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Parry W, Fraser C, Crellin E, Hughes J, Vestesson E, Clarke GM. Continuity of care and consultation mode in general practice: a cross-sectional and longitudinal study using patient-level and practice-level data from before and during the COVID-19 pandemic in England. BMJ Open 2023; 13:e075152. [PMID: 37968008 PMCID: PMC10660661 DOI: 10.1136/bmjopen-2023-075152] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023] Open
Abstract
OBJECTIVES Investigate trends in continuity of care with a general practitioner (GP) before and during the COVID-19 pandemic. Identify whether continuity of care is associated with consultation mode, controlling for other patient and practice characteristics. DESIGN Retrospective cross-sectional and longitudinal observational studies. SETTING Primary care records from 389 general practices participating in Clinical Practice Research Datalink Aurum in England. PARTICIPANTS In the descriptive analysis, 100 000+ patients were included each month between April 2018 and April 2021. Modelling of the association between continuity of care and consultation mode focused on 153 475 and 125 298 patients in index months of February 2020 (before the pandemic) and February 2021 (during the pandemic) respectively, and 76 281 patients in both index months. PRIMARY AND SECONDARY OUTCOMES MEASURES The primary outcome measure was the Usual Provider of Care index. Secondary outcomes included the Bice-Boxerman index and count of consultations with the most frequently seen GP. RESULTS Continuity of care was gradually declining before the pandemic but stabilised during it. There were consistent demographic, socioeconomic and regional differences in continuity of care. An average of 23% of consultations were delivered remotely in the year to February 2020 compared with 76% in February 2021. We found little evidence consultation mode was associated with continuity at the patient level, controlling for a range of covariates. In contrast, patient characteristics and practice-level supply and demand were associated with continuity. CONCLUSIONS We set out to examine the association of consultation mode with continuity of care but found that GP supply and patient demand were much more important. To improve continuity for patients, primary care capacity needs to increase. This requires sufficient, long-term investment in clinicians, staff, facilities and digital infrastructure. General practice also needs to transform ways of working to ensure continuity for those that need it, even in a capacity-constrained environment.
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Affiliation(s)
| | | | | | - Jay Hughes
- Data Analytics, The Health Foundation, London EC4Y 8AP, UK
| | - Emma Vestesson
- Data Analytics, The Health Foundation, London EC4Y 8AP, UK
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Vestesson E, De Corte K, Chappell P, Crellin E, Clarke GM. Antibiotic prescribing in remote versus face-to-face consultations for acute respiratory infections in primary care in England: an observational study using target maximum likelihood estimation. EClinicalMedicine 2023; 64:102245. [PMID: 37842171 PMCID: PMC10568332 DOI: 10.1016/j.eclinm.2023.102245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Revised: 08/28/2023] [Accepted: 09/13/2023] [Indexed: 10/17/2023] Open
Abstract
Background The COVID-19 pandemic has led to an ongoing increase in the use of remote consultations in general practice in England. Although the evidence is limited, there are concerns that the increase in remote consultations could lead to more antibiotic prescribing. Methods In this cohort study, we used patient-level primary care data from the Clinical Practice Research Datalink to estimate the association between consultation mode (remote versus face-to-face) and antibiotic prescribing in England for acute respiratory infections (ARI) between April 2021 and March 2022. Eligibility criteria were applied at both practice-level and patient-level. 400 practices in England were sampled at random and then 600,000 patients were randomly sampled from the eligible patients (whose sex was recorded). Consultations for acute respiratory infections were identified. All antibiotic prescriptions were included, with the exception of antituberculosis drugs and antileprotic drugs, as identified through chapter 5.1 of the British National Formulary. The CPRD Aurum data was linked to the COVID-19 ONS infection survey by region. All analyses were done at the individual level. Repeated consultations from the same patient within 7 days were grouped together. We used targeted maximum likelihood estimation, a causal machine learning method with adjustment for infection type and patient-level, clinician-level and practice-level factors. Findings There were 45,997 ARI consultations (34,555 unique patients) within the study period, of which 28,127 were remote and 17,870 were face-to-face. For children, 48% of consultations were remote and, for adults, 66% were remote. For children, 42% of remote and 43% of face-to-face consultations led to an antibiotic prescription; the equivalent values for adults were 52% and 42%, respectively. After adjustment with TMLE, adults with a remote consultation had 23% (odds ratio [OR] 1.23, 95% CI: 1.18-1.29) higher chance of being prescribed antibiotics than if they had been seen face-to-face. We found no significant association between consultation mode and antibiotic prescribing in children (OR 1.04 95% CI: 0.98-1.11). Interpretation The higher rates of antibiotic prescribing in remote consultations for adults are cause for concern. We see no significant difference in antibiotic prescribing between consultation mode for children. These findings should inform antimicrobial stewardship activities for health-care professionals and policy makers. Future research should examine differences in guideline-compliance between remote and face-to-face consultations to understand the factors driving antibiotic prescribing in different consultation modes. Funding None.
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Affiliation(s)
- Emma Vestesson
- The Health Foundation, London, UK
- University College London Great Ormond Street Institute of Child Health, London, UK
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Chappell P, Dias A, Bakhai M, Ledger J, Clarke GM. How is primary care access changing? A retrospective, repeated cross-sectional study of patient-initiated demand at general practices in England using a modern access model, 2019-2022. BMJ Open 2023; 13:e072944. [PMID: 37591638 PMCID: PMC10441067 DOI: 10.1136/bmjopen-2023-072944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 07/26/2023] [Indexed: 08/19/2023] Open
Abstract
OBJECTIVES To explore trends in patient-initiated requests for general practice services and the association between patient characteristics including demographics, preferences for care and clinical needs and modes of patient contact (online vs telephone), and care delivery (face-to-face vs remote) at practices using a modern access model. DESIGN Retrospective repeated cross-sectional study spanning March 2019 to February 2022. SETTING General practices in England using the askmyGP online consultation system to implement a modern general practice access model using digital and non-digital (multimodal) access pathways and digitally supported triage to manage patient-initiated requests. PARTICIPANTS 10 435 465 patient-initiated requests from 1 488 865 patients at 154 practices. RESULTS Most requests were initiated online (72.1% in 2021/2022) rather than by telephone. Online users were likely to be female, younger than 45 years, asking about existing medical problems, had used the system before and frequent attenders (familiar patients). During the pandemic, request rates for face-to-face consultations fell while those for telephone consultations and online messages increased, with telephone consultations being most popular (53.8% in 2021/2022). Video was seldom requested. More than 60% of requests were consistently delivered in the mode requested. Face-to-face consultations were more likely to be used for the youngest and oldest patients, new medical problems, non-frequent attenders (unfamiliar patients) and those who requested a face-to-face consultation. Over the course of the study, request rates for patients aged over 44 years increased, for example, by 15.4% (p<0.01) for patients aged over 74 years. Rates for younger patients decreased by 32.6% (p<0.001) in 2020/2021, compared with 2019/2020, before recovering to prepandemic levels in 2021/2022. CONCLUSIONS Demand patterns shed light on the characteristics of patients making requests for general practice services and the composition of the care backlog with implications for policy and practice. A modern general practice access model can be used effectively to manage patient-initiated demand.
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Affiliation(s)
- Paul Chappell
- NHS England, London, UK
- Improvement Analytics Unit, The Health Foundation, London, UK
| | - Alison Dias
- NHS England, London, UK
- Improvement Analytics Unit, The Health Foundation, London, UK
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Berman DM, Lee AY, Lesurf R, Patel PG, Ebrahimizadeh W, Bayani J, Lee LA, Boufaied N, Selvarajah S, Jamaspishvili T, Guérard KP, Dion D, Kawashima A, Clarke GM, How N, Jackson CL, Scarlata E, Siddiqui K, Okello JBA, Aprikian AG, Moussa M, Finelli A, Chin J, Brimo F, Bauman G, Loblaw A, Venkateswaran V, Buttyan R, Chevalier S, Thomson A, Park PC, Siemens DR, Lapointe J, Boutros PC, Bartlett JMS. Multimodal Biomarkers That Predict the Presence of Gleason Pattern 4: Potential Impact for Active Surveillance. J Urol 2023; 210:257-271. [PMID: 37126232 DOI: 10.1097/ju.0000000000003507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 04/20/2023] [Indexed: 05/02/2023]
Abstract
PURPOSE Latent grade group ≥2 prostate cancer can impact the performance of active surveillance protocols. To date, molecular biomarkers for active surveillance have relied solely on RNA or protein. We trained and independently validated multimodal (mRNA abundance, DNA methylation, and/or DNA copy number) biomarkers that more accurately separate grade group 1 from grade group ≥2 cancers. MATERIALS AND METHODS Low- and intermediate-risk prostate cancer patients were assigned to training (n=333) and validation (n=202) cohorts. We profiled the abundance of 342 mRNAs, 100 DNA copy number alteration loci, and 14 hypermethylation sites at 2 locations per tumor. Using the training cohort with cross-validation, we evaluated methods for training classifiers of pathological grade group ≥2 in centrally reviewed radical prostatectomies. We trained 2 distinct classifiers, PRONTO-e and PRONTO-m, and validated them in an independent radical prostatectomy cohort. RESULTS PRONTO-e comprises 353 mRNA and copy number alteration features. PRONTO-m includes 94 clinical, mRNAs, copy number alterations, and methylation features at 14 and 12 loci, respectively. In independent validation, PRONTO-e and PRONTO-m predicted grade group ≥2 with respective true-positive rates of 0.81 and 0.76, and false-positive rates of 0.43 and 0.26. Both classifiers were resistant to sampling error and identified more upgrading cases than a well-validated presurgical risk calculator, CAPRA (Cancer of the Prostate Risk Assessment; P < .001). CONCLUSIONS Two grade group classifiers with superior accuracy were developed by incorporating RNA and DNA features and validated in an independent cohort. Upon further validation in biopsy samples, classifiers with these performance characteristics could refine selection of men for active surveillance, extending their treatment-free survival and intervals between surveillance.
