~39 500 days) using approach 2. The two approaches require different assumptions. Increased understanding of the mechanisms through which ELEX/TEZ/IVA acts on these outcomes would enable further refinements to our projections. CONCLUSIONS This work contributes to increased understanding of the changing healthcare needs of people with CF and illustrates how Registry data can be used in combination with RCT evidence to estimate population-level treatment impacts.
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Affiliation(s)
- Ruth H Keogh
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK
| | | | | | | | - Siobhán B Carr
- Department of Paediatric Respiratory Medicine, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Karla Diaz-Ordaz
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK
| | - Emily Granger
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK
| | - Nicholas P Jewell
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK
| | - Alex Lewin
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK
| | - Clemence Leyrat
- Department of Medical Statistics, London School of Hygiene & Tropical Medicine, London, UK
| | - Daniela K Schlüter
- Department of Public Health, Policy and Systems, Institute of Population Health, University of Liverpool, Liverpool, UK
| | - Maarten van Smeden
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Rhonda D Szczesniak
- Division of Biostatistics & Epidemiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA,Department of Pediatrics, University of Cincinnati, Cincinnati, Ohio, USA
| | - Gary J Connett
- National Institute for Health Research, Southampton Respiratory Biomedical Research Centre, University Hospital Southampton NHS Foundation Trust, Southampton, UK
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15
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Who are the 10%? - Non eligibility of cystic fibrosis (CF) patients for highly effective modulator therapies. Respir Med 2022; 199:106878. [DOI: 10.1016/j.rmed.2022.106878] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 03/28/2022] [Accepted: 05/09/2022] [Indexed: 11/19/2022]
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16
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Newsome SJ, Daniel RM, Carr SB, Bilton D, Keogh RH. Using Negative Control Outcomes and Difference-in-Differences Analysis to Estimate Treatment Effects in an Entirely Treated Cohort: The Effect of Ivacaftor in Cystic Fibrosis. Am J Epidemiol 2022; 191:505-515. [PMID: 34753177 PMCID: PMC8914944 DOI: 10.1093/aje/kwab263] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 09/26/2021] [Accepted: 10/27/2021] [Indexed: 11/15/2022] Open
Abstract
When an entire cohort of patients receives a treatment, it is difficult to estimate the treatment effect in the treated because there are no directly comparable untreated patients. Attempts can be made to find a suitable control group (e.g., historical controls), but underlying differences between the treated and untreated can result in bias. Here we show how negative control outcomes combined with difference-in-differences analysis can be used to assess bias in treatment effect estimates and obtain unbiased estimates under certain assumptions. Causal diagrams and potential outcomes are used to explain the methods and assumptions. We apply the methods to UK Cystic Fibrosis Registry data to investigate the effect of ivacaftor, introduced in 2012 for a subset of the cystic fibrosis population with a particular genotype, on lung function and annual rate (days/year) of receiving intravenous (IV) antibiotics (i.e., IV days). We consider 2 negative control outcomes: outcomes measured in the pre-ivacaftor period and outcomes among persons ineligible for ivacaftor because of their genotype. Ivacaftor was found to improve lung function in year 1 (an approximately 6.5–percentage-point increase in ppFEV1), was associated with reduced lung function decline (an approximately 0.5–percentage-point decrease in annual ppFEV1 decline, though confidence intervals included 0), and reduced the annual rate of IV days (approximately 60% over 3 years).
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Affiliation(s)
| | | | | | | | - Ruth H Keogh
- Correspondence to Dr. Ruth H. Keogh, Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, United Kingdom (e-mail: )
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17
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Schlüter DK, Griffiths R, Akbari A, Taylor-Robinson D. Educational achievements of children aged 10-11 years with cystic fibrosis. A data linkage study in Wales. Int J Popul Data Sci 2022; 7:1725. [PMID: 35909577 PMCID: PMC9284509 DOI: 10.23889/ijpds.v7i1.1725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Introduction As people with cystic fibrosis (CF) lead longer, healthier lives, educational qualifications and employment prospects are increasingly important. However, little is known about the social consequences of CF, in particular, any impact on educational achievements and the support children with CF receive in schools. Objectives To assess the educational achievements of children with CF in Wales compared to the general Welsh population, and the additional learning support children with CF receive in schools. Methods We conducted a population-scale data linkage study of all children born in Wales using the Secure Anonymised Information Linkage (SAIL) Databank. We used anonymised individual-level population-scale health and administrative data sources to identify children with CF born between 2000 - 2015, linked to educational attainment records. We calculated the percentage of children that reached expected levels in statutory assessment at age 10-11, Key Stage 2 (KS2), and compared this to educational outcomes in the general population. We also assessed the percentage of children with CF that received extra learning support. Results Out of 150 eligible children, 119 had KS2 results. 77% (95% CI: 69%-84%) of children achieved expected levels in English, 81% (95% CI: 73% -87%) in Mathematics and 82% (95% CI: 75% - 88%) in Science. In the comparable general Welsh population, 83.4% to 91.1% achieved the expected level in English, 84.9% to 91.6% in Maths, and 87.1% to 92.2% in Science across the years of the study. 70% of children with CF received extra learning support. Conclusions Children with CF in Wales may have worse educational achievements than the general population. More research is needed to inform policies and interventions to better support children with CF to reach their full educational potential and employment opportunities.
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Affiliation(s)
- Daniela K Schlüter
- Department of Public Health, Policy and Systems, University of Liverpool, Liverpool, UK
| | - Rowena Griffiths
- Population Data Science, Health Data Research UK, Swansea University, Swansea, UK
| | - Ashley Akbari
- Population Data Science, Health Data Research UK, Swansea University, Swansea, UK
| | - David Taylor-Robinson
- Department of Public Health, Policy and Systems, University of Liverpool, Liverpool, UK
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18
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van Rhijn N, Coleman J, Collier L, Moore C, Richardson MD, Bright-Thomas RJ, Jones AM. Meteorological Factors Influence the Presence of Fungi in the Air; A 14-Month Surveillance Study at an Adult Cystic Fibrosis Center. Front Cell Infect Microbiol 2021; 11:759944. [PMID: 34900752 PMCID: PMC8662344 DOI: 10.3389/fcimb.2021.759944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 11/05/2021] [Indexed: 11/17/2022] Open
Abstract
Background Cystic fibrosis is an inherited disease that predisposes to progressive lung damage. Cystic fibrosis patients are particularly prone to developing pulmonary infections. Fungal species are commonly isolated in lower airway samples from patients with cystic fibrosis. Fungal spores are prevalent in the air. Methods We performed environmental air sampling surveillance at the Manchester Adult Cystic Fibrosis Centre, UK (MACFC) over a 14-month period to assess fungal growth inside and outside the CF center. Results Airborne counts of fungal spores peaked from May to October, both in outdoor and indoor samples. Collection of meteorological data allowed us to correlate fungal presence in the air with elevated temperatures and low wind speeds. Additionally, we demonstrated patient rooms containing windows had elevated fungal counts compared to rooms not directly connected to the outdoors. Conclusions This study suggests that airborne Aspergillus fumigatus spores were more abundant during the summer months of the survey period, which appeared to be driven by increased temperatures and lower wind speeds. Indoor counts directly correlated to outdoor A. fumigatus levels and were elevated in patient rooms that were directly connected to the outdoor environment via an openable window designed for ventilation purposes. Further studies are required to determine the clinical implications of these findings for cystic fibrosis patients who are predisposed to Aspergillus related diseases, and in particular whether there is seasonal influence on incidence of Aspergillus related conditions and if screening for such complications such be increased during summer months and precautions intensified for those with a known history of Aspergillus related disease.
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Affiliation(s)
- Norman van Rhijn
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, United Kingdom
| | - James Coleman
- Manchester Adult Cystic Fibrosis Centre, Manchester University National Health Service (NHS) Foundation Trust, Manchester, United Kingdom.,Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Lisa Collier
- Manchester Adult Cystic Fibrosis Centre, Manchester University National Health Service (NHS) Foundation Trust, Manchester, United Kingdom.,Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Caroline Moore
- Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Mycology Reference Centre, European Confederation of Medical Mycology (ECMM) Excellence Centre of Medical Mycology, Manchester University National Health Service (NHS) Foundation Trust, Manchester, United Kingdom
| | - Malcolm D Richardson
- Manchester Fungal Infection Group, Division of Infection, Immunity and Respiratory Medicine, University of Manchester, Manchester, United Kingdom.,Mycology Reference Centre, European Confederation of Medical Mycology (ECMM) Excellence Centre of Medical Mycology, Manchester University National Health Service (NHS) Foundation Trust, Manchester, United Kingdom
| | - Rowland J Bright-Thomas
- Manchester Adult Cystic Fibrosis Centre, Manchester University National Health Service (NHS) Foundation Trust, Manchester, United Kingdom.,Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom
| | - Andrew M Jones
- Manchester Adult Cystic Fibrosis Centre, Manchester University National Health Service (NHS) Foundation Trust, Manchester, United Kingdom.,Faculty of Biology Medicine and Health, The University of Manchester, Manchester, United Kingdom.,Mycology Reference Centre, European Confederation of Medical Mycology (ECMM) Excellence Centre of Medical Mycology, Manchester University National Health Service (NHS) Foundation Trust, Manchester, United Kingdom
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19
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Al-Selwi Y, Shaw JA, Kattner N. Understanding the Pancreatic Islet Microenvironment in Cystic Fibrosis and the Extrinsic Pathways Leading to Cystic Fibrosis Related Diabetes. CLINICAL MEDICINE INSIGHTS-ENDOCRINOLOGY AND DIABETES 2021; 14:11795514211048813. [PMID: 34675737 PMCID: PMC8524685 DOI: 10.1177/11795514211048813] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022]
Abstract
Cystic fibrosis (CF) is an autosomal recessive chronic condition
effecting approximately 70 000 to 100 000 people globally and is
caused by a loss-of-function mutation in the CF transmembrane
conductance regulator. Through improvements in clinical care, life
expectancy in CF has increased considerably associated with rising
incidence of secondary complications including CF-related diabetes
(CFRD). CFRD is believed to result from β-cell loss as well as
insufficient insulin secretion due to β-cell dysfunction, but the
underlying pathophysiology is not yet fully understood. Here we review
the morphological and cellular changes in addition to the
architectural remodelling of the pancreatic exocrine and endocrine
compartments in CF and CFRD pancreas. We consider also potential
underlying proinflammatory signalling pathways impacting on endocrine
and specifically β-cell function, concluding that further research
focused on these mechanisms may uncover novel therapeutic targets
enabling restoration of normal insulin secretion.