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Affiliation(s)
- D M Berman
- Queen's University Cancer Research Institute, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - A Y Lee
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - R Lesurf
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Now with Hospital for Sick Children, Toronto, Ontario, Canada
| | - P G Patel
- Queen's University Cancer Research Institute, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Now with Hospital for Sick Children, Toronto, Ontario, Canada
| | - W Ebrahimizadeh
- Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Now with IMV Inc, Dartmouth, Nova Scotia, Canada
| | - J Bayani
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario, Canada
| | - L A Lee
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - N Boufaied
- Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - S Selvarajah
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Now with University Health Network, Toronto, Ontario, Canada
| | - T Jamaspishvili
- Queen's University Cancer Research Institute, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - K-P Guérard
- Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - D Dion
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - A Kawashima
- Queen's University Cancer Research Institute, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Now with Osaka University, Osaka, Japan
| | - G M Clarke
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - N How
- Queen's University Cancer Research Institute, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Hamilton Health Sciences, Hamilton, Ontario, Canada
| | - C L Jackson
- Queen's University Cancer Research Institute, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - E Scarlata
- Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - K Siddiqui
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- Now with Sultan Qaboos University Hospital, Seeb, Oman
| | - J B A Okello
- Queen's University Cancer Research Institute, Kingston, Ontario, Canada
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
| | - A G Aprikian
- Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - M Moussa
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - A Finelli
- Princess Margaret Cancer Centre. Toronto, Ontario, Canada
- Departments of Surgery and Oncology, University of Toronto, Toronto, Ontario, Canada
| | - J Chin
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - F Brimo
- Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Department of Pathology, McGill University, Montreal, Quebec, Canada
| | - G Bauman
- Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
- London Regional Cancer Program, London Health Sciences Centre, London, Ontario, Canada
| | - A Loblaw
- Department of Radiation Oncology, Sunnybrook Health Sciences Centre, Toronto, Ontario, Canada
- Departments of Radiation Oncology and Health Policy Management and Evaluation, University of Toronto, Toronto
| | - V Venkateswaran
- Departments of Surgery and Oncology, University of Toronto, Toronto, Ontario, Canada
- Institute of Medical Science, University of Toronto, Toronto, Ontario, Canada
| | - R Buttyan
- Vancouver Prostate Centre, Vancouver, British Columbia, Canada
- Departments of Experimental Medicine and Interdisciplinary Oncology, Vancouver, British Columbia, Canada
| | - S Chevalier
- Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - A Thomson
- Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
- Now with College of Science and Engineering Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - P C Park
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, Ontario, Canada
- Now with Department of Pathology, Shared Health, Winnipeg, Manitoba, Canada
| | - D R Siemens
- Queen's University Cancer Research Institute, Kingston, Ontario, Canada
- Departments of Urology, Oncology and Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada
| | - J Lapointe
- Department of Surgery, McGill University and the Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - P C Boutros
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Ontario, Canada
- Now with University of California, Los Angeles, Los Angeles, California, United States
| | - J M S Bartlett
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathology, University of Toronto, Toronto, Ontario, Canada
- Edinburgh Cancer Research Centre, University of Edinburgh, Edinburgh, United Kingdom
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Vestesson EM, De Corte KLA, Crellin E, Ledger J, Bakhai M, Clarke GM. Consultation Rate and Mode by Deprivation in English General Practice From 2018 to 2022: Population-Based Study. JMIR Public Health Surveill 2023; 9:e44944. [PMID: 37129943 DOI: 10.2196/44944] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/03/2023] [Accepted: 03/14/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND The COVID-19 pandemic has had a significant impact on primary care service delivery with an increased use of remote consultations. With general practice delivering record numbers of appointments and rising concerns around access, funding, and staffing in the UK National Health Service, we assessed contemporary trends in consultation rate and modes (ie, face-to-face versus remote). OBJECTIVE This paper describes trends in consultation rates in general practice in England for key demographics before and during the COVID-19 pandemic. We explore the use of remote and face-to-face consultations with regard to socioeconomic deprivation to understand the possible effect of changes in consultation modes on health inequalities. METHODS We did a retrospective analysis of 9,429,919 consultations by general practitioners, nurses, or other health care professionals between March 2018 and February 2022 for patients registered at 397 general practices in England. We used routine electronic health records from Clinical Practice Research Datalink Aurum with linkage to national data sets. Negative binomial models were used to predict consultation rates and modes (ie, remote versus face-to-face) by age, sex, and socioeconomic deprivation over time. RESULTS Overall consultation rates increased by 15% from 4.92 in 2018-2019 to 5.66 in 2021-2022 with some fluctuation during the start of the COVID-19 pandemic. The breakdown into face-to-face and remote consultations shows that the pandemic precipitated a rapid increase in remote consultations across all groups, but the extent varies by age. Consultation rates increased with increasing levels of deprivation. Socioeconomic differences in consultation rates, adjusted for sex and age, halved during the pandemic (from 0.36 to 0.18, indicating more consultations in the most deprived), effectively narrowing relative differences between deprivation quintiles. This trend remains when stratified by sex, but the difference across deprivation quintiles is smaller for men. The most deprived saw a relatively larger increase in remote and decrease in face-to-face consultation rates compared to the least deprived. CONCLUSIONS The substantial increases in consultation rates observed in this study imply an increased pressure on general practice. The narrowing of consultation rates between deprivation quintiles is cause for concern, given ample evidence that health needs are greater in more deprived areas.
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Affiliation(s)
- Emma Maria Vestesson
- The Health Foundation, London, United Kingdom
- Great Ormond Street Institute of Child Health, University College London, London, United Kingdom
| | | | | | - Jean Ledger
- National Health Service England, London, United Kingdom
| | - Minal Bakhai
- National Health Service England, London, United Kingdom
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Clarke GM, Steventon A, O'Neill S. A comparison of synthetic control approaches for the evaluation of policy interventions using observational data: Evaluating the impact of redesigning urgent and emergency care in Northumberland. Health Serv Res 2023; 58:445-457. [PMID: 36573610 PMCID: PMC10012235 DOI: 10.1111/1475-6773.14126] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
OBJECTIVE To compare the original synthetic control (OSC) method with alternative approaches (Generalized [GSC], Micro [MSC], and Bayesian [BSC] synthetic control methods) and re-evaluate the impact of a significant restructuring of urgent and emergency care in Northeast England, which included the opening of the UK's first purpose-built specialist emergency care hospital. DATA SOURCES Simulations and data from Secondary Uses Service data, a single comprehensive repository for patient-level health care data in England. STUDY DESIGN Hospital use of individuals exposed and unexposed to the restructuring is compared. We estimate the impact using OSC, MSC, BSC, and GSC applied at the general practice level. We contrast the estimation methods' performance in a Monte Carlo simulation study. DATA COLLECTION/EXTRACTION METHODS Hospital activity data from Secondary Uses Service for patients aged over 18 years registered at a general practice in England from April 2011 to March 2019. PRINCIPAL FINDINGS None of the methods dominated all simulation scenarios. GSC was generally preferred. In contrast to an earlier evaluation that used OSC, GSC reported a smaller impact of the opening of the hospital on Accident and Emergency (A&E) department (also known as emergency department or casualty) visits and no evidence for any impact on the proportion of A&E patients seen within 4 h. CONCLUSIONS The simulation study highlights cases where the considered methods may lead to biased estimates in health policy evaluations. GSC was found to be the most reliable method of those considered. Considering more disaggregated data over a longer time span and applying GSC indicates that the specialist emergency care hospitals in Northumbria had less impact on A&E visits and waiting times than suggested by the original evaluation which applied OSC to more aggregated data.
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Affiliation(s)
| | | | - Stephen O'Neill
- Department of Health Services Research & Policy, London School of Hygiene and Tropical Medicine, London, UK
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Tridente A, Holloway PAH, Hutton P, Gordon AC, Mills GH, Clarke GM, Chiche JD, Stuber F, Garrard C, Hinds C, Bion J. Methodological challenges in European ethics approvals for a genetic epidemiology study in critically ill patients: the GenOSept experience. BMC Med Ethics 2019; 20:30. [PMID: 31064358 PMCID: PMC6503539 DOI: 10.1186/s12910-019-0370-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 04/22/2019] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND During the set-up phase of an international study of genetic influences on outcomes from sepsis, we aimed to characterise potential differences in ethics approval processes and outcomes in participating European countries. METHODS Between 2005 and 2007 of the FP6-funded international Genetics Of Sepsis and Septic Shock (GenOSept) project, we asked national coordinators to complete a structured survey of research ethic committee (REC) approval structures and processes in their countries, and linked these data to outcomes. Survey findings were reconfirmed or modified in 2017. RESULTS Eighteen countries participated in the study, recruiting 2257 patients from 160 ICUs. National practices differed widely in terms of composition of RECs, procedures and duration of the ethics approval process. Eight (44.4%) countries used a single centralised process for approval, seven (38.9%) required approval by an ethics committee in each participating hospital, and three (16.7%) required both. Outcomes of the application process differed widely between countries because of differences in national legislation, and differed within countries because of interpretation of the ethics of conducting research in patients lacking capacity. The RECs in four countries had no lay representation. The median time from submission to final decision was 1.5 (interquartile range 1-7) months; in nine (50%) approval was received within 1 month; six took over 6 months, and in one 24 months; had all countries been able to match the most efficient approvals processes, an additional 74 months of country or institution-level recruitment would have been available. In three countries, rejection of the application by some local RECs resulted in loss of centres; and one country rejected the application outright. CONCLUSIONS The potential benefits of the single application portal offered by the European Clinical Trials Regulation will not be realised without harmonisation of research ethics committee practices as well as national legislation.
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Affiliation(s)
- Ascanio Tridente
- Whiston Hospital, Prescot, Merseyside and Department of Molecular and Clinical Pharmacology, University of Liverpool, Liverpool, UK
| | | | - Paula Hutton
- Intensive Care Unit, John Radcliffe Hospital, Oxford, UK
| | | | | | | | | | - Frank Stuber
- Department of Anaesthesiology and Pain Medicine, Bern University Hospital and University of Bern, Bern, Switzerland
| | | | - Charles Hinds
- Barts and the London Queen Mary School of Medicine, London, UK
| | - Julian Bion
- Institute of Clinical Sciences, University of Birmingham, Birmingham, UK
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Clarke GM, Holloway CMB, Zubovits JT, Nofech-Mozes S, Murray M, Liu K, Wang D, Kiss A, Yaffe MJ. Three-dimensional tumor visualization of invasive breast carcinomas using whole-mount serial section histopathology: implications for tumor size assessment. Breast Cancer Res Treat 2019; 174:669-677. [PMID: 30612274 DOI: 10.1007/s10549-018-05122-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 12/26/2018] [Indexed: 12/30/2022]
Abstract
PURPOSE Linear tumor size (T-size) estimated with conventional histology informs breast cancer management. Previously we demonstrated significant differences in margin and focality estimates using conventional histology versus digital whole-mount serial sections (WMSS). Using WMSS we can measure T-size or volume. Here, we compare WMSS T-size with volume, and with T-size measured conventionally. We also compare the ellipsoid model for calculating tumor volume to direct, WMSS measurement. METHODS Two pathologists contoured regions of invasive carcinoma and measured T-size from both WMSS and (simulated) conventional sections in 55 consecutive lumpectomy specimens. Volume was measured directly from the contours. Measurements were compared using the paired t-test or Spearman's rank-order correlation. A five-point 'border index' was devised and assigned to each case to parametrize tumor shape considering 'compactness' or cellularity. Tumor volumes calculated assuming ellipsoid geometry were compared with direct, WMSS measurements. RESULTS WMSS reported significantly larger T-size than conventional histology in the majority of cases [61.8%, 34/55; means = (2.34 cm; 1.99 cm), p < 0.001], with a 16.4% (9/55) rate of 'upstaging'. The majority of discordances were due to undersampling. T-size and volume were strongly correlated (r = 0.838, p < 0.001). Significantly lower volume was obtained with WMSS versus ellipsoid modeling [means = (1.18 cm3; 1.45 cm3), p < 0.001]. CONCLUSIONS Significantly larger T-size is measured with WMSS than conventionally, due primarily to undersampling in the latter. Volume and linear size are highly correlated. Diffuse tumors interspersed with normal or non-invasive elements may be sampled less extensively than more localized masses. The ellipsoid model overestimates tumor volume.
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Affiliation(s)
- G M Clarke
- Physical Sciences Platform, Sunnybrook Research Institute, Room C7-27c 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - C M B Holloway
- Department of Surgery, Faculty of Medicine, University of Toronto, Toronto, Canada
- Department of Surgery, Sunnybrook Health Sciences Centre, Room T2-015 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - J T Zubovits
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
- Department of Pathology, Scarborough and Rouge Hospital, 3030 Birchmount Road, Toronto, ON, M1W 3W3, Canada
| | - S Nofech-Mozes
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
- Sunnybrook Health Sciences Centre, Room E423a 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - M Murray
- Physical Sciences Platform, Sunnybrook Research Institute, Room C7-48a 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - K Liu
- Physical Sciences Platform, Sunnybrook Research Institute, Room C7-27a 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - D Wang
- Physical Sciences Platform, Sunnybrook Research Institute, Room C7-27a 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - A Kiss
- Research Design and Biostatistics, Sunnybrook Research Institute, Toronto, ON, Canada
- Institute of Health Policy, Management and Evaluation, University of Toronto, Room G106 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada
| | - M J Yaffe
- Departments of Medical Biophysics and Medical Imaging, Faculty of Medicine, University of Toronto, Toronto, Canada.
- Physical Sciences Platform, Sunnybrook Research Institute, Room S6-57 2075 Bayview Avenue, Toronto, ON, M4N 3M5, Canada.
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Leffler EM, Band G, Busby GBJ, Kivinen K, Le QS, Clarke GM, Bojang KA, Conway DJ, Jallow M, Sisay-Joof F, Bougouma EC, Mangano VD, Modiano D, Sirima SB, Achidi E, Apinjoh TO, Marsh K, Ndila CM, Peshu N, Williams TN, Drakeley C, Manjurano A, Reyburn H, Riley E, Kachala D, Molyneux M, Nyirongo V, Taylor T, Thornton N, Tilley L, Grimsley S, Drury E, Stalker J, Cornelius V, Hubbart C, Jeffreys AE, Rowlands K, Rockett KA, Spencer CCA, Kwiatkowski DP. Resistance to malaria through structural variation of red blood cell invasion receptors. Science 2017; 356:science.aam6393. [PMID: 28522690 DOI: 10.1126/science.aam6393] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 05/08/2017] [Indexed: 12/29/2022]
Abstract
The malaria parasite Plasmodium falciparum invades human red blood cells by a series of interactions between host and parasite surface proteins. By analyzing genome sequence data from human populations, including 1269 individuals from sub-Saharan Africa, we identify a diverse array of large copy-number variants affecting the host invasion receptor genes GYPA and GYPB We find that a nearby association with severe malaria is explained by a complex structural rearrangement involving the loss of GYPB and gain of two GYPB-A hybrid genes, which encode a serologically distinct blood group antigen known as Dantu. This variant reduces the risk of severe malaria by 40% and has recently increased in frequency in parts of Kenya, yet it appears to be absent from west Africa. These findings link structural variation of red blood cell invasion receptors with natural resistance to severe malaria.
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Affiliation(s)
- Ellen M Leffler
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - George B J Busby
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Katja Kivinen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Quang Si Le
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kalifa A Bojang
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia
| | - David J Conway
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia.,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Muminatou Jallow
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia.,Royal Victoria Teaching Hospital, Independence Drive, Post Office Box 1515, Banjul, The Gambia
| | - Fatoumatta Sisay-Joof
- Medical Research Council Unit, Atlantic Boulevard, Fajara, Post Office Box 273, The Gambia
| | - Edith C Bougouma
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso
| | | | - David Modiano
- University of Rome La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - Sodiomon B Sirima
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), 01 BP 2208 Ouagadougou 01, Burkina Faso
| | - Eric Achidi
- Department of Medical Laboratory Sciences, University of Buea, Post Office Box 63, Buea, South West Region, Cameroon
| | - Tobias O Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Post Office Box 63, Buea, South West Region, Cameroon
| | - Kevin Marsh
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya.,Nuffield Department of Medicine, NDM Research Building, Roosevelt Drive, Headington, Oxford OX3 7FZ, UK
| | - Carolyne M Ndila
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya
| | - Norbert Peshu
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya
| | - Thomas N Williams
- Kenyan Medical Research Institute (KEMRI)-Wellcome Trust Research Programme, Post Office Box 230-80108, Kilifi, Kenya.,Faculty of Medicine, Department of Medicine, Imperial College, Exhibition Road, London SW7 2AZ, UK
| | - Chris Drakeley
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Post Office Box 2228, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Post Office Box 2228, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK.,National Institute for Medical Research, Mwanza Research Centre, Mwanza City, Tanzania
| | - Hugh Reyburn
- Joint Malaria Programme, Kilimanjaro Christian Medical Centre, Post Office Box 2228, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - Eleanor Riley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
| | - David Kachala
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi
| | - Malcolm Molyneux
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi.,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Vysaul Nyirongo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi
| | - Terrie Taylor
- Blantyre Malaria Project, Queen Elizabeth Central Hospital, College of Medicine, Post Office Box 30096, Chichiri, Blantyre 3, Malawi.,College of Osteopathic Medicine, Michigan State University, East Lansing, MI 48824, USA
| | - Nicole Thornton
- International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, 500 North Bristol Park, Filton, Bristol BS34 7QH, UK
| | - Louise Tilley
- International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, 500 North Bristol Park, Filton, Bristol BS34 7QH, UK
| | - Shane Grimsley
- International Blood Group Reference Laboratory, National Health Service (NHS) Blood and Transplant, 500 North Bristol Park, Filton, Bristol BS34 7QH, UK
| | - Eleanor Drury
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Jim Stalker
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Victoria Cornelius
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Christina Hubbart
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Anna E Jeffreys
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kate Rowlands
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Chris C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK. .,Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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11
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Mägi R, Suleimanov YV, Clarke GM, Kaakinen M, Fischer K, Prokopenko I, Morris AP. SCOPA and META-SCOPA: software for the analysis and aggregation of genome-wide association studies of multiple correlated phenotypes. BMC Bioinformatics 2017; 18:25. [PMID: 28077070 PMCID: PMC5225593 DOI: 10.1186/s12859-016-1437-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2016] [Accepted: 12/17/2016] [Indexed: 11/10/2022] Open
Abstract
Background Genome-wide association studies (GWAS) of single nucleotide polymorphisms (SNPs) have been successful in identifying loci contributing genetic effects to a wide range of complex human diseases and quantitative traits. The traditional approach to GWAS analysis is to consider each phenotype separately, despite the fact that many diseases and quantitative traits are correlated with each other, and often measured in the same sample of individuals. Multivariate analyses of correlated phenotypes have been demonstrated, by simulation, to increase power to detect association with SNPs, and thus may enable improved detection of novel loci contributing to diseases and quantitative traits. Results We have developed the SCOPA software to enable GWAS analysis of multiple correlated phenotypes. The software implements “reverse regression” methodology, which treats the genotype of an individual at a SNP as the outcome and the phenotypes as predictors in a general linear model. SCOPA can be applied to quantitative traits and categorical phenotypes, and can accommodate imputed genotypes under a dosage model. The accompanying META-SCOPA software enables meta-analysis of association summary statistics from SCOPA across GWAS. Application of SCOPA to two GWAS of high-and low-density lipoprotein cholesterol, triglycerides and body mass index, and subsequent meta-analysis with META-SCOPA, highlighted stronger association signals than univariate phenotype analysis at established lipid and obesity loci. The META-SCOPA meta-analysis also revealed a novel signal of association at genome-wide significance for triglycerides mapping to GPC5 (lead SNP rs71427535, p = 1.1x10−8), which has not been reported in previous large-scale GWAS of lipid traits. Conclusions The SCOPA and META-SCOPA software enable discovery and dissection of multiple phenotype association signals through implementation of a powerful reverse regression approach.