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Affiliation(s)
- Yara Al-Selwi
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
| | - James Am Shaw
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK.,Institute of Transplantation, Freeman Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Nicole Kattner
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, UK
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20
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Esan OB, Schlüter DK, Phillips R, Cosgriff R, Paranjothy S, Williams D, Norman R, Carr SB, Duckers J, Taylor-Robinson D. Pregnancy rates and outcomes in women with cystic fibrosis in the UK: comparisons with the general population before and after the introduction of disease-modifying treatment, 2003-17. BJOG 2021; 129:743-751. [PMID: 34597459 DOI: 10.1111/1471-0528.16957] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/21/2021] [Accepted: 09/26/2021] [Indexed: 11/27/2022]
Abstract
OBJECTIVE To compare pregnancy rates and outcomes for women with cystic fibrosis in the UK with those of the general population and assess the effect of the introduction of disease-modifying treatment. DESIGN A population-based longitudinal study, 2003-17. SETTING United Kingdom. POPULATION Women aged 15-44 years in the UK cystic fibrosis (CF) Registry compared with women in England and Wales. METHODS We calculated pregnancy and live-birth rates for the CF population and the general population of England and Wales. For women with CF we compared pregnancy rates before and after ivacaftor was introduced in 2013. We further used CF registry data to assess pregnancy outcomes for mothers with CF, and to assess the relationship between maternal pre-pregnancy lung function and nutritional status and child gestational age. MAIN OUTCOME MEASURES Pregnancy and live-birth rates and child gestational age. RESULTS Of 3831 women with CF, 661 reported 818 pregnancies. Compared with the general population, the pregnancy rate was 3.3 times lower in the CF population (23.5 versus 77.7 per 1000 woman-years); the live-birth rate was 3.5 times lower (17.4 versus 61.4 per 1000 woman-years) with 70% of pregnancies in CF women resulting in live births; termination of pregnancy rates were also lower (9% versus 22%). Pregnancy rates increased post-ivacaftor for eligible women with CF, from 29.7 to 45.7 per 1000 woman-years. There was no association between pre-pregnancy lung function/nutrition status and gestational age. CONCLUSIONS Pregnancy rates in women with CF are about one-third of the rates in the general population with favourable outcomes, and increased for eligible women post-ivacaftor. TWEETABLE ABSTRACT Pregnancy rates in women with CF are about a third of the rate in England and Wales with 70% live births. Ivacaftor increases the rate.
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Affiliation(s)
- O B Esan
- Department of Public Health, Policy and Systems, University of Liverpool, Liverpool, UK
| | - D K Schlüter
- Department of Public Health, Policy and Systems, University of Liverpool, Liverpool, UK
| | - R Phillips
- Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - R Cosgriff
- Data Quality and Improvement, Cystic Fibrosis Trust, London, UK
| | - S Paranjothy
- Aberdeen Centre for Health Data Science, Institute of Applied Health Sciences, University of Aberdeen, Aberdeen, UK
| | - D Williams
- Cardiff School of Sport and Health Sciences, Cardiff Metropolitan University, Cardiff, UK
| | - R Norman
- Research and Development, University Hospital of Wales, Cardiff, UK
| | - S B Carr
- Department of Respiratory Paediatrics, Royal Brompton Hospital, London, UK
| | - J Duckers
- All Wales Adult CF Centre, Cardiff and Vale University Health Board, Cardiff, UK
| | - D Taylor-Robinson
- Department of Public Health, Policy and Systems, University of Liverpool, Liverpool, UK
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21
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Granger E, Davies G, Keogh RH. Treatment patterns in people with cystic fibrosis: have they changed since the introduction of ivacaftor? J Cyst Fibros 2021; 21:316-322. [PMID: 34497037 PMCID: PMC9097695 DOI: 10.1016/j.jcf.2021.08.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/11/2021] [Accepted: 08/18/2021] [Indexed: 11/28/2022]
Abstract
Longitudinal treatment patterns among the ivacaftor-treated cystic fibrosis population in the UK differ from those seen in a contemporary cohort of individuals untreated due to their genotype, despite minimal differences between the genotype groups prior to the introduction of ivacaftor. People who are treated with ivacaftor were less likely to continue other treatments such as inhaled antibiotics, dornase alfa, hypertonic saline, chronic oral antibiotics and supplementary feeding, compared to people who are not treated with ivacaftor. The differences in use of dornase alfa and hypertonic saline solution between ivacaftor-treated and non-ivacaftor-treated people, are larger for people with higher lung function.
Background In late 2012, ivacaftor became available in the UK for people with cystic fibrosis (CF) aged 6 years and over with a G551D mutation. Long-term changes in treatment patterns have not previously been reported. We investigated long-term treatment patterns in people with CF with a G551D mutation who took ivacaftor and compared these with non-ivacaftor-treated cohorts using the UK Cystic Fibrosis Registry. Methods Using 2007-2018 data we compared treatment patterns between four cohorts: 1: ivacaftor-treated; 2: ivacaftor era (2013-2018), ineligible genotype (no G551D mutation); 3: pre-ivacaftor era (2007-2012), eligible genotype (G551D mutation); 4: pre-ivacaftor era, ineligible genotype. Treatments included: inhaled antibiotics, dornase alfa, hypertonic saline, chronic oral antibiotics and supplementary feeding. Results Up to 2012 the percentages of people taking each treatment were similar between the two cohorts defined by genotype and tended to increase by year with a similar slope. Once ivacaftor was introduced, the use of other treatments tended to decrease or remain stable by year for the ivacaftor-treated cohort, whereas it remained stable or increased in the non-ivacaftor-treated cohort. This led to differences in treatment use between the two cohorts in the ivacaftor-era, which became more marked over time. Conclusions We have shown a clear divergence in treatment patterns since the introduction of ivacaftor in a number of key treatments widely used in CF. Further research is needed to investigate whether the differences in treatment patterns are associated with changes in health outcomes.
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Affiliation(s)
- Emily Granger
- Department of Medical Statistics, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, United Kingdom.
| | - Gwyneth Davies
- Population, Policy and Practice Research and Teaching Department, UCL Great Ormond Street Institute of Child Health (UCL GOS ICH), London WC1N 1EH, United Kingdom
| | - Ruth H Keogh
- Department of Medical Statistics, Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, United Kingdom; Centre for Statistical Methodology, London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London WC1E 7HT, United Kingdom
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Ratnayake I, Ahern S, Ruseckaite R. Acceptability of patient reported outcome measures (PROMs) in a cystic fibrosis data registry. BMJ Open Respir Res 2021; 8:8/1/e000927. [PMID: 34281916 PMCID: PMC8291302 DOI: 10.1136/bmjresp-2021-000927] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 06/27/2021] [Indexed: 11/23/2022] Open
Abstract
Introduction Improvements in the treatment of cystic fibrosis (CF) have resulted in longer survival and an increased focus on optimising daily functioning with the condition. Patient-reported outcome measures (PROMs) are valuable tools in evaluating the health-related quality of life of persons with chronic diseases. PROMs may be incorporated into clinical registries to assess and provide feedback regarding the health-related quality of life of the affected population. This study uses qualitative methodology to describe the views of patients with CF, caregivers and clinicians on the usefulness and practicality of incorporating a PROM in the Australian Cystic Fibrosis Data Registry (ACFDR). Methods We conducted semistructured interviews with a convenience sample of patients with CF (n=5), caregivers (n=7) and clinicians (n=13) on their opinions on incorporating the Cystic Fibrosis Questionnaire-Revised or the Cystic Fibrosis Quality of Life Questionnaire into the ACFDR. We analysed data into topics and subtopics using conventional content analysis. Results Participants believed that PROMs could generate useful aggregate health-related quality of life data to support better understanding of the experiences of the modern CF population. Participants emphasised that implementation must be supported by processes to feedback data to patients and clinicians. Most participants preferred electronic PROMs administration for easy integration into existing systems and the potential to support feedback. Conclusion Patients, caregivers and clinicians in this study generally supported the usefulness and practicality of PROM implementation in the ACFDR.
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Affiliation(s)
- Irushi Ratnayake
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Susannah Ahern
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
| | - Rasa Ruseckaite
- Department of Epidemiology and Preventive Medicine, Monash University, Melbourne, Victoria, Australia
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Schlüter DK, Ostrenga JS, Carr SB, Fink AK, Faro A, Szczesniak RD, Keogh RH, Charman SC, Marshall BC, Goss CH, Taylor-Robinson D. Lung function in children with cystic fibrosis in the USA and UK: a comparative longitudinal analysis of national registry data. Thorax 2021; 77:136-142. [PMID: 33975926 PMCID: PMC8581063 DOI: 10.1136/thoraxjnl-2021-216849] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/30/2021] [Accepted: 04/18/2021] [Indexed: 12/18/2022]
Abstract
Rationale A previous analysis found significantly higher lung function in the US paediatric cystic fibrosis (CF) population compared with the UK with this difference apparently decreasing in adolescence and adulthood. However, the cross-sectional nature of the study makes it hard to interpret these results. Objectives To compare longitudinal trajectories of lung function in children with CF between the USA and UK and to explore reasons for any differences. Methods We used mixed effects regression analysis to model lung function trajectories in the study populations. Using descriptive statistics, we compared early growth and nutrition (height, weight, body mass index), infections (Pseudomonas aeruginosa, Staphylococcus aureus) and treatments (rhDnase, hypertonic saline, inhaled antibiotics). Results We included 9463 children from the USA and 3055 children from the UK with homozygous F508del genotype. Lung function was higher in the USA than in the UK when first measured at age six and remained higher throughout childhood. We did not find important differences in early growth and nutrition, or P.aeruginosa infection. Prescription of rhDNase and hypertonic saline was more common in the USA. Inhaled antibiotics were prescribed at similar levels in both countries, but Tobramycin was prescribed more in the USA and colistin in the UK. S. aureus infection was more common in the USA than the UK. Conclusions Children with CF and homozygous F508del genotype in the USA had better lung function than UK children. These differences do not appear to be explained by early growth or nutrition, but differences in the use of early treatments need further investigation.