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Affiliation(s)
- Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Yury V Suleimanov
- Computation-based Science and Technology Research Center, Cyprus Institute, Nicosia, Cyprus.,Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | | | - Krista Fischer
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - Andrew P Morris
- Estonian Genome Center, University of Tartu, Tartu, Estonia. .,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. .,Department of Biostatistics, University of Liverpool, Liverpool, UK.
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12
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Clarke GM, Rockett K, Kivinen K, Hubbart C, Jeffreys AE, Rowlands K, Jallow M, Conway DJ, Bojang KA, Pinder M, Usen S, Sisay-Joof F, Sirugo G, Toure O, Thera MA, Konate S, Sissoko S, Niangaly A, Poudiougou B, Mangano VD, Bougouma EC, Sirima SB, Modiano D, Amenga-Etego LN, Ghansah A, Koram KA, Wilson MD, Enimil A, Evans J, Amodu OK, Olaniyan S, Apinjoh T, Mugri R, Ndi A, Ndila CM, Uyoga S, Macharia A, Peshu N, Williams TN, Manjurano A, Sepúlveda N, Clark TG, Riley E, Drakeley C, Reyburn H, Nyirongo V, Kachala D, Molyneux M, Dunstan SJ, Phu NH, Quyen NN, Thai CQ, Hien TT, Manning L, Laman M, Siba P, Karunajeewa H, Allen S, Allen A, Davis TME, Michon P, Mueller I, Molloy SF, Campino S, Kerasidou A, Cornelius VJ, Hart L, Shah SS, Band G, Spencer CCA, Agbenyega T, Achidi E, Doumbo OK, Farrar J, Marsh K, Taylor T, Kwiatkowski DP. Characterisation of the opposing effects of G6PD deficiency on cerebral malaria and severe malarial anaemia. eLife 2017; 6:e15085. [PMID: 28067620 PMCID: PMC5222559 DOI: 10.7554/elife.15085] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Accepted: 11/03/2016] [Indexed: 01/27/2023] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) deficiency is believed to confer protection against Plasmodium falciparum malaria, but the precise nature of the protective effecthas proved difficult to define as G6PD deficiency has multiple allelic variants with different effects in males and females, and it has heterogeneous effects on the clinical outcome of P. falciparum infection. Here we report an analysis of multiple allelic forms of G6PD deficiency in a large multi-centre case-control study of severe malaria, using the WHO classification of G6PD mutations to estimate each individual's level of enzyme activity from their genotype. Aggregated across all genotypes, we find that increasing levels of G6PD deficiency are associated with decreasing risk of cerebral malaria, but with increased risk of severe malarial anaemia. Models of balancing selection based on these findings indicate that an evolutionary trade-off between different clinical outcomes of P. falciparum infection could have been a major cause of the high levels of G6PD polymorphism seen in human populations.
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Affiliation(s)
- Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom,MRC Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom, (GMC)
| | - Kirk Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom,MRC Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom,The Wellcome Trust Sanger Institute, Cambridge, United Kingdom, (KRoc)
| | - Katja Kivinen
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Christina Hubbart
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Anna E Jeffreys
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Kate Rowlands
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Muminatou Jallow
- Medical Research Council Unit The Gambia, Fajara, Gambia,Edward Francis Small Teaching Hospital, Independence Drive, Banjul, Gambia
| | - David J Conway
- Medical Research Council Unit The Gambia, Fajara, Gambia,Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | | | | | - Stanley Usen
- Medical Research Council Unit The Gambia, Fajara, Gambia
| | | | - Giorgio Sirugo
- Medical Research Council Unit The Gambia, Fajara, Gambia
| | - Ousmane Toure
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Mahamadou A Thera
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Salimata Konate
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Sibiry Sissoko
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Amadou Niangaly
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Belco Poudiougou
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | | | - Edith C Bougouma
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso
| | - Sodiomon B Sirima
- Centre National de Recherche et de Formation sur le Paludisme (CNRFP), Ouagadougou, Burkina Faso
| | | | | | - Anita Ghansah
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Kwadwo A Koram
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Michael D Wilson
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | | - Jennifer Evans
- Department of Molecular Medicine, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany,Kumasi Centre for Collaborative Research, Kumasi, Ghana
| | | | | | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | - Regina Mugri
- Department of Medical Laboratory Sciences, University of Buea, Buea, Cameroon
| | - Andre Ndi
- Department of Medical Laboratory Sciences, University of Buea, Buea, Cameroon
| | | | - Sophie Uyoga
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Norbert Peshu
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya,Department of Medicine, Faculty of Medicine, Imperial College, London, United Kingdom
| | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Nuno Sepúlveda
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Taane G Clark
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Eleanor Riley
- Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Chris Drakeley
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Hugh Reyburn
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Vysaul Nyirongo
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, University of Malawi, Blantyre, Malawi
| | - David Kachala
- Oxford University Clinical Research Unit, University of Oxford, Ho Chi Minh City, Vietnam
| | - Malcolm Molyneux
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, University of Malawi, Blantyre, Malawi,Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, United Kingdom
| | - Sarah J Dunstan
- The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Australia
| | - Nguyen Hoan Phu
- Oxford University Clinical Research Unit, University of Oxford, Ho Chi Minh City, Vietnam,Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | - Nguyen Ngoc Quyen
- Oxford University Clinical Research Unit, University of Oxford, Ho Chi Minh City, Vietnam
| | - Cao Quang Thai
- Oxford University Clinical Research Unit, University of Oxford, Ho Chi Minh City, Vietnam,Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam
| | - Tran Tinh Hien
- Oxford University Clinical Research Unit, University of Oxford, Ho Chi Minh City, Vietnam,Hospital for Tropical Diseases, Ho Chi Minh City, Viet Nam,Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Laurens Manning
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Moses Laman
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Peter Siba
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | | | | | - Angela Allen
- Weatherall Institute of Molecular Medicine, Oxford University, Oxford, United Kingdom
| | | | - Pascal Michon
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea,Faculty of Medicine and Health Sciences, Divine Word University, Madang, Papua New Guinea
| | - Ivo Mueller
- Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea,Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia,Barcelona Centre for International Health Research, Barcelona, Spain
| | - Síle F Molloy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Susana Campino
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Angeliki Kerasidou
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom,Nuffield Department of Population Health, The Ethox Centre, University of Oxford, Oxford, United Kingdom
| | - Victoria J Cornelius
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom,MRC Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
| | - Lee Hart
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Shivang S Shah
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom,Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, United States
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom,MRC Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom
| | - Chris CA Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Tsiri Agbenyega
- Komfo Anoyke Teaching Hospital, Kumasi, Ghana,Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Eric Achidi
- Department of Medical Laboratory Sciences, University of Buea, Buea, Cameroon
| | - Ogobara K Doumbo
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, University of Oxford, Ho Chi Minh City, Vietnam,Nuffield Department of Clinical Medicine, Center for Tropical Medicine, Oxford University, Oxford, United Kingdom
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Terrie Taylor
- Blantyre Malaria Project at the College of Medicine, University of Malawi, Blantyre, Malawi
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom,MRC Centre for Genomics and Global Health, University of Oxford, Oxford, United Kingdom,The Wellcome Trust Sanger Institute, Cambridge, United Kingdom, (DPK)
| | - MalariaGEN Consortium
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom,The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
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13
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Hong NJL, Clarke GM, Yaffe MJ, Holloway CMB. Cost-effectiveness analysis of whole-mount pathology processing for patients with early breast cancer undergoing breast conservation. ACTA ACUST UNITED AC 2016; 23:S23-31. [PMID: 26985143 DOI: 10.3747/co.23.2917] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Obtaining accurate histopathologic detail for breast lumpectomy specimens is challenging because of sampling and loss of three-dimensional conformational features with conventional processing. The whole-mount (wm) technique is a novel method of serial pathologic sectioning designed to optimize cross-sectional visualization of resected specimens and determination of margin status. METHODS Using a Markov chain cohort simulation cost-effectiveness model, we compared conventional processing with wm technique for breast lumpectomies. Cost-effectiveness was evaluated from the perspective of the Canadian health care system and compared using incremental cost-effectiveness ratios (icers) for cost per quality-adjusted life-year (qaly) over a 10-year time horizon. Deterministic and probabilistic sensitivity analyses were performed to test the robustness of the model with willingness-to-pay (wtp) thresholds of $0-$100,000. Costs are reported in adjusted 2014 Canadian dollars, discounted at a rate of 3%. RESULTS Compared with conventional processing, wm processing is more costly ($19,989 vs. $18,427) but generates 0.03 more qalys over 10 years. The icer is $45,414, indicating that this additional amount is required for each additional qaly obtained. The model was robust to all variance in parameters, with the prevalence of positive margins accounting for most of the model's variability. CONCLUSIONS After a wtp threshold of $45,414, wm processing becomes cost-effective and ultimately generates fewer recurrences and marginally more qalys over time. Excellent baseline outcomes for the current treatment of breast cancer mean that incremental differences in survival are small. However, the overall benefit of the wm technique should be considered in the context of achieving improved accuracy and not just enhancements in clinical effectiveness.
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Affiliation(s)
- N J Look Hong
- Division of Surgical Oncology, Sunnybrook Health Sciences Centre, Toronto, ON;; Department of Surgery, University of Toronto, Toronto, ON
| | - G M Clarke
- Sunnybrook Research Institute, Toronto, ON
| | - M J Yaffe
- Sunnybrook Research Institute, Toronto, ON
| | - C M B Holloway
- Division of Surgical Oncology, Sunnybrook Health Sciences Centre, Toronto, ON;; Department of Surgery, University of Toronto, Toronto, ON
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14
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Uyoga S, Ndila CM, Macharia AW, Nyutu G, Shah S, Peshu N, Clarke GM, Kwiatkowski DP, Rockett KA, Williams TN. Glucose-6-phosphate dehydrogenase deficiency and the risk of malaria and other diseases in children in Kenya: a case-control and a cohort study. Lancet Haematol 2015; 2:e437-44. [PMID: 26686045 PMCID: PMC4703047 DOI: 10.1016/s2352-3026(15)00152-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/17/2015] [Revised: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 12/01/2022]
Abstract
Background The global prevalence of X-linked glucose-6-phosphate dehydrogenase (G6PD) deficiency is thought to be a result of selection by malaria, but epidemiological studies have yielded confusing results. We investigated the relationships between G6PD deficiency and both malaria and non-malarial illnesses among children in Kenya. Methods We did this study in Kilifi County, Kenya, where the G6PD c.202T allele is the only significant cause of G6PD deficiency. We tested the associations between G6PD deficiency and severe and complicated Plasmodium falciparum malaria through a case-control study of 2220 case and 3940 control children. Cases were children aged younger than 14 years, who visited the high dependency ward of Kilifi County Hospital with severe malaria between March 1, 1998, and Feb 28, 2010. Controls were children aged between 3–12 months who were born within the same study area between August 2006, and September 2010. We assessed the association between G6PD deficiency and both uncomplicated malaria and other common diseases of childhood in a cohort study of 752 children aged younger than 10 years. Participants of this study were recruited from a representative sample of households within the Ngerenya and Chonyi areas of Kilifi County between Aug 1, 1998, and July 31, 2001. The primary outcome measure for the case-control study was the odds ratio for hospital admission with severe malaria (computed by logistic regression) while for the cohort study it was the incidence rate ratio for uncomplicated malaria and non-malaria illnesses (computed by Poisson regression), by G6PD deficiency category. Findings 2863 (73%) children in the control group versus 1643 (74%) in the case group had the G6PD normal genotype, 639 (16%) versus 306 (14%) were girls heterozygous for G6PD c.202T, and 438 (11%) versus 271 (12%) children were either homozygous girls or hemizygous boys. Compared with boys and girls without G6PD deficiency, we found significant protection from severe malaria (odds ratio [OR] 0·82, 95% CI 0·70–0·97; p=0·020) among G6PD c.202T heterozygous girls but no evidence for protection among G6PD c.202T hemizygous boys and homozygous girls (OR 1·18, 0·99–1·40; p=0·056). Median follow-up for the mild disease cohort study was 2·24 years (IQR 2·22–2·85). G6PD c.202T had no effect on other common diseases of childhood in heterozygous girls (incidence rate ratio 0·98, 95% CI 0·86–1·11; p=0·82) or homozygous girls or hemizygous boys (0·93, 0·82–1·04; p=0·25), with the sole exception of a marginally significant increase in the incidence of helminth infections among heterozygous girls. Interpretation Heterozygous girls might be the driving force for the positive selection of G6PD deficiency alleles. Further studies are needed to definitively establish the mechanisms by which G6PD deficiency confers an advantage against malaria in heterozygous individuals. Such studies could lead to the development of new treatments. Funding Wellcome Trust, UK Medical Research Council, European Union, and Foundation for the National Institutes of Health (as part of the Bill & Melinda Gates Grand Challenges in Global Health Initiative).
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Affiliation(s)
- Sophie Uyoga
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Carolyne M Ndila
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Alex W Macharia
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Gideon Nyutu
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Shivang Shah
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Laboratory of Malaria and Vector Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Norbert Peshu
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK; Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Thomas N Williams
- Department of Epidemiology and Demography, KEMRI-Wellcome Trust Research Programme, Kilifi, Kenya; Department of Medicine, Imperial College, St Mary's Hospital, London, UK.
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15
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Shelton JMG, Corran P, Risley P, Silva N, Hubbart C, Jeffreys A, Rowlands K, Craik R, Cornelius V, Hensmann M, Molloy S, Sepulveda N, Clark TG, Band G, Clarke GM, Spencer CCA, Kerasidou A, Campino S, Auburn S, Tall A, Ly AB, Mercereau-Puijalon O, Sakuntabhai A, Djimdé A, Maiga B, Touré O, Doumbo OK, Dolo A, Troye-Blomberg M, Mangano VD, Verra F, Modiano D, Bougouma E, Sirima SB, Ibrahim M, Hussain A, Eid N, Elzein A, Mohammed H, Elhassan A, Elhassan I, Williams TN, Ndila C, Macharia A, Marsh K, Manjurano A, Reyburn H, Lemnge M, Ishengoma D, Carter R, Karunaweera N, Fernando D, Dewasurendra R, Drakeley CJ, Riley EM, Kwiatkowski DP, Rockett KA. Genetic determinants of anti-malarial acquired immunity in a large multi-centre study. Malar J 2015; 14:333. [PMID: 26314886 PMCID: PMC4552443 DOI: 10.1186/s12936-015-0833-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Accepted: 08/03/2015] [Indexed: 01/01/2023] Open
Abstract
Background Many studies report associations between human genetic factors and immunity to malaria but few have been reliably replicated. These studies are usually country-specific, use small sample sizes and are
not directly comparable due to differences in methodologies. This study brings together samples and data collected from multiple sites across Africa and Asia to use standardized methods to look for consistent genetic effects on anti-malarial antibody levels. Methods Sera, DNA samples and clinical data were collected from 13,299 individuals from ten sites in Senegal, Mali, Burkina Faso, Sudan, Kenya, Tanzania, and Sri Lanka using standardized methods. DNA was extracted and typed for 202 Single Nucleotide Polymorphisms with known associations to malaria or antibody production, and antibody levels to four clinical grade malarial antigens [AMA1, MSP1, MSP2, and (NANP)4] plus total IgE were measured by ELISA techniques. Regression models were used to investigate the associations of clinical and genetic factors with antibody levels. Results Malaria infection increased levels of antibodies to malaria antigens and, as expected, stable predictors of anti-malarial antibody levels included age, seasonality, location, and ethnicity. Correlations between antibodies to blood-stage antigens AMA1, MSP1 and MSP2 were higher between themselves than with antibodies to the (NANP)4 epitope of the pre-erythrocytic circumsporozoite protein, while there was little or no correlation with total IgE levels. Individuals with sickle cell trait had significantly lower antibody levels to all blood-stage antigens, and recessive homozygotes for CD36 (rs321198) had significantly lower anti-malarial antibody levels to MSP2. Conclusion Although the most significant finding with a consistent effect across sites was for sickle cell trait, its effect is likely to be via reducing a microscopically positive parasitaemia rather than directly on antibody levels. However, this study does demonstrate a framework for the feasibility of combining data from sites with heterogeneous malaria transmission levels across Africa and Asia with which to explore genetic effects on anti-malarial immunity. Electronic supplementary material The online version of this article (doi:10.1186/s12936-015-0833-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Jennifer M G Shelton
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Patrick Corran
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK. .,National Institute for Biological Standards and Controls, South Mimms, Hertfordshire, UK.
| | - Paul Risley
- National Institute for Biological Standards and Controls, South Mimms, Hertfordshire, UK.
| | - Nilupa Silva
- National Institute for Biological Standards and Controls, South Mimms, Hertfordshire, UK.
| | - Christina Hubbart
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Anna Jeffreys
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Kate Rowlands
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Rachel Craik
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Victoria Cornelius
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Meike Hensmann
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Sile Molloy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Nuno Sepulveda
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK.
| | - Taane G Clark
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK.
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Christopher C A Spencer
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Angeliki Kerasidou
- Nuffield Department of Population Health, The Ethox Centre, University of Oxford, Richard Doll Building, Old Road Campus, Oxford, OX3 7LF, UK.
| | - Susana Campino
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Sarah Auburn
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK.
| | - Adama Tall
- Infectious Diseases Epidemiology Unit, Institut Pasteur, BP 220, Dakar, Senegal.
| | - Alioune Badara Ly
- Infectious Diseases Epidemiology Unit, Institut Pasteur, BP 220, Dakar, Senegal.
| | - Odile Mercereau-Puijalon
- Parasite Molecular Immunology Unit, Institut Pasteur, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France.
| | - Anavaj Sakuntabhai
- Unité de Génétique Fonctionnelle des Maladies Infectieuses, Institut Pasteur, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France. .,Centre National de la Recherche Scientifique, URA3012, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France.
| | - Abdoulaye Djimdé
- Department of Epidemiology of Parasitic Diseases, Faculty of Medicine, Pharmacy and Odonto-Stomatology, Malaria Research and Training Center, USTTB, BP 1805, Bamako, Mali.
| | - Boubacar Maiga
- Department of Epidemiology of Parasitic Diseases, Faculty of Medicine, Pharmacy and Odonto-Stomatology, Malaria Research and Training Center, USTTB, BP 1805, Bamako, Mali.
| | - Ousmane Touré
- Department of Epidemiology of Parasitic Diseases, Faculty of Medicine, Pharmacy and Odonto-Stomatology, Malaria Research and Training Center, USTTB, BP 1805, Bamako, Mali.
| | - Ogobara K Doumbo
- Department of Epidemiology of Parasitic Diseases, Faculty of Medicine, Pharmacy and Odonto-Stomatology, Malaria Research and Training Center, USTTB, BP 1805, Bamako, Mali.
| | - Amagana Dolo
- Department of Epidemiology of Parasitic Diseases, Faculty of Medicine, Pharmacy and Odonto-Stomatology, Malaria Research and Training Center, USTTB, BP 1805, Bamako, Mali.