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Affiliation(s)
- Daniela K Schlüter
- Department of Public Health, Policy and Systems, University of Liverpool, Liverpool, UK
| | | | - Siobhán B Carr
- Royal Brompton Hospital, London, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Aliza K Fink
- Cystic Fibrosis Foundation, Bethesda, Maryland, USA
| | - Albert Faro
- Cystic Fibrosis Foundation, Bethesda, Maryland, USA
| | - Rhonda D Szczesniak
- Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, USA
| | - Ruth H Keogh
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK
| | | | | | - Christopher H Goss
- Departments of Medicine and Pediatrics, University of Washington, Seattle, Washington, USA
| | - David Taylor-Robinson
- Department of Public Health, Policy and Systems, University of Liverpool, Liverpool, UK
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24
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Seaman SR, Keogh RH, Dukes O, Vansteelandt S. Using generalized linear models to implement g-estimation for survival data with time-varying confounding. Stat Med 2021; 40:3779-3790. [PMID: 33942919 PMCID: PMC7612171 DOI: 10.1002/sim.8997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 11/17/2022]
Abstract
Using data from observational studies to estimate the causal effect of a time-varying exposure, repeatedly measured over time, on an outcome of interest requires careful adjustment for confounding. Standard regression adjustment for observed time-varying confounders is unsuitable, as it can eliminate part of the causal effect and induce bias. Inverse probability weighting, g-computation, and g-estimation have been proposed as being more suitable methods. G-estimation has some advantages over the other two methods, but until recently there has been a lack of flexible g-estimation methods for a survival time outcome. The recently proposed Structural Nested Cumulative Survival Time Model (SNCSTM) is such a method. Efficient estimation of the parameters of this model required bespoke software. In this article we show how the SNCSTM can be fitted efficiently via g-estimation using standard software for fitting generalised linear models.The ability to implement g-estimation for a survival outcome using standard statistical software greatly increases the potential uptake of this method. We illustrate the use of this method of fitting the SNCSTM by reanalyzing data from the UK Cystic Fibrosis Registry, and provide example R code to facilitate the use of this approach by other researchers.
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Affiliation(s)
- Shaun R Seaman
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Ruth H Keogh
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK
| | - Oliver Dukes
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Stijn Vansteelandt
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, London, UK.,Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
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25
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Hughes DA, Archangelidi O, Coates M, Armstrong-James D, Elborn SJ, Carr SB, Davies JC. Clinical characteristics of Pseudomonas and Aspergillus co-infected cystic fibrosis patients: A UK registry study. J Cyst Fibros 2021; 21:129-135. [PMID: 33958279 DOI: 10.1016/j.jcf.2021.04.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 04/13/2021] [Accepted: 04/14/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa (Pa) and Aspergillus species (Asp) are the most common bacterial and fungal organisms respectively in CF airways. Our aim was to examine impacts of Asp infection and Pa/Asp co-infection. METHODS Patients on the UK CF Registry in 2016 were grouped into: absent (Pa-), intermittent (Pai) or chronic Pa (Pac), each with Asp positive (Asp+) or negative (Asp-). Primary outcome was best percentage predicted FEV1 (ppFEV1) that year. Secondary outcomes were intravenous (IV) antibiotic courses, growth (height, weight, BMI) and additional disease complications. Associations between outcomes and infection-status were assessed using regression models adjusting for significant confounders (age, sex, Phe508del homozygosity and CF-related diabetes (CFRD)). RESULTS 9,270 patients were included (median age 19 [IQR 9-30] years, 54% male, 50% Phe508del/F508del). 4,142 patients (45%) isolated Pa, 1,460 (16%) Asp. Pa-/Asp+ subjects had an adjusted ppFEV1 that was 5.9% lower than Pa-/Asp- (p < 0.0001). In patients with Pai or Pac, there was no additional impact of Asp on ppFEV1. However, there was a higher probability that Pac/Asp+ patients had required IV antibiotics than Pac/Asp- group (OR 1.23 [1.03-1.48]). Low BMI, ABPA, CF-liver disease and CFRD were all more frequent with Asp alone than Pa-/Asp-, though not more common in Pac/Asp+ than Pac/Asp-. CONCLUSIONS Co-infection with Pa and Asp was not associated with reduced lung function compared with Pa alone, but was associated with additional use of IV antibiotics. Asp infection itself is associated with several important indicators of disease severity. Longitudinal analyses should explore the impact of co-infection on disease progression.
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Affiliation(s)
- Dominic A Hughes
- National Heart & Lung Institute, Imperial College London, UK; Royal Brompton and Harefield Hospitals, London, UK.
| | | | - Matthew Coates
- National Heart & Lung Institute, Imperial College London, UK
| | - Darius Armstrong-James
- Royal Brompton and Harefield Hospitals, London, UK; Department of Infectious Diseases, Imperial College London, UK
| | | | - Siobhán B Carr
- National Heart & Lung Institute, Imperial College London, UK; Royal Brompton and Harefield Hospitals, London, UK
| | - Jane C Davies
- National Heart & Lung Institute, Imperial College London, UK; Royal Brompton and Harefield Hospitals, London, UK
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26
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Yang S, Zhu F, Ling X, Liu Q, Zhao P. Intelligent Health Care: Applications of Deep Learning in Computational Medicine. Front Genet 2021; 12:607471. [PMID: 33912213 PMCID: PMC8075004 DOI: 10.3389/fgene.2021.607471] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/05/2021] [Indexed: 12/24/2022] Open
Abstract
With the progress of medical technology, biomedical field ushered in the era of big data, based on which and driven by artificial intelligence technology, computational medicine has emerged. People need to extract the effective information contained in these big biomedical data to promote the development of precision medicine. Traditionally, the machine learning methods are used to dig out biomedical data to find the features from data, which generally rely on feature engineering and domain knowledge of experts, requiring tremendous time and human resources. Different from traditional approaches, deep learning, as a cutting-edge machine learning branch, can automatically learn complex and robust feature from raw data without the need for feature engineering. The applications of deep learning in medical image, electronic health record, genomics, and drug development are studied, where the suggestion is that deep learning has obvious advantage in making full use of biomedical data and improving medical health level. Deep learning plays an increasingly important role in the field of medical health and has a broad prospect of application. However, the problems and challenges of deep learning in computational medical health still exist, including insufficient data, interpretability, data privacy, and heterogeneity. Analysis and discussion on these problems provide a reference to improve the application of deep learning in medical health.
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Affiliation(s)
- Sijie Yang
- School of Computer Science and Technology, Soochow University, Suzhou, China
| | - Fei Zhu
- School of Computer Science and Technology, Soochow University, Suzhou, China
| | - Xinghong Ling
- School of Computer Science and Technology, Soochow University, Suzhou, China
- WenZheng College of Soochow University, Suzhou, China
| | - Quan Liu
- School of Computer Science and Technology, Soochow University, Suzhou, China
| | - Peiyao Zhao
- School of Computer Science and Technology, Soochow University, Suzhou, China
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27
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Abstract
BACKGROUND Male sex is associated with better lung function and survival in people with cystic fibrosis but it is unclear whether the survival benefit is solely due to the sex-effect on lung function. METHODS This study analyzes data between 1996 and 2015 from the longitudinal registry study of the UK Cystic Fibrosis Registry. We jointly analyze repeated measurements and time-to-event outcomes to assess how much of the sex effect on lung function also explains survival. These novel methods allow examination of association between percent of forced expiratory volume in 1 second (%FEV1) and covariates such as sex and genotype, and survival, in the same modeling framework. We estimate the probability of surviving one more year with a probit model. RESULTS The dataset includes 81,129 lung function measurements of %FEV1 on 9,741 patients seen between 1996 and 2015 and captures 1,543 deaths. Males compared with females experienced a more gradual decline in %FEV1 (difference 0.11 per year 95% confidence interval [CI] = 0.08, 0.14). After adjusting for confounders, both overall level of %FEV1 and %FEV1 rate of change are associated with the concurrent hazard for death. There was evidence of a male survival advantage (probit coefficient 0.15; 95% CI = 0.10, 0.19) which changed little after adjustment for %FEV1 using conventional approaches but was attenuated by 37% on adjustment for %FEV1 level and slope in the joint model (0.09; 95% CI = 0.06, 0.12). CONCLUSIONS We estimate that about 37% of the association of sex on survival in cystic fibrosis is mediated through lung function.
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28
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Ahern S, Dean J, Liman J, Ruseckaite R, Burke N, Gollan M, Keatley L, King S, Kotsimbos T, Middleton PG, Schultz A, Wainwright C, Wark P, Bell S. Redesign of the Australian Cystic Fibrosis Data Registry: A multidisciplinary collaboration. Paediatr Respir Rev 2021; 37:37-43. [PMID: 32331762 DOI: 10.1016/j.prrv.2020.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 03/19/2020] [Indexed: 10/24/2022]
Abstract
Clinical registries that monitor and review outcomes for patients with cystic fibrosis have existed internationally for many decades. However, their purpose continues to evolve and now includes the capability to support clinical effectiveness research, clinical trials and Phase IV studies, and international data comparisons and projects. To achieve this, registries must regularly update the information that they collect and ensure design that is adaptable and flexible to changing needs. The Australian Cystic Fibrosis Data Registry commenced in 1998, and in 2018-19 undertook a transformation to enable it to meet the needs of multiple stakeholders into the future. This included a comprehensive, multidisciplinary review of the registry's data elements, and a redesign and rebuild of the registry's database. The data element review comprised the processes of alignment, comparison, selection, consolidation, revision and definition of finalised data elements. The database redesign included attention to each of the registry functions of data collection, storage and management, and reporting. The revision of a national data collection system is a time-intensive process, and requires significant clinical and other expert engagement. The resulting database, while being continually refined, is now fit for purpose to support Australian clinicians and patients with CF to receive best practice care.