| | - Marita Troye-Blomberg
- Department of Molecular Biosciences, Wenner-Gren Institute, Stockholm University, Svante Arrheniusväg 20B, 106 91, Stockholm, Sweden.
| | - Valentina D Mangano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Frederica Verra
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - David Modiano
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185, Rome, Italy.
| | - Edith Bougouma
- Centre de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso.
| | - Sodiomon B Sirima
- Centre de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso.
| | - Muntaser Ibrahim
- Institute of Endemic Diseases, University of Khartoum, Medical Sciences Campus, Qasser Street, Khartoum, Sudan.
| | - Ayman Hussain
- Institute of Endemic Diseases, University of Khartoum, Medical Sciences Campus, Qasser Street, Khartoum, Sudan.
| | - Nahid Eid
- Institute of Endemic Diseases, University of Khartoum, Medical Sciences Campus, Qasser Street, Khartoum, Sudan.
| | - Abier Elzein
- Institute of Endemic Diseases, University of Khartoum, Medical Sciences Campus, Qasser Street, Khartoum, Sudan.
| | - Hiba Mohammed
- Institute of Endemic Diseases, University of Khartoum, Medical Sciences Campus, Qasser Street, Khartoum, Sudan.
| | - Ahmed Elhassan
- Institute of Endemic Diseases, University of Khartoum, Medical Sciences Campus, Qasser Street, Khartoum, Sudan.
| | - Ibrahim Elhassan
- Institute of Endemic Diseases, University of Khartoum, Medical Sciences Campus, Qasser Street, Khartoum, Sudan.
| | - Thomas N Williams
- KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230-80108, Kilifi, Kenya. .,Department of Medicine, Imperial College, St Mary's Campus, Norfolk Place, London, W2 1PG, UK.
| | - Carolyne Ndila
- KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230-80108, Kilifi, Kenya.
| | - Alexander Macharia
- KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230-80108, Kilifi, Kenya.
| | - Kevin Marsh
- KEMRI-Wellcome Trust Research Programme, CGMRC, PO Box 230-80108, Kilifi, Kenya.
| | - Alphaxard Manjurano
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK. .,Kilimanjaro Christian Medical College, Tumaini University, Moshi, Tanzania.
| | - Hugh Reyburn
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK. .,Kilimanjaro Christian Medical College, Tumaini University, Moshi, Tanzania.
| | - Martha Lemnge
- National Institute for Medical Research, Ocean Road, Dar es Salaam, Tanzania.
| | - Deus Ishengoma
- National Institute for Medical Research, Ocean Road, Dar es Salaam, Tanzania.
| | - Richard Carter
- Division of Biological Sciences, Ashworth Laboratories, University of Edinburgh, West Mains Rd., Edinburgh, EH9 3JT, UK.
| | - Nadira Karunaweera
- Department of Parasitology, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo, Sri Lanka.
| | - Deepika Fernando
- Department of Parasitology, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo, Sri Lanka.
| | - Rajika Dewasurendra
- Department of Parasitology, Faculty of Medicine, University of Colombo, Kynsey Road, Colombo, Sri Lanka.
| | - Christopher J Drakeley
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK. .,Kilimanjaro Christian Medical College, Tumaini University, Moshi, Tanzania.
| | - Eleanor M Riley
- London School of Hygiene and Tropical Medicine, Keppel Street, London, UK. .,Kilimanjaro Christian Medical College, Tumaini University, Moshi, Tanzania.
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK. .,Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
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Tridente A, Clarke GM, Walden A, Gordon AC, Hutton P, Chiche JD, Holloway PAH, Mills GH, Bion J, Stüber F, Garrard C, Hinds C. Association between trends in clinical variables and outcome in intensive care patients with faecal peritonitis: analysis of the GenOSept cohort. Crit Care 2015; 19:210. [PMID: 25939380 PMCID: PMC4432819 DOI: 10.1186/s13054-015-0931-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 04/16/2015] [Indexed: 01/20/2023]
Abstract
Introduction Patients admitted to intensive care following surgery for faecal peritonitis present particular challenges in terms of clinical management and risk assessment. Collaborating surgical and intensive care teams need shared perspectives on prognosis. We aimed to determine the relationship between dynamic assessment of trends in selected variables and outcomes. Methods We analysed trends in physiological and laboratory variables during the first week of intensive care unit (ICU) stay in 977 patients at 102 centres across 16 European countries. The primary outcome was 6-month mortality. Secondary endpoints were ICU, hospital and 28-day mortality. For each trend, Cox proportional hazards (PH) regression analyses, adjusted for age and sex, were performed for each endpoint. Results Trends over the first 7 days of the ICU stay independently associated with 6-month mortality were worsening thrombocytopaenia (mortality: hazard ratio (HR) = 1.02; 95% confidence interval (CI), 1.01 to 1.03; P <0.001) and renal function (total daily urine output: HR =1.02; 95% CI, 1.01 to 1.03; P <0.001; Sequential Organ Failure Assessment (SOFA) renal subscore: HR = 0.87; 95% CI, 0.75 to 0.99; P = 0.047), maximum bilirubin level (HR = 0.99; 95% CI, 0.99 to 0.99; P = 0.02) and Glasgow Coma Scale (GCS) SOFA subscore (HR = 0.81; 95% CI, 0.68 to 0.98; P = 0.028). Changes in renal function (total daily urine output and renal component of the SOFA score), GCS component of the SOFA score, total SOFA score and worsening thrombocytopaenia were also independently associated with secondary outcomes (ICU, hospital and 28-day mortality). We detected the same pattern when we analysed trends on days 2, 3 and 5. Dynamic trends in all other measured laboratory and physiological variables, and in radiological findings, changes inrespiratory support, renal replacement therapy and inotrope and/or vasopressor requirements failed to be retained as independently associated with outcome in multivariate analysis. Conclusions Only deterioration in renal function, thrombocytopaenia and SOFA score over the first 2, 3, 5 and 7 days of the ICU stay were consistently associated with mortality at all endpoints. These findings may help to inform clinical decision making in patients with this common cause of critical illness. Electronic supplementary material The online version of this article (doi:10.1186/s13054-015-0931-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ascanio Tridente
- Intensive Care Unit, Whiston Hospital, Prescot, Warrington Road, Prescot, Merseyside, L35 5DR, UK. .,Department of Infection and Immunity, The Medical School, University of Sheffield, Beech Hill Rd, Sheffield, South Yorkshire, S10 2RX, Sheffield, UK.
| | - Geraldine M Clarke
- The Wellcome Trust Centre for Human Genetics, University of Oxford, University Offices, Wellington Square, Oxford, OX1 2JD, Oxford, UK.
| | - Andrew Walden
- Intensive Care Unit, Royal Berkshire Hospital, Craven Road, RG1 5AN, Reading, UK.
| | | | - Paula Hutton
- Intensive Care Unit, John Radcliffe Hospital, Headley Way, OX3 9DU, Oxford, UK.
| | - Jean-Daniel Chiche
- Medical Intensive Care Unit, Hôpital Cochin, 27 rue du Faubourg Saint-Jacques, 75014, Paris, France.
| | | | - Gary H Mills
- Department of Infection and Immunity, The Medical School, University of Sheffield, Beech Hill Rd, Sheffield, South Yorkshire, S10 2RX, Sheffield, UK. .,Intensive Care Unit, Sheffield Teaching Hospitals NHS Trust, Northern General Hospital, Herries Road, South Yorkshire, S5 7AU, Sheffield, UK.
| | - Julian Bion
- Department of Anaesthesia and Critical Care, School of Clinical and Experimental Medicine, University of Birmingham, Office 1, Ground Floor East, old Queen Elizabeth Hospital, Edgbaston, Birmingham, B15 2TH, UK.
| | - Frank Stüber
- Department of Anaesthesiology and Pain Medicine, University Hospital Inselspital, Bern, and University of Bern, Bern, Switzerland.
| | - Christopher Garrard
- Intensive Care Unit, John Radcliffe Hospital, Headley Way, OX3 9DU, Oxford, UK.
| | - Charles Hinds
- Barts and The School of Medicine and Dentistry, Queen Mary University of London, Turner Street, London, E1 2AD, UK.
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17
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Langenberg C, Sharp SJ, Franks PW, Scott RA, Deloukas P, Forouhi NG, Froguel P, Groop LC, Hansen T, Palla L, Pedersen O, Schulze MB, Tormo MJ, Wheeler E, Agnoli C, Arriola L, Barricarte A, Boeing H, Clarke GM, Clavel-Chapelon F, Duell EJ, Fagherazzi G, Kaaks R, Kerrison ND, Key TJ, Khaw KT, Kröger J, Lajous M, Morris AP, Navarro C, Nilsson PM, Overvad K, Palli D, Panico S, Quirós JR, Rolandsson O, Sacerdote C, Sánchez MJ, Slimani N, Spijkerman AMW, Tumino R, van der A DL, van der Schouw YT, Barroso I, McCarthy MI, Riboli E, Wareham NJ. Gene-lifestyle interaction and type 2 diabetes: the EPIC interact case-cohort study. PLoS Med 2014; 11:e1001647. [PMID: 24845081 PMCID: PMC4028183 DOI: 10.1371/journal.pmed.1001647] [Citation(s) in RCA: 155] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 04/11/2014] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Understanding of the genetic basis of type 2 diabetes (T2D) has progressed rapidly, but the interactions between common genetic variants and lifestyle risk factors have not been systematically investigated in studies with adequate statistical power. Therefore, we aimed to quantify the combined effects of genetic and lifestyle factors on risk of T2D in order to inform strategies for prevention. METHODS AND FINDINGS The InterAct study includes 12,403 incident T2D cases and a representative sub-cohort of 16,154 individuals from a cohort of 340,234 European participants with 3.99 million person-years of follow-up. We studied the combined effects of an additive genetic T2D risk score and modifiable and non-modifiable risk factors using Prentice-weighted Cox regression and random effects meta-analysis methods. The effect of the genetic score was significantly greater in younger individuals (p for interaction = 1.20×10-4). Relative genetic risk (per standard deviation [4.4 risk alleles]) was also larger in participants who were leaner, both in terms of body mass index (p for interaction = 1.50×10-3) and waist circumference (p for interaction = 7.49×10-9). Examination of absolute risks by strata showed the importance of obesity for T2D risk. The 10-y cumulative incidence of T2D rose from 0.25% to 0.89% across extreme quartiles of the genetic score in normal weight individuals, compared to 4.22% to 7.99% in obese individuals. We detected no significant interactions between the genetic score and sex, diabetes family history, physical activity, or dietary habits assessed by a Mediterranean diet score. CONCLUSIONS The relative effect of a T2D genetic risk score is greater in younger and leaner participants. However, this sub-group is at low absolute risk and would not be a logical target for preventive interventions. The high absolute risk associated with obesity at any level of genetic risk highlights the importance of universal rather than targeted approaches to lifestyle intervention.
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Affiliation(s)
- Claudia Langenberg
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Stephen J. Sharp
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Paul W. Franks
- Lund University, Malmö, Sweden
- Umeå University, Umeå, Sweden
| | - Robert A. Scott
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Panos Deloukas
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Nita G. Forouhi
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | | | - Leif C. Groop
- University Hospital Scania, Malmö, Sweden
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Torben Hansen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Sciences, University of Southern Denmark, Odense, Denmark
| | - Luigi Palla
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Oluf Pedersen
- The Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
- Faculty of Health Science, University of Aarhus, Aarhus, Denmark
- Institute of Biomedical Science, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Maria-Jose Tormo
- Department of Epidemiology, Murcia Regional Health Council, Murcia, Spain
- Consorcio de Investigación Biomédica de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
- Department of Health and Social Sciences, Universidad de Murcia, Spain
| | - Eleanor Wheeler
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | | | - Larraitz Arriola
- Consorcio de Investigación Biomédica de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
- Public Health Division of Gipuzkoa, San Sebastian, Spain
- Instituto de Investigación Sanitaria BioDonostia, Basque Government, San Sebastian, Spain
| | - Aurelio Barricarte
- Consorcio de Investigación Biomédica de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
- Navarre Public Health Institute, Pamplona, Spain
| | - Heiner Boeing
- German Institute of Human Nutrition, Potsdam-Rehbruecke, Germany
| | - Geraldine M. Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | | | - Eric J. Duell
- Catalan Institute of Oncology, Bellvitge Biomedical Research Institute, Barcelona, Spain
| | - Guy Fagherazzi
- Inserm, CESP U1018, Villejuif, France
- Université Paris-Sud, UMRS 1018, Villejuif, France
| | - Rudolf Kaaks
- German Cancer Research Center, Heidelberg, Germany
| | - Nicola D. Kerrison
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
| | | | - Kay Tee Khaw
- University of Cambridge, Cambridge, United Kingdom
| | - Janine Kröger
- German Institute of Human Nutrition, Potsdam-Rehbruecke, Germany
| | - Martin Lajous
- Inserm, CESP U1018, Villejuif, France
- Center for Research on Population Health, National Institute of Public Health of Mexico, Cuernavaca, Mexico
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Andrew P. Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
| | - Carmen Navarro
- Department of Epidemiology, Murcia Regional Health Council, Murcia, Spain
- Consorcio de Investigación Biomédica de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
- Unit of Preventive Medicine and Public Health, School of Medicine, University of Murcia, Murcia, Spain
| | | | - Kim Overvad
- Department of Public Health, Aarhus University, Aarhus, Denmark
- Aalborg University Hospital, Aalborg, Denmark
| | - Domenico Palli
- Cancer Research and Prevention Institute, Florence, Italy
| | - Salvatore Panico
- Dipartimento di Medicina Clinica e Chirurgia, Federico II University, Naples, Italy
| | | | | | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Azienda Ospedaliero Universitaria Città della Salute e della Scienza, University of Turin, Turin, Italy
- Piedmont Reference Center for Epidemiology and Cancer Prevention, Torino, Italy
- Human Genetics Foundation, Torino, Italy
| | - María-José Sánchez
- Consorcio de Investigación Biomédica de Epidemiología y Salud Pública, Instituto de Salud Carlos III, Madrid, Spain
- Andalusian School of Public Health, Granada, Spain
| | - Nadia Slimani
- International Agency for Research on Cancer, Lyon, France
| | | | - Rosario Tumino
- Azienda Sanitaria Provinciale di Ragusa, Ragusa, Italy
- Aire Onlus, Ragusa, Italy
| | - Daphne L. van der A
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | | | - Inês Barroso
- The Wellcome Trust Sanger Institute, Cambridge, United Kingdom
- University of Cambridge Metabolic Research Laboratories, Cambridge, United Kingdom
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, United Kingdom
- NIHR Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Elio Riboli
- School of Public Health, Imperial College London, London, United Kingdom
| | - Nicholas J. Wareham
- Medical Research Council Epidemiology Unit, University of Cambridge, Cambridge, United Kingdom
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18
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Tridente A, Clarke GM, Walden A, McKechnie S, Hutton P, Mills GH, Gordon AC, Holloway PAH, Chiche JD, Bion J, Stuber F, Garrard C, Hinds CJ. Patients with faecal peritonitis admitted to European intensive care units: an epidemiological survey of the GenOSept cohort. Intensive Care Med 2013; 40:202-210. [PMID: 24306080 DOI: 10.1007/s00134-013-3158-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 11/07/2013] [Indexed: 01/14/2023]
Abstract
INTRODUCTION Faecal peritonitis (FP) is a common cause of sepsis and admission to the intensive care unit (ICU). The Genetics of Sepsis and Septic Shock in Europe (GenOSept) project is investigating the influence of genetic variation on the host response and outcomes in a large cohort of patients with sepsis admitted to ICUs across Europe. Here we report an epidemiological survey of the subset of patients with FP. OBJECTIVES To define the clinical characteristics, outcomes and risk factors for mortality in patients with FP admitted to ICUs across Europe. METHODS Data was extracted from electronic case report forms. Phenotypic data was recorded using a detailed, quality-assured clinical database. The primary outcome measure was 6-month mortality. Patients were followed for 6 months. Kaplan-Meier analysis was used to determine mortality rates. Cox proportional hazards regression analysis was employed to identify independent risk factors for mortality. RESULTS Data for 977 FP patients admitted to 102 centres across 16 countries between 29 September 2005 and 5 January 2011 was extracted. The median age was 69.2 years (IQR 58.3-77.1), with a male preponderance (54.3%). The most common causes of FP were perforated diverticular disease (32.1%) and surgical anastomotic breakdown (31.1%). The ICU mortality rate at 28 days was 19.1%, increasing to 31.6% at 6 months. The cause of FP, pre-existing co-morbidities and time from estimated onset of symptoms to surgery did not impact on survival. The strongest independent risk factors associated with an increased rate of death at 6 months included age, higher APACHE II score, acute renal and cardiovascular dysfunction within 1 week of admission to ICU, hypothermia, lower haematocrit and bradycardia on day 1 of ICU stay. CONCLUSIONS In this large cohort of patients admitted to European ICUs with FP the 6 month mortality was 31.6%. The most consistent predictors of mortality across all time points were increased age, development of acute renal dysfunction during the first week of admission, lower haematocrit and hypothermia on day 1 of ICU admission.
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Affiliation(s)
- Ascanio Tridente
- Whiston Hospital, Prescot, Merseyside and Academic Unit of Medical Education, The Medical School, University of Sheffield, Sheffield, UK
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Clarke GM, Rivas MA, Morris AP. A flexible approach for the analysis of rare variants allowing for a mixture of effects on binary or quantitative traits. PLoS Genet 2013; 9:e1003694. [PMID: 23966874 PMCID: PMC3744430 DOI: 10.1371/journal.pgen.1003694] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 06/19/2013] [Indexed: 11/18/2022] Open
Abstract
Multiple rare variants either within or across genes have been hypothesised to collectively influence complex human traits. The increasing availability of high throughput sequencing technologies offers the opportunity to study the effect of rare variants on these traits. However, appropriate and computationally efficient analytical methods are required to account for collections of rare variants that display a combination of protective, deleterious and null effects on the trait. We have developed a novel method for the analysis of rare genetic variation in a gene, region or pathway that, by simply aggregating summary statistics at each variant, can: (i) test for the presence of a mixture of effects on a trait; (ii) be applied to both binary and quantitative traits in population-based and family-based data; (iii) adjust for covariates to allow for non-genetic risk factors and; (iv) incorporate imputed genetic variation. In addition, for preliminary identification of promising genes, the method can be applied to association summary statistics, available from meta-analysis of published data, for example, without the need for individual level genotype data. Through simulation, we show that our method is immune to the presence of bi-directional effects, with no apparent loss in power across a range of different mixtures, and can achieve greater power than existing approaches as long as summary statistics at each variant are robust. We apply our method to investigate association of type-1 diabetes with imputed rare variants within genes in the major histocompatibility complex using genotype data from the Wellcome Trust Case Control Consortium.
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Affiliation(s)
- Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom.
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Affiliation(s)
- G M Clarke
- Department of Pharmacy, Heriot-Watt University, Edinburgh
| | - G C Jefferson
- Department of Pharmacy, Heriot-Watt University, Edinburgh
| | - R J McBride
- Department of Pharmacy, Heriot-Watt University, Edinburgh
| | - P C Priestley
- Department of Dermatology, University of Edinburgh
- Department of Pharmacy, Heriot-Watt University, Edinburgh
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21
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Abstract
This protocol describes how to perform basic statistical analysis in a population-based genetic association case-control study. The steps described involve the (i) appropriate selection of measures of association and relevance of disease models; (ii) appropriate selection of tests of association; (iii) visualization and interpretation of results; (iv) consideration of appropriate methods to control for multiple testing; and (v) replication strategies. Assuming no previous experience with software such as PLINK, R or Haploview, we describe how to use these popular tools for handling single-nucleotide polymorphism data in order to carry out tests of association and visualize and interpret results. This protocol assumes that data quality assessment and control has been performed, as described in a previous protocol, so that samples and markers deemed to have the potential to introduce bias to the study have been identified and removed. Study design, marker selection and quality control of case-control studies have also been discussed in earlier protocols. The protocol should take ~1 h to complete.