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Affiliation(s)
- Susannah Ahern
- Monash University, Department of Epidemiology and Preventive Medicine. 553 St Kilda Rd, Melbourne, Victoria 3004, Australia.
| | - Joanne Dean
- Monash University, Department of Epidemiology and Preventive Medicine. 553 St Kilda Rd, Melbourne, Victoria 3004, Australia.
| | - John Liman
- Monash University, Department of Epidemiology and Preventive Medicine. 553 St Kilda Rd, Melbourne, Victoria 3004, Australia.
| | - Rasa Ruseckaite
- Monash University, Department of Epidemiology and Preventive Medicine. 553 St Kilda Rd, Melbourne, Victoria 3004, Australia.
| | - Nettie Burke
- Cystic Fibrosis Australia, 2 Richardson Place North, Ryde, NSW 2113, Australia.
| | - Morgan Gollan
- Australian Cystic Fibrosis Data Registry, Victoria 3004, Australia
| | - Lucy Keatley
- Westmead Hospital, Cnr Hawkesbury Rd and Darcy Rd, NSW 2145, Australia.
| | - Susannah King
- The Alfred, 55 Commercial Rd, Melbourne, Victoria 3004, Australia; Department of Dietetics, Nutrition and Sport, LaTrobe University, Bundoora, Victoria 3086, Australia.
| | - Tom Kotsimbos
- The Alfred, 55 Commercial Rd, Melbourne, Victoria 3004, Australia.
| | - Peter G Middleton
- Westmead Hospital, Cnr Hawkesbury Rd and Darcy Rd, NSW 2145, Australia; Westmead Clinical School, University of Sydney, Australia.
| | - Andre Schultz
- Perth Children's Hospital, 15 Hospital Avenue, Nedlands, Western Australia 6009, Australia.
| | - Claire Wainwright
- Queensland Children's Hospital, 501 Stanley St South, Brisbane, Queensland 4101, Australia.
| | - Peter Wark
- John Hunter Hospital, Newcastle, Lookout Rd, New Lambton Heights, NSW 2305, Australia.
| | - Scott Bell
- Translational Research Institute 37 Kent Street Woolloongabba, Queensland 4102, Australia.
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29
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Dayasiri K, Hull J, Rao S. NICE guidance on diagnosis and management of cystic fibrosis. Arch Dis Child Educ Pract Ed 2021; 106:31-34. [PMID: 32447278 DOI: 10.1136/archdischild-2019-316882] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 04/17/2020] [Accepted: 04/26/2020] [Indexed: 11/03/2022]
Affiliation(s)
- Kavinda Dayasiri
- Department of Paediatrics, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Jeremy Hull
- Department of Paediatrics, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
| | - Sahana Rao
- Department of Paediatrics, Oxford University Hospitals NHS Foundation Trust, Oxford, Oxfordshire, UK
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30
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Frost F, Nazareth D, Shaw M, Al-Aloul M. Assessing the validity and applicability of the French 3-year prognostic score in the UK cystic fibrosis population - a national cohort study. Transpl Int 2021; 34:436-444. [PMID: 33486768 DOI: 10.1111/tri.13805] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Revised: 08/11/2020] [Accepted: 12/14/2020] [Indexed: 12/01/2022]
Abstract
Models that predict outcomes, aid prognostication and inform the assessment of urgency for lung transplantation (LT) in CF are in demand. A prognostic score derived from the French adult CF registry to predict death or LT over 3-year follow-up was described in 2017 and validated using Canadian CF registry data. We assessed its performance in the UK CF population. The French prognostic score was applied to untransplanted adults with CF. The index year (2014) and outcomes (Death or LT) were evaluated to 2017. Receiver operator characteristics plots and area under curve (AUC) was computed. 4407 adults with CF met the inclusion criteria. After 3 years, 7.1% (P < 0.001) were dead or had received LT compared to the French (12.8%) and Canadian (9.4%) cohorts. The French score deemed 592 (26.2%) 'High-risk' - death/LT occurred in 189/592 (30.2%), less than previously reported in France and Canada (P < 0.0001). The discriminatory power of the French score was lower (AUC 0.830) than reported. Recalibration yielded only marginal improvement in model performance (AUC 0.833). The French prognostic score does not perform as well in the UK as reported elsewhere. Bespoke UK scores are needed to aid prognostication and inform LT decision-making.
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Affiliation(s)
- Freddy Frost
- Adult CF Unit, Liverpool Heart and Chest Hospital NHS Trust, Liverpool, UK
| | - Dilip Nazareth
- Adult CF Unit, Liverpool Heart and Chest Hospital NHS Trust, Liverpool, UK
| | - Matthew Shaw
- Liverpool Heart and Chest Hospital NHS Trust, Liverpool, UK
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31
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Alawsi F, Sawbridge D, Fitzgerald R. Orthodontics in patients with significant medical co-morbidities. J Orthod 2020; 47:4-24. [PMID: 32985344 DOI: 10.1177/1465312520949881] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A wide variety of patients with medical co-morbidities may present to general orthodontic practice. It is important for the treating clinician to have a general understanding of key medical conditions that may impact upon the treatment and management options. This clinical supplement provides a treatment-focused summative update for the orthodontist regarding significant medical co-morbidities, their general prevalence and an exploration of potential impacts upon orthodontic treatment. This review also discusses the significance of key medications and provides suggestions for the safe provision of orthodontic treatment.
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Affiliation(s)
- Fahad Alawsi
- Orthodontic Department, Royal Preston Hospital, Preston, UK
| | - David Sawbridge
- Intestinal Failure Unit, Salford Royal NHS Foundation Trust, Salford, UK
| | - Rhian Fitzgerald
- Orthodontic Department, Royal Preston Hospital, Preston, UK.,Alder Hey Children's Hospital, Liverpool, UK
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Harrington NE, Sweeney E, Harrison F. Building a better biofilm - Formation of in vivo-like biofilm structures by Pseudomonas aeruginosa in a porcine model of cystic fibrosis lung infection. Biofilm 2020; 2:100024. [PMID: 33381751 PMCID: PMC7762787 DOI: 10.1016/j.bioflm.2020.100024] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/24/2020] [Accepted: 04/24/2020] [Indexed: 12/20/2022] Open
Abstract
Pseudomonas aeruginosa biofilm infections in the cystic fibrosis (CF) lung are highly resistant to current antimicrobial treatments and are associated with increased mortality rates. The existing models for such infections are not able to reliably mimic the clinical biofilms observed. We aimed to further optimise an ex vivo pig lung (EVPL) model for P. aeruginosa CF lung infection that can be used to increase understanding of chronic CF biofilm infection. The EVPL model will facilitate discovery of novel infection prevention methods and treatments, and enhanced exploration of biofilm architecture. We investigated purine metabolism and biofilm formation in the model using transposon insertion mutants in P. aeruginosa PA14 for key genes: purD, gacA and pelA. Our results demonstrate that EVPL recapitulates a key aspect of in vivo P. aeruginosa infection metabolism, and that the pathogen forms a biofilm with a clinically realistic structure not seen in other in vitro studies. Two pathways known to be required for in vivo biofilm infection - the Gac regulatory pathway and production of the Pel exopolysaccharide - are essential to the formation of this mature, structured biofilm on EVPL tissue. We propose the high-throughput EVPL model as a validated biofilm platform to bridge the gap between in vitro work and CF lung infection.
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Affiliation(s)
- Niamh E. Harrington
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Esther Sweeney
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, United Kingdom
| | - Freya Harrison
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, United Kingdom
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Abidin NZ, Gardner AI, Robinson HL, Haq IJ, Thomas MF, Brodlie M. Trends in nontuberculous mycobacteria infection in children and young people with cystic fibrosis. J Cyst Fibros 2020; 20:737-741. [PMID: 32950411 PMCID: PMC8490157 DOI: 10.1016/j.jcf.2020.09.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/13/2020] [Accepted: 09/14/2020] [Indexed: 11/18/2022]
Abstract
NTM infection in children with CF is a major clinical concern and challenge. Prevalence of NTM in children in the UK CF registry stabilised from 2016 to 18. This prevalence, however, remained substantially higher than in 2010. We highlight the need for high quality studies in this area.
Nontuberculous mycobacteria (NTM) infection is of growing concern in cystic fibrosis (CF). UK CF Registry data were analyzed from 2016 to 2018. Prevalence of infection stabilized in the pediatric age-group during this period but remained substantially higher than in 2010. Allergic bronchopulmonary aspergillosis and Pseudomonas aeruginosa infection were associated with NTM infection.
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Affiliation(s)
- Noreen Zainal Abidin
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH. United Kingdom; Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, Queen Victoria Road, Newcastle upon Tyne, UK, NE1 4LP. United Kingdom
| | - Aaron Ions Gardner
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH. United Kingdom
| | - Hannah-Louise Robinson
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH. United Kingdom
| | - Iram J Haq
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH. United Kingdom; Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, Queen Victoria Road, Newcastle upon Tyne, UK, NE1 4LP. United Kingdom
| | - Matthew F Thomas
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH. United Kingdom; Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, Queen Victoria Road, Newcastle upon Tyne, UK, NE1 4LP. United Kingdom
| | - Malcolm Brodlie
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH. United Kingdom; Paediatric Respiratory Medicine, Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, Queen Victoria Road, Newcastle upon Tyne, UK, NE1 4LP. United Kingdom.
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Kaplan S, Lee A, Caine N, Charman SC, Bilton D. Long-term safety study of colistimethate sodium (Colobreathe®): Findings from the UK Cystic Fibrosis Registry. J Cyst Fibros 2020; 20:324-329. [PMID: 32807645 DOI: 10.1016/j.jcf.2020.08.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2020] [Revised: 07/17/2020] [Accepted: 08/04/2020] [Indexed: 10/23/2022]
Abstract
BACKGROUND As part of the risk management plan in Europe, a long-term observational study was conducted to monitor the safety of colistimethate sodium dry powder for inhalation (CMS-DPI) compared to other inhaled antibiotics. METHODS A cohort of CMS-DPI patients and a matched cohort were identified from the UK Cystic Fibrosis Registry (UKCFR) from 2014-2018. The primary outcome was a composite endpoint, defined as adverse events (AEs) or new cystic fibrosis (CF) complications. Other outcomes included pulmonary exacerbations and treatment discontinuations. RESULTS Of 1466 and 3503 patients in the CMS-DPI and comparator cohorts, respectively, 82.7% and 79.4% had AEs. Among the most common new CF complications were osteopenia, CF-related diabetes, and increased liver enzymes. The adjusted event rate ratio (ERR) for the primary outcome was 1.25 (95% confidence interval [CI]: 1.18-1.33, p<0.001). After excluding new CF complications, there was no difference between cohorts (ERR=1.04, 95% CI: 0.79-1.38, p=0.785). Pulmonary exacerbations were common in CMS-DPI and comparator cohorts (78.0% and 79.9% of patients, respectively), with adjusted ERR of 1.02 (95% CI: 0.95-1.10, p=0.523). Rates of discontinuation were similar in the CMS-DPI and Tobramycin inhalation powder comparator cohorts (37.8% and 39.8% of patients, respectively). CONCLUSIONS There was no difference in the rate of adverse events between CMS-DPI and comparator cohorts. The safety profile of CMS-DPI is similar to those of other inhaled antibiotics, supporting its long-term safety in people with CF. The UKCFR has developed a successful model for partnership with industry to conduct long-term studies aimed at assessing drug safety.
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Affiliation(s)
- Sigal Kaplan
- Teva Pharmaceutical Industries Ltd., Netanya, Israel.
| | - Andrew Lee
- UK Cystic Fibrosis Trust (UKCFT), London, United Kingdom
| | - Noreen Caine
- UK Cystic Fibrosis Trust (UKCFT), London, United Kingdom
| | | | - Diana Bilton
- National Heart and Lung Institute, Imperial College, London & Royal Brompton Hospital, London, United Kingdom
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Griffiths R, Schlüter DK, Akbari A, Cosgriff R, Tucker D, Taylor-Robinson D. Identifying children with Cystic Fibrosis in population-scale routinely collected data in Wales: A Retrospective Review. Int J Popul Data Sci 2020; 5:1346. [PMID: 33644411 PMCID: PMC7898022 DOI: 10.23889/ijpds.v5i1.1346] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
INTRODUCTION The challenges in identifying a cohort of people with a rare condition can be addressed by routinely collected, population-scale electronic health record (EHR) data, which provide large volumes of data at a national level. This paper describes the challenges of accurately identifying a cohort of children with Cystic Fibrosis (CF) using EHR and their validation against the UK CF Registry. OBJECTIVES To establish a proof of principle and provide insight into the merits of linked data in CF research; to identify the benefits of access to multiple data sources, in particular the UK CF Registry data, and to demonstrate the opportunity it represents as a resource for future CF research. METHODS Three EHR data sources were used to identify children with CF born in Wales between 1st January 1998 and 31st August 2015 within the Secure Anonymised Information Linkage (SAIL) Databank. The UK CF Registry was later acquired by SAIL and linked to the EHR cohort to validate the cases and explore the reasons for misclassifications. RESULTS We identified 352 children with CF in the three EHR data sources. This was greater than expected based on historical incidence rates in Wales. Subsequent validation using the UK CF Registry found that 257 (73%) of these were true cases. Approximately 98.7% (156/158) of individuals identified as CF cases in all three EHR data sources were confirmed as true cases; but this was only the case for 19.8% (20/101) of all those identified in just a single data source. CONCLUSION Identifying health conditions in EHR data can be challenging, so data quality assurance and validation is important or the merit of the research is undermined. This retrospective review identifies some of the challenges in identifying CF cases and demonstrates the benefits of linking cases across multiple data sources to improve quality.
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Affiliation(s)
- R Griffiths
- Swansea University Medical School, Swansea University
- Health Data Research UK
| | - DK Schlüter
- Department of Public Health and Policy, University of Liverpool, Liverpool L69 7ZX
| | - A Akbari
- Swansea University Medical School, Swansea University
- Health Data Research UK
- Administrative Data Research Wales
| | - R Cosgriff
- Cystic Fibrosis Trust, One Aldgate, London EC3N 1R
| | - D Tucker
- Public Health Wales, Capital Quarter 2, Tyndall Street, Cardiff. CF10 4BZ\break † Joint First Authors
| | - D Taylor-Robinson
- Department of Public Health and Policy, University of Liverpool, Liverpool L69 7ZX
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Vijayasingam A, Frost E, Wilkins J, Gillen L, Premachandra P, Mclaren K, Gilmartin D, Picinali L, Vidal-Diez A, Borsci S, Ni MZ, Tang WY, Morris-Rosendahl D, Harcourt J, Elston C, Simmonds NJ, Shah A. Tablet and web-based audiometry to screen for hearing loss in adults with cystic fibrosis. Thorax 2020; 75:632-639. [PMID: 32409613 DOI: 10.1136/thoraxjnl-2019-214177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 04/18/2020] [Accepted: 04/20/2020] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Individuals with chronic lung disease (eg, cystic fibrosis (CF)) often receive antimicrobial therapy including aminoglycosides resulting in ototoxicity. Extended high-frequency audiometry has increased sensitivity for ototoxicity detection, but diagnostic audiometry in a sound-booth is costly, time-consuming and requires a trained audiologist. This cross-sectional study analysed tablet-based audiometry (Shoebox MD) performed by non-audiologists in an outpatient setting, alongside home web-based audiometry (3D Tune-In) to screen for hearing loss in adults with CF. METHODS Hearing was analysed in 126 CF adults using validated questionnaires, a web self-hearing test (0.5 to 4 kHz), tablet (0.25 to 12 kHz) and sound-booth audiometry (0.25 to 12 kHz). A threshold of ≥25 dB hearing loss at ≥1 audiometric frequency was considered abnormal. Demographics and mitochondrial DNA sequencing were used to analyse risk factors, and accuracy and usability of hearing tests determined. RESULTS Prevalence of hearing loss within any frequency band tested was 48%. Multivariate analysis showed age (OR 1.127; (95% CI: 1.07 to 1.18; p value<0.0001) per year older) and total intravenous antibiotic days over 10 years (OR 1.006; (95% CI: 1.002 to 1.010; p value=0.004) per further intravenous day) were significantly associated with increased risk of hearing loss. Tablet audiometry had good usability, was 93% sensitive, 88% specific with 94% negative predictive value to screen for hearing loss compared with web self-test audiometry and questionnaires which had poor sensitivity (17% and 13%, respectively). Intraclass correlation (ICC) of tablet versus sound-booth audiometry showed high correlation (ICC >0.9) at all frequencies ≥4 kHz. CONCLUSIONS Adults with CF have a high prevalence of drug-related hearing loss and tablet-based audiometry can be a practical, accurate screening tool within integrated ototoxicity monitoring programmes for early detection.
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Affiliation(s)
- Anitha Vijayasingam
- Adult Cystic Fibrosis Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Emily Frost
- Department of Audiology, Imperial College Healthcare NHS Trust, London, UK
| | - Julie Wilkins
- Department of Audiology, Imperial College Healthcare NHS Trust, London, UK
| | - Lise Gillen
- Department of Audiology, Guy's and Saint Thomas' Hospitals NHS Trust, London, UK
| | | | - Kate Mclaren
- Adult Cystic Fibrosis Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Desmond Gilmartin
- Adult Cystic Fibrosis Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK
| | - Lorenzo Picinali
- Dyson School of Design Engineering, Imperial College London, London, UK
| | - Alberto Vidal-Diez
- London In Vitro Diagnostics Collaborative, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Simone Borsci
- London In Vitro Diagnostics Collaborative, Department of Surgery and Cancer, Imperial College London, London, UK.,Department of Cognitive Psychology and Ergonomics, Faculty of Behavioural Management and Social sciences, University of Twente, Enschede, Overijssel, Netherlands
| | - Melody Zhifang Ni
- London In Vitro Diagnostics Collaborative, Department of Surgery and Cancer, Imperial College London, London, UK
| | - Wai Y Tang
- Clinical Genetics and Genomics, Royal Brompton and Harefield NHS Foundation Trust, London, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Deborah Morris-Rosendahl
- Clinical Genetics and Genomics, Royal Brompton and Harefield NHS Foundation Trust, London, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Jonny Harcourt
- Department of Ear, Nose and Throat, Imperial College Healthcare NHS Trust, London, UK
| | - Caroline Elston
- Department of Cystic Fibrosis, King's College Hospital NHS Foundation Trust, London, London, UK
| | - N J Simmonds
- Adult Cystic Fibrosis Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK.,National Heart and Lung Institute, Imperial College London, London, UK
| | - Anand Shah
- Adult Cystic Fibrosis Centre, Royal Brompton and Harefield NHS Foundation Trust, London, UK .,National Heart and Lung Institute, Imperial College London, London, UK
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Brown A, Jenkins L, Reid A, Leavy A, McDowell G, McIlroy C, Thompson A, McNaughten B. How to perform and interpret the sweat test. Arch Dis Child Educ Pract Ed 2020; 105:230-235. [PMID: 31744807 DOI: 10.1136/archdischild-2018-316615] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 11/05/2019] [Indexed: 12/12/2022]
Abstract
Cystic fibrosis (CF) is the most common life-threatening autosomal-recessive disease affecting Caucasians in the western world. The sweat test is the main diagnostic test for CF. It is indicated as part of the clinical assessment for infants that have picked up on the national neonatal screening programme. It may also be requested where clinical suspicion of a diagnosis of CF exists despite normal screening results. This article outlines the physiological basis behind sweat testing and the technical aspects of performing the test. Indications for performing the test are also considered. The article aims to provide clinicians with a guide to interpretation of results.
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Affiliation(s)
- Anthony Brown
- The Royal Belfast Hospital for Sick Children, Belfast, UK
| | - Laura Jenkins
- Respiratory Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK
| | - Alastair Reid
- Respiratory Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK
| | - Anne Leavy
- Respiratory Paediatrics, Royal Belfast Hospital for Sick Children, Belfast, UK
| | - Glen McDowell
- Biomedical Science, Royal Group of Hospitals and Dental Hospital Health and Social Services Trust, Belfast, UK
| | - Claire McIlroy
- Neonatal Screening, Royal Belfast Hospital for Sick Children, Belfast, UK
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Keogh RH, Tanner K, Simmonds NJ, Bilton D. The changing demography of the cystic fibrosis population: forecasting future numbers of adults in the UK. Sci Rep 2020; 10:10660. [PMID: 32606329 PMCID: PMC7327064 DOI: 10.1038/s41598-020-67353-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Accepted: 06/01/2020] [Indexed: 12/01/2022] Open
Abstract
Improvements in management of cystic fibrosis (CF) through specialist centres in the UK have been associated with a step-change in life expectancy. With increasing numbers of adult patients there is a need to review health care provision to ensure it is sufficient to meet future needs. We used UK CF Registry data to project the number of patients aged 16–17 and 18 and older up to 2030, and numbers therefore requiring specialist adult CF care. Survival modelling was used to estimate age-specific mortality rates. New-diagnosis rates were estimated using diagnoses observed in the Registry and national population figures. Uncertainty in projections was captured through 95% prediction intervals (PI). The number of adults (aged 18 and older) is expected to increase by 28% from 6,225 in 2017 to 7,988 in 2030 (95% PI 7,803–8,169), assuming current mortality rates. If mortality rates improve at the rate seen over recent years, the projected number increases to 8,579 (95% PI 8,386–8,764). The age distribution is also expected to change, with 36% of CF adults being over 40 in 2030, versus 21% in 2017. There is an urgent requirement to review adult CF health care provision, due to both increasing numbers and the changing care needs of an older population.
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Affiliation(s)
- Ruth H Keogh
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
| | - Kamaryn Tanner
- Department of Medical Statistics, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Nicholas J Simmonds
- National Heart and Lung Institute, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London, SW3 6LR, UK.,Royal Brompton Hospital, Sydney Street, London, SW3 6NP, UK
| | - Diana Bilton
- National Heart and Lung Institute, Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London, SW3 6LR, UK.,Royal Brompton Hospital, Sydney Street, London, SW3 6NP, UK
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Seaman S, Dukes O, Keogh R, Vansteelandt S. Adjusting for time-varying confounders in survival analysis using structural nested cumulative survival time models. Biometrics 2020; 76:472-483. [PMID: 31562652 PMCID: PMC7317577 DOI: 10.1111/biom.13158] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Accepted: 09/19/2019] [Indexed: 11/28/2022]
Abstract
Accounting for time-varying confounding when assessing the causal effects of time-varying exposures on survival time is challenging. Standard survival methods that incorporate time-varying confounders as covariates generally yield biased effect estimates. Estimators using weighting by inverse probability of exposure can be unstable when confounders are highly predictive of exposure or the exposure is continuous. Structural nested accelerated failure time models (AFTMs) require artificial recensoring, which can cause estimation difficulties. Here, we introduce the structural nested cumulative survival time model (SNCSTM). This model assumes that intervening to set exposure at time t to zero has an additive effect on the subsequent conditional hazard given exposure and confounder histories when all subsequent exposures have already been set to zero. We show how to fit it using standard software for generalized linear models and describe two more efficient, double robust, closed-form estimators. All three estimators avoid the artificial recensoring of AFTMs and the instability of estimators that use weighting by the inverse probability of exposure. We examine the performance of our estimators using a simulation study and illustrate their use on data from the UK Cystic Fibrosis Registry. The SNCSTM is compared with a recently proposed structural nested cumulative failure time model, and several advantages of the former are identified.
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Affiliation(s)
- Shaun Seaman
- MRC Biostatistics Unit, University of CambridgeInstitute of Public HealthCambridgeUK
| | - Oliver Dukes
- Department of Applied Mathematics, Computer Science and StatisticsGhent UniversityGhentBelgium
| | - Ruth Keogh
- London School of Hygiene and Tropical MedicineLondonUK
| | - Stijn Vansteelandt
- Department of Applied Mathematics, Computer Science and StatisticsGhent UniversityGhentBelgium
- London School of Hygiene and Tropical MedicineLondonUK
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40
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Salvatore M, Amato A, Floridia G, Censi F, Ferrari G, Tosto F, Padoan R, Raia V, Cirilli N, Castaldo G, Capoluongo E, Caruso U, Corbetta C, Taruscio D. The Italian External Quality Assessment Program for Cystic Fibrosis Sweat Chloride Test: Does Active Participation Improve the Quality? INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17093196. [PMID: 32375358 PMCID: PMC7246827 DOI: 10.3390/ijerph17093196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 04/26/2020] [Accepted: 04/27/2020] [Indexed: 05/28/2023]
Abstract
(1) Background: Diagnostic testing for cystic fibrosis (CF) is based on a sweat chloride test (SCT) considering the appropriate signs and symptoms of the disease and results of a gene mutation analysis. In 2014, the Istituto Superiore di Sanità (ISS) established a pilot Italian external quality assessment program for CF SCT (Italian EQA-SCT), which is now a third party service carried out by the ISS. (2) Methods: The ongoing scheme is prospective, enrollment is voluntary, and the payment of a fee is required. Results are shared through a dedicated web-facility. Assessment covers the analysis, interpretation, and reporting of results. (3) Results: Thirteen, fifteen, sixteen, and fifteen different laboratories, respectively, participated from 2015 to 2016 and from 2018 to 2019 in the Italian EQA-SCT scheme. Eleven different laboratories participated each year in all four rounds of the Italian EQA-SCT. (4) Conclusions: The overall results obtained from the laboratories participating constantly clearly show that their qualitative and quantitative performance improved significantly. This is due to the opportunity-after receiving the EQA results-to constantly review their performance and address any inconsistencies. We firmly believe that participation in the EQA program will improve the quality of participating laboratories and that EQA participation should become mandatory as a fundamental requirement for laboratory accreditation.
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Affiliation(s)
- Marco Salvatore
- Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, National Center Rare Diseases, 00161 Rome, Italy; (A.A.); (F.C.); (G.F.); (F.T.); (D.T.)
| | - Annalisa Amato
- Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, National Center Rare Diseases, 00161 Rome, Italy; (A.A.); (F.C.); (G.F.); (F.T.); (D.T.)
| | - Giovanna Floridia
- Unità di Bioetica, Istituto Superiore di Sanità, 00161 Roma, Italia;
| | - Federica Censi
- Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, National Center Rare Diseases, 00161 Rome, Italy; (A.A.); (F.C.); (G.F.); (F.T.); (D.T.)
| | - Gianluca Ferrari
- Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, National Center Rare Diseases, 00161 Rome, Italy; (A.A.); (F.C.); (G.F.); (F.T.); (D.T.)
| | - Fabrizio Tosto
- Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, National Center Rare Diseases, 00161 Rome, Italy; (A.A.); (F.C.); (G.F.); (F.T.); (D.T.)
| | - Rita Padoan
- Centro di Supporto Fibrosi Cistica, Dipartimento Pediatrico, Università di Brescia, ASST Spedali Civili, 25123 Brescia, Italia;
| | - Valeria Raia
- Centro Regionale Fibrosi Cistica, Unità di Pediatria, Dipartimento di Scienze Mediche Traslazionali, Università degli Studi di Napoli, Federico II, 80145 Napoli, Italia;
| | - Natalia Cirilli
- Centro di Riferimento Fibrosi Cistica, Dipartimento Materno Infantile, AOU Ospedali Riuniti, 60121 Ancona, Italia;
| | - Giuseppe Castaldo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II; CEINGE-Biotecnologie avanzate, scarl, 80131 Napoli, Italia; (G.C.); (E.C.)
| | - Ettore Capoluongo
- Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università di Napoli Federico II; CEINGE-Biotecnologie avanzate, scarl, 80131 Napoli, Italia; (G.C.); (E.C.)
| | - Ubaldo Caruso
- LABSIEM—Laboratorio per lo Studio degli Errori Congeniti del Metabolismo, Università degli Studi di Genova—DINOGMI, 16132 Genova, Italia;
| | - Carlo Corbetta
- SC Laboratorio di Riferimento Regionale per lo Screening Neonatale—Regione Lombardia, ASST Fatebenefratelli Sacco, 20157 Milano, Italia;
| | - Domenica Taruscio
- Undiagnosed Rare Diseases Interdepartmental Unit, Istituto Superiore di Sanità, National Center Rare Diseases, 00161 Rome, Italy; (A.A.); (F.C.); (G.F.); (F.T.); (D.T.)
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Higgins M, Volkova N, Moy K, Marshall BC, Bilton D. Real-World Outcomes Among Patients with Cystic Fibrosis Treated with Ivacaftor: 2012-2016 Experience. Pulm Ther 2020; 6:141-149. [PMID: 32304091 PMCID: PMC7229122 DOI: 10.1007/s41030-020-00115-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Indexed: 01/30/2023] Open
Abstract
Introduction In this long-term, postapproval, observational study, data from the US Cystic Fibrosis Foundation Patient Registry and the UK Cystic Fibrosis Registry were used to evaluate the impact of ivacaftor treatment on cystic fibrosis (CF) by comparing outcomes in ivacaftor-treated patients with those in matched untreated comparator patients. Registry data from up to 5 years of ivacaftor availability in the US and up to 4 years of availability in the UK were evaluated. Methods Starting in the first year of ivacaftor availability, ivacaftor-treated patients in each registry were matched 1:5 to comparator patients who never received ivacaftor. Clinical endpoints were evaluated in annual cross-sectional safety analyses. The key endpoints were death, organ transplants, pulmonary exacerbation, and hospitalization. Relative risks and 95% CIs were calculated to compare the ivacaftor and comparator cohorts in each registry. Results Here, we report the complete and final results of the annual cross-sectional safety analyses across the duration of the study, with up to 5 years of follow-up. Data show a pattern of lower risk of death, transplant, pulmonary exacerbation, and hospitalization among ivacaftor-treated patients in both registries. Conclusions Ivacaftor-treated patients had consistently favorable clinical outcomes relative to untreated comparators, and no new safety concerns were identified. While general limitations of observational research apply, these findings support disease modification by CF transmembrane conductance regulator (CFTR) modulator therapy with ivacaftor. Future research of novel CFTR modulators will need to explore alternative methods for comparator selection for evaluation of clinical data given the evolving landscape of CF treatment. We performed a study to better understand the long-term impact of treatment with a drug called ivacaftor for patients with cystic fibrosis (CF). Our study used data from CF patient registries in the United Kingdom and the United States. These registries collect information about patients with CF, their health, and the treatments they receive. Using data from these registries, we compared patients treated with ivacaftor with a similar group of patients (similar age, sex, and disease severity) who did not receive ivacaftor. We looked at the clinical outcomes of each group every year for up to 5 years. In the final analysis from our study, we found no new safety concerns associated with ivacaftor treatment. Additionally, we found that patients treated with ivacaftor tended to have lower risks of death, organ transplant, pulmonary exacerbations, and hospitalizations. Overall, these results demonstrate the favorable impact of ivacaftor treatment on long-term outcomes of patients with CF.
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Affiliation(s)
- Mark Higgins
- Vertex Pharmaceuticals (Europe) Limited, 2 Kingdom St, London, W2 6BD, UK.
| | - Nataliya Volkova
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, MA, USA
| | - Kristin Moy
- Vertex Pharmaceuticals Incorporated, 50 Northern Ave, Boston, MA, USA
| | - Bruce C Marshall
- US Cystic Fibrosis Foundation, 4550 Montgomery Ave, Suite 1100 N, Bethesda, MD, USA
| | - Diana Bilton
- The Cystic Fibrosis Trust, 1 Aldgate, London, EC3N 1RE, UK.,National Heart and Lung Institute, Imperial College London, London, UK.,Royal Brompton Hospital, London, UK
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Gardner AI, McClenaghan E, Saint G, McNamara PS, Brodlie M, Thomas MF. Epidemiology of Nontuberculous Mycobacteria Infection in Children and Young People With Cystic Fibrosis: Analysis of UK Cystic Fibrosis Registry. Clin Infect Dis 2020; 68:731-737. [PMID: 29982302 PMCID: PMC6376093 DOI: 10.1093/cid/ciy531] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 06/29/2018] [Indexed: 12/30/2022] Open
Abstract
Background Infection with nontuberculous mycobacteria (NTM) is of growing clinical concern in people with cystic fibrosis (CF). The epidemiology of infection in children and young people remains poorly understood. Our goal was to investigate the epidemiology of NTM infection in the pediatric age group using data from the UK CF Registry. Methods Data from 2010–2015 for individuals aged <16 years (23200 observations from 5333 unique individuals) were obtained. Univariate analysis of unique individuals comparing all key clinical factors and health outcomes to NTM status was performed. The significant factors that were identified were used to generate a multivariate logistic regression model that, following step-wise removal, generated a final parsimonious model. Results The prevalence of individuals with a NTM-positive respiratory culture increased every year from 2010 (45 [1.3%]) to 2015 (156 [3.8%]). Allergic bronchopulmonary aspergillosis (odds ratio [OR], 2.66; P = 5.0 × 10−8), age (OR, 1.08; P = 3.4 × 10−10), and intermittent Pseudomonas aeruginosa infection (OR, 1.51; P = .004) were significantly associated with NTM infection. Conclusions NTM infection is of increasing prevalence in the UK pediatric CF population. This study highlights the urgent need for work to establish effective treatment and prevention strategies for NTM infection in young people with CF.
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Affiliation(s)
- Aaron I Gardner
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne
| | - Elliot McClenaghan
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne
| | - Gemma Saint
- Department of Child Health, University of Liverpool
- Alder Hey Children’s National Health Service Foundation Trust
| | - Paul S McNamara
- Department of Child Health, University of Liverpool
- Alder Hey Children’s National Health Service Foundation Trust
| | - Malcolm Brodlie
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne
- Department of Paediatric Respiratory Medicine, Great North Children’s Hospital, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, United Kingdom
- Correspondence: M. Brodlie, Level 3, Clinical Resource Building, Royal Victoria Infirmary, Newcastle upon Tyne NE1 4LP, UK ()
| | - Matthew F Thomas
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne
- Department of Paediatric Respiratory Medicine, Great North Children’s Hospital, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, United Kingdom
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43
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Mohindru B, Turner D, Sach T, Bilton D, Carr S, Archangelidi O, Bhadhuri A, Whitty JA. Health State Utility Data in Cystic Fibrosis: A Systematic Review. PHARMACOECONOMICS - OPEN 2020; 4:13-25. [PMID: 31054048 PMCID: PMC7018933 DOI: 10.1007/s41669-019-0144-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
INTRODUCTION Cystic fibrosis (CF) is a life-limiting, hereditable condition, with the highest prevalence in Europe. CF treatments have led to improvements in clinical symptoms, disease management and decelerated disease progression. However, little is known about the health state utility (HSU) associated with CF disease states, adverse events, and changes in disease severity. Although HSU data have contributed to existing health economic modelling studies, a lack of such data have been highlighted. This systematic review aims to provide a summary of HSU-related research in CF and highlight related research gaps. METHODS Online searches were performed in six databases and studies in any of the following categories were included: (1) estimation of HSUs in CF; (2) mapping studies between patient-reported outcome measures (PROMs) and HSUs; (3) economic evaluations on the management of CF that report primary HSU data; and (4) any CF clinical trial that reported HSU as an outcome. RESULTS A total of 17 studies were reviewed, of which 12 provided HSU values for specific CF populations. The remaining five articles provided HSU data that were broken down by CF relevant health states, including lung transplantations, pulmonary exacerbation (PEx) events and forced expiratory volume in 1 s (FEV1). CONCLUSION Current HSU data in CF are limited and there is considerable scope for further research, both in providing HSU values for CF and in investigating methods for HSU elicitation/evaluation in CF populations.
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Affiliation(s)
- Bishal Mohindru
- Norwich Medical School, Norwich Research Park, University of East Anglia, Norwich Norfolk, NR4 7TJ, UK.
| | - David Turner
- Norwich Medical School, Norwich Research Park, University of East Anglia, Norwich Norfolk, NR4 7TJ, UK
| | - Tracey Sach
- Norwich Medical School, Norwich Research Park, University of East Anglia, Norwich Norfolk, NR4 7TJ, UK
| | - Diana Bilton
- Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London, SW3 6LR, UK
| | - Siobhan Carr
- Imperial College London, Emmanuel Kaye Building, 1B Manresa Road, London, SW3 6LR, UK
| | | | - Arjun Bhadhuri
- The University of Sheffield, Regent Court, 30 Regent Street, Sheffield, S1 4DA, UK
| | - Jennifer A Whitty
- Norwich Medical School, Norwich Research Park, University of East Anglia, Norwich Norfolk, NR4 7TJ, UK
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Goutaki M, Papon JF, Boon M, Casaulta C, Eber E, Escudier E, Halbeisen FS, Harris A, Hogg C, Honore I, Jung A, Karadag B, Koerner-Rettberg C, Legendre M, Maitre B, Nielsen KG, Rubbo B, Rumman N, Schofield L, Shoemark A, Thouvenin G, Willkins H, Lucas JS, Kuehni CE. Standardised clinical data from patients with primary ciliary dyskinesia: FOLLOW-PCD. ERJ Open Res 2020; 6:00237-2019. [PMID: 32055632 PMCID: PMC7008138 DOI: 10.1183/23120541.00237-2019] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 12/12/2019] [Indexed: 12/31/2022] Open
Abstract
Clinical data on primary ciliary dyskinesia (PCD) are limited, heterogeneous and mostly derived from retrospective chart reviews, leading to missing data and unreliable symptoms and results of physical examinations. We need standardised prospective data collection to study phenotypes, severity and prognosis and improve standards of care. A large, international and multidisciplinary group of PCD experts developed FOLLOW-PCD, a standardised clinical PCD form and patient questionnaire. We identified existing forms for clinical data collection via the Better Experimental Approaches to Treat PCD (BEAT-PCD) COST Action network and a literature review. We selected and revised the content items with the working group and patient representatives. We then revised several drafts in an adapted Delphi process, refining the content and structure. FOLLOW-PCD has a modular structure, to allow flexible use based on local practice and research focus. It includes patient-completed versions for the modules on symptoms and lifestyle. The form allows a comprehensive standardised clinical assessment at baseline and for annual reviews and a short documentation for routine follow-up. It can either be completed using printable paper forms or using an online REDCap database. Data collected in FOLLOW-PCD version 1.0 is available in real-time for national and international monitoring and research. The form will be adapted in the future after extensive piloting in different settings and we encourage the translation of the patient questionnaires to multiple languages. FOLLOW-PCD will facilitate quality research based on prospective standardised data from routine care, which can be pooled between centres, to provide first-line and real-time evidence for clinical decision-making. Standardised follow-up of PCD patients enables quality research with real-time data from routine care, providing evidence for clinical decision-makinghttp://bit.ly/2PDfISF
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Affiliation(s)
- Myrofora Goutaki
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.,Paediatric Respiratory Medicine, Children's University Hospital of Bern, University of Bern, Bern, Switzerland
| | - Jean-François Papon
- AP-HP, Hôpital Kremlin-Bicetre, Service d'ORL et de Chirurgie Cervico-Faciale, Le Kremlin-Bicêtre, France.,Faculté de Médecine, Université Paris-Saclay, Le Kremlin-Bicêtre, France.,INSERM, U955, Créteil, France.,CNRS, ERL 7240, Créteil, France
| | - Mieke Boon
- Dept of Paediatrics, University Hospital Gasthuisberg, Leuven, Belgium
| | - Carmen Casaulta
- Paediatric Respiratory Medicine, Children's University Hospital of Bern, University of Bern, Bern, Switzerland
| | - Ernst Eber
- Division of Paediatric Pulmonology and Allergology, Dept of Paediatrics and Adolescent Medicine, Medical University of Graz, Graz, Austria
| | - Estelle Escudier
- Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Florian S Halbeisen
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Amanda Harris
- Primary Ciliary Dyskinesia Centre, NIHR Respiratory Biomedical Research Centre, University of Southampton, Southampton, UK
| | - Claire Hogg
- Primary Ciliary Dyskinesia Centre, Royal Brompton and Harefield Foundation Trust, London, UK
| | - Isabelle Honore
- Assistance Publique-Hôpitaux de Paris, Hôpital Cochin, Service de Pneumologie, Paris, France
| | - Andreas Jung
- Division of Respiratory Medicine, University Children's Hospital of Zurich, Zurich, Switzerland
| | - Bulent Karadag
- Dept of Pediatric Pulmonology, Marmara University, School of Medicine, Istanbul, Turkey
| | - Cordula Koerner-Rettberg
- Dept of Paediatric Pneumology, University Children's Hospital of Ruhr University Bochum, Bochum, Germany
| | - Marie Legendre
- Service de Génétique et Embryologie Médicales, Hôpital Armand-Trousseau, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Bernard Maitre
- Centre Hospitalier Intercommunal de Créteil, Service de Pneumologie et de Pathologie Professionnelle, DHU A-TVB, Université Paris Est-Créteil, Créteil, France.,INSERM U955, Institut Mondor de Recherche Biomédicale (IMRB) Equipe 04, Créteil, France
| | - Kim G Nielsen
- Danish PCD Centre Copenhagen, Paediatric Pulmonary Service, Copenhagen University Hospital, Copenhagen, Denmark
| | - Bruna Rubbo
- Primary Ciliary Dyskinesia Centre, NIHR Respiratory Biomedical Research Centre, University of Southampton, Southampton, UK
| | - Nisreen Rumman
- Al-Quds University, Faculty of Medicine, East Jerusalem, Palestine
| | - Lynne Schofield
- Leeds Teaching Hospital NHS Foundation Trust Leeds, Leeds, UK
| | - Amelia Shoemark
- Tayside Respiratory Research Group, University of Dundee, Dundee, UK
| | - Guillaume Thouvenin
- Paediatric Pulmonary Dept, Trousseau Hospital APHP, Sorbonne Universities and Pierre et Marie Curie University, Paris, France.,Sorbonne Université, INSERM, Centre de Recherche Saint-Antoine, CRSA, Paris, France
| | - Hannah Willkins
- Primary Ciliary Dyskinesia Centre, NIHR Respiratory Biomedical Research Centre, University of Southampton, Southampton, UK
| | - Jane S Lucas
- Primary Ciliary Dyskinesia Centre, NIHR Respiratory Biomedical Research Centre, University of Southampton, Southampton, UK
| | - Claudia E Kuehni
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland.,Paediatric Respiratory Medicine, Children's University Hospital of Bern, University of Bern, Bern, Switzerland
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Volkova N, Moy K, Evans J, Campbell D, Tian S, Simard C, Higgins M, Konstan MW, Sawicki GS, Elbert A, Charman SC, Marshall BC, Bilton D. Disease progression in patients with cystic fibrosis treated with ivacaftor: Data from national US and UK registries. J Cyst Fibros 2020; 19:68-79. [DOI: 10.1016/j.jcf.2019.05.015] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 04/22/2019] [Accepted: 05/20/2019] [Indexed: 11/25/2022]
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Shukla SD, Swaroop Vanka K, Chavelier A, Shastri MD, Tambuwala MM, Bakshi HA, Pabreja K, Mahmood MQ, O’Toole RF. Chronic respiratory diseases: An introduction and need for novel drug delivery approaches. TARGETING CHRONIC INFLAMMATORY LUNG DISEASES USING ADVANCED DRUG DELIVERY SYSTEMS 2020. [PMCID: PMC7499075 DOI: 10.1016/b978-0-12-820658-4.00001-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Globally, chronic respiratory diseases (CRDs), both communicable and noncommunicable, are among the leading causes of mortality, morbidity, economic and societal burden, and disability-adjusted life years (DALYs). CRDs affect multiple components of respiratory system, including the airways, parenchyma, and pulmonary vasculature. Although noncommunicable respiratory diseases, such as asthma, chronic obstructive pulmonary disease (COPD), interstitial lung disease (ILD), cystic fibrosis (CF), and lung cancer (LC), account for enormous disease burden, the currently available therapies only focus on alleviating the symptoms of diseases rather than providing optimal treatment and/or prevention. Similarly a major respiratory communicable disease, that is, tuberculosis (TB), is associated with the challenge of increasingly developing antibiotic resistance in the bacterial pathogen Mycobacterium tuberculosis. In light of these challenges, we aim to summarize the underlying molecular and cellular mechanisms that lead to hallmark pathophysiology of CRDs. Moreover, we will also highlight the limitations of current therapeutic strategies and explore novel drug delivery options that may be potentially more effective in the management of CRDs.
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Schlüter DK, Southern KW, Dryden C, Diggle P, Taylor-Robinson D. Impact of newborn screening on outcomes and social inequalities in cystic fibrosis: a UK CF registry-based study. Thorax 2019; 75:123-131. [PMID: 31771956 PMCID: PMC7029232 DOI: 10.1136/thoraxjnl-2019-213179] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 10/07/2019] [Accepted: 10/31/2019] [Indexed: 12/30/2022]
Abstract
Background Newborn bloodspot screening (NBS) for cystic fibrosis (CF) was introduced across the UK in 2007 but the impact on clinical outcomes and health inequalities for children with CF is unclear. Methods We undertook longitudinal analyses of UK CF registry data on over 3000 children with CF born between 2000 and 2015. Clinical outcomes were the trajectories of percent predicted forced expiratory volume in one second (%FEV1) from age 5, weight for age and body mass index (BMI) SD-scores from age one, and time to chronic Pseudomonas aeruginosa (cPA) infection. Using mixed effects and time-to-event models we assessed the association of NBS with outcomes and potential interactions with childhood socioeconomic conditions, while adjusting for confounders. Results NBS was associated with higher average lung function trajectory (+1.56 FEV1 percentage points 95% CI 0.1 to 3.02, n=2216), delayed onset of cPA, and higher average weight trajectory intercept at age one (+0.16 SD; 95% CI 0.07 to 0.26, n=3267) but negative rate of weight change thereafter (−0.02 SD per year; 95% CI −0.03 to −0.00). We found no significant association of NBS with BMI or rate of change of lung function. There was no clear evidence of an impact of NBS on health inequalities early in life. Conclusions Children diagnosed with CF by NBS in the UK have better lung function and increased early weight but NBS does not appear to have narrowed early health inequalities.
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Affiliation(s)
- Daniela K Schlüter
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, UK
| | - Kevin W Southern
- Department of Women's and Children's Health, University of Liverpool, Liverpool, UK
| | - Carol Dryden
- Department of Paediatrics, Wishaw General Hospital, Wishaw, UK
| | - Peter Diggle
- Centre for Health Informatics, Computing and Statistics, Lancaster Medical School, Lancaster University, Lancaster, UK
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Miah KM, Hyde SC, Gill DR. Emerging gene therapies for cystic fibrosis. Expert Rev Respir Med 2019; 13:709-725. [PMID: 31215818 DOI: 10.1080/17476348.2019.1634547] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 06/18/2019] [Indexed: 01/06/2023]
Abstract
Introduction: Cystic fibrosis (CF) remains a life-threatening genetic disease, with few clinically effective treatment options. Gene therapy and gene editing strategies offer the potential for a one-time CF cure, irrespective of the CFTR mutation class. Areas covered: We review emerging gene therapies and gene delivery strategies for the treatment of CF particularly viral and non-viral approaches with potential to treat CF. Expert opinion: It was initially anticipated that the challenge of developing a gene therapy for CF lung disease would be met relatively easily. Following early proof-of-concept clinical studies, CF gene therapy has entered a new era with innovative vector designs, approaches to subvert the humoral immune system and increase gene delivery and gene correction efficiencies. Developments include integrating adenoviral vectors, rapamycin-loaded nanoparticles, and lung-tropic lentiviral vectors. The characterization of novel cell types in the lung epithelium, including pulmonary ionocytes, may also encourage cell type-specific targeting for CF correction. We anticipate preclinical studies to further validate these strategies, which should pave the way for clinical trials. We also expect gene editing efficiencies to improve to clinically translatable levels, given advancements in viral and non-viral vectors. Overall, gene delivery technologies look more convincing in producing an effective CF gene therapy.
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Affiliation(s)
- Kamran M Miah
- a Gene Medicine Group, Nuffield Division of Clinical Laboratory Science, Radcliffe Department of Medicine, University of Oxford , Oxford , UK
| | - Stephen C Hyde
- a Gene Medicine Group, Nuffield Division of Clinical Laboratory Science, Radcliffe Department of Medicine, University of Oxford , Oxford , UK
| | - Deborah R Gill
- a Gene Medicine Group, Nuffield Division of Clinical Laboratory Science, Radcliffe Department of Medicine, University of Oxford , Oxford , UK
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The emerging burden of liver disease in cystic fibrosis patients: A UK nationwide study. PLoS One 2019; 14:e0212779. [PMID: 30947265 PMCID: PMC6448894 DOI: 10.1371/journal.pone.0212779] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 02/08/2019] [Indexed: 02/08/2023] Open
Abstract
Objective Cystic fibrosis associated liver disease (CFLD) is the third largest cause of mortality in CF. Our aim was to define the burden of CFLD in the UK using national registry data and identify risk factors for progressive disease. Methods A longitudinal population-based cohort study was conducted. Cases were defined as all patients with CFLD identified from the UK CF Registry, 2008–2013 (n = 3417). Denominator data were derived from the entire UK CF Registry. The burden of CFLD was characterised. Regression analysis was undertaken to identify risk factors for cirrhosis and progression. Results Prevalence of CFLD increased from 203.4 to 228.3 per 1000 patients during 2008–2013. Mortality in CF patients with CFLD was more than double those without; cirrhotic patients had higher all-cause mortality (HR 1.54, 95% CI 1.09 to 2.18, p = 0.015). Median recorded age of cirrhosis diagnosis was 19 (range 5–53) years. Male sex, Pseudomonas airway infection and CF related diabetes were independent risk factors for cirrhosis. Ursodeoxycholic acid use was associated with prolonged survival in patients without cirrhosis. Conclusions This study highlights an important changing disease burden of CFLD. The prevalence is slowly increasing and, importantly, the disease is not just being diagnosed in childhood. Although the role of ursodeoxycholic acid remains controversial, this study identified a positive association with survival.
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Abstract
BACKGROUND Cystic fibrosis (CF) is an inherited, chronic, progressive condition affecting around 10,000 individuals in the United Kingdom and over 70,000 worldwide. Survival in CF has improved considerably over recent decades, and it is important to provide up-to-date information on patient prognosis. METHODS The UK Cystic Fibrosis Registry is a secure centralized database, which collects annual data on almost all CF patients in the United Kingdom. Data from 43,592 annual records from 2005 to 2015 on 6181 individuals were used to develop a dynamic survival prediction model that provides personalized estimates of survival probabilities given a patient's current health status using 16 predictors. We developed the model using the landmarking approach, giving predicted survival curves up to 10 years from 18 to 50 years of age. We compared several models using cross-validation. RESULTS The final model has good discrimination (C-indexes: 0.873, 0.843, and 0.804 for 2-, 5-, and 10-year survival prediction) and low prediction error (Brier scores: 0.036, 0.076, and 0.133). It identifies individuals at low and high risk of short- and long-term mortality based on their current status. For patients 20 years of age during 2013-2015, for example, over 80% had a greater than 95% probability of 2-year survival and 40% were predicted to survive 10 years or more. CONCLUSIONS Dynamic personalized prediction models can guide treatment decisions and provide personalized information for patients. Our application illustrates the utility of the landmarking approach for making the best use of longitudinal and survival data and shows how models can be defined and compared in terms of predictive performance.
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