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Affiliation(s)
- Geraldine M Clarke
- Genetic and Genomic Epidemiology Unit, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK.
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22
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Cho EY, Jang Y, Shin ES, Jang HY, Yoo YK, Kim S, Jang JH, Lee JY, Yun MH, Park MY, Chae JS, Lim JW, Shin DJ, Park S, Lee JH, Han BG, Rae KH, Cardon LR, Morris AP, Lee JE, Clarke GM. Genome-wide association analysis and replication of coronary artery disease in South Korea suggests a causal variant common to diverse populations. Heart Asia 2010; 2:104-8. [PMID: 27325954 DOI: 10.1136/ha.2009.001370] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Accepted: 05/07/2010] [Indexed: 12/26/2022]
Abstract
BACKGROUND Recent genome-wide association (GWA) studies have identified and replicated several genetic loci associated with the risk of development of coronary artery disease (CAD) in samples from populations of Caucasian and Asian descent. However, only chromosome 9p21 has been confirmed as a major susceptibility locus conferring risk for development of CAD across multiple ethnic groups. The authors aimed to find evidence of further similarities and differences in genetic risk of CAD between Korean and other populations. METHODS The authors performed a GWA study comprising 230 cases and 290 controls from a Korean population typed on 490 032 single nucleotide polymorphisms (SNPs). A total of 3148 SNPs were taken forward for genotyping in a subsequent replication study using an independent sample of 1172 cases and 1087 controls from the same population. RESULTS The association previously observed on chromosome 9p21 was independently replicated (p=3.08e-07). Within this region, the same risk haplotype was observed in samples from both Korea and of Western European descent, suggesting that the causal mutation carried on this background occurred on a single ancestral allele. Other than 9p21, the authors were unable to replicate any of the previously reported signals for association with CAD. Furthermore, no evidence of association was found at chromosome 1q41 for risk of myocardial infarction, previously identified as conferring risk in a Japanese population. CONCLUSION A common causal variant is likely to be responsible for risk of CAD in Korean and Western European populations at chromosome 9p21.3. Further investigations are required to confirm non-replication of any other cross-race genetic risk factors.
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Affiliation(s)
| | - Yangsoo Jang
- Clinical Nutrigenetics/Nutrigenomics Lab, Department of Food & Nutrition, College of Human Ecology, Yonsei University Research Institute of Science for Ageing, Yonsei University, Seoul, Republic of Korea
| | | | | | | | - Sook Kim
- DNA Link, Seoul, Republic of Korea
| | | | | | | | | | - Jey Sook Chae
- Clinical Nutrigenetics/Nutrigenomics Lab, Department of Food & Nutrition, College of Human Ecology, Yonsei University Research Institute of Science for Ageing, Yonsei University, Seoul, Republic of Korea
| | - Jin Woo Lim
- Division of Cardiology, Cardiovascular Genome Center, Yonsei Medical Institute, Yonsei University, Seoul, Republic of Korea
| | - Dong Jik Shin
- Division of Cardiology, Cardiovascular Genome Center, Yonsei Medical Institute, Yonsei University, Seoul, Republic of Korea
| | - Sungha Park
- Division of Cardiology, Cardiovascular Genome Center, Yonsei Medical Institute, Yonsei University, Seoul, Republic of Korea
| | - Jong Ho Lee
- Clinical Nutrigenetics/Nutrigenomics Lab, Department of Food & Nutrition, College of Human Ecology, Yonsei University Research Institute of Science for Ageing, Yonsei University, Seoul, Republic of Korea
| | - Bok Ghee Han
- National Genome Research Institute, Korean National Institute of Health, Seoul, Korea
| | - Kim Hyung Rae
- National Genome Research Institute, Korean National Institute of Health, Seoul, Korea
| | - Lon R Cardon
- GlaxoSmithKline, Philadelphia, Pennsylvania, USA
| | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | | | - Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
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Abstract
Significant allele flipping, where associations for the same disease occur at opposite alleles of the same bi-allelic locus, is increasing. But when is a significant allele flip genuine? We address the statistical issues of claiming and observing genuine allele flips in actual samples. We show that unless an allele flip is genuine, the probability of observing a significant allele flip in samples ascertained similarly from a common population is negligible. We derive expressions for the expected values of commonly used measures of association, which confirm previous findings that the underlying mechanism of a genuine allele flip is variation in the haplotype frequencies and show further how this variation interacts with variation in the genetic effects to impact allele flipping. We show that for association testing at proxy SNPs, common in genome-wide association studies, variation in haplotype frequencies must coincide with a reversal in the sign of linkage disequilibrium (LD) to trigger genuine allele flips. Using HapMap data and r, rather than r(2), to highlight previously unobserved effects, we show that unless genetic effects are large, variation in LD is unlikely to cause genuine allele flips in samples drawn from the same population. However, as populations diverge, it is an increasingly viable cause of a genuine allele flip for sufficiently large genetic effect and/or sample sizes. We conclude that evidence of variation in local patterns of LD, ancestral composition of study samples, and environmental exposures between study populations can provide compelling practical evidence in defense of a genuine allele flip.
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Affiliation(s)
- Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom.
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An P, Mukherjee O, Chanda P, Yao L, Engelman CD, Huang CH, Zheng T, Kovac IP, Dubé MP, Liang X, Li J, de Andrade M, Culverhouse R, Malzahn D, Manning AK, Clarke GM, Jung J, Province MA. The challenge of detecting epistasis (G x G interactions): Genetic Analysis Workshop 16. Genet Epidemiol 2010; 33 Suppl 1:S58-67. [PMID: 19924703 DOI: 10.1002/gepi.20474] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Interest is increasing in epistasis as a possible source of the unexplained variance missed by genome-wide association studies. The Genetic Analysis Workshop 16 Group 9 participants evaluated a wide variety of classical and novel analytical methods for detecting epistasis, in both the statistical and machine learning paradigms, applied to both real and simulated data. Because the magnitude of epistasis is clearly relative to scale of penetrance, and therefore to some extent, to the choice of model framework, it is not surprising that strong interactions under one model might be minimized or even disappear entirely under a different modeling framework.
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Affiliation(s)
- Ping An
- Division of Statistical Genomics and Department of Genetics, Washington University School of Medicine, St. Louis, Missouri 63108, USA
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Abstract
Assuming continuous, normally distributed environmental and categorical genotype variables, the authors compare 6 case-only designs for tests of association in gene-environment interaction. Novel tests modeling the environmental variable as either the response or the predictor and allowing a genetic variable with multiallelic variants are included. The authors show that tests imposing the same genotypic pattern of inheritance perform similarly regardless of whether genotype is the response variable or the predictor variable. The novel tests using the genetic variable as the response variable are advantageous because they are robust to non-normally distributed environmental exposures. Dominance deviance—deviation from additivity in the main or interaction effects—is key to test performance: When it is zero or modest, tests searching for a trend with increasing risk alleles are optimal; when it is large, tests for genotypic effects are optimal. However, the authors show that dominance deviance is attenuated when it is observed at a proxy locus, which is common in genome-wide association studies, so large dominance deviance is likely to be rare. The authors conclude that the trend test is the appropriate tool for large-scale association scans where the true gene-environment interaction model is unknown. The common practice of assuming a dominant pattern of inheritance can cause serious losses of power in the presence of any recessive, or modest dominant, effects.
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Affiliation(s)
- Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
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Clarke GM, Pettersson FH, Morris AP. A comparison of case-only designs for detecting gene x gene interaction in rheumatoid arthritis using genome-wide case-control data in Genetic Analysis Workshop 16. BMC Proc 2009; 3 Suppl 7:S73. [PMID: 20018068 PMCID: PMC2795975 DOI: 10.1186/1753-6561-3-s7-s73] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
We compare and contrast case-only designs for detecting gene x gene (G x G) interaction in rheumatoid arthritis (RA) using the genome-wide data provided by Genetic Analysis Workshop 16 Problem 1. Logistic as well as novel multinomial and proportional odds models that do not depend on the specification of additive or dominant models for susceptibility loci were applied to the case-only sample. We identified 519 significant interactions (p < 1 x 10-4 in at least one test). All methods detected unique significant interactions; 169 were common to more than one model and only 21 were common to all models. Results emphasize that categorization of the genetic variables and choice of regression model are critical and hugely influential in the identification of G x G. Porportional odds and multinomial methods provide new tools for identification of G x G interactions.
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Affiliation(s)
- Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.
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Pettersson FH, Anderson CA, Clarke GM, Barrett JC, Cardon LR, Morris AP, Zondervan KT. Marker selection for genetic case-control association studies. Nat Protoc 2009; 4:743-52. [PMID: 19390530 DOI: 10.1038/nprot.2009.38] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Association studies can focus on candidate gene(s), a particular genomic region, or adopt a genome-wide association approach, each of which has implications for marker selection. The strategy for marker selection will affect the statistical power of the study to detect a disease association and is a crucial element of study design. The abundant single nucleotide polymorphisms (SNPs) are the markers of choice in genetic case-control association studies. The genotypes of neighboring SNPs are often highly correlated ('in linkage disequilibrium', LD) within a population, which is utilized for selecting specific 'tagSNPs' to serve as proxies for other nearby SNPs in high LD. General guidelines for SNP selection in candidate genes/regions and genome-wide studies are provided in this protocol, along with illustrative examples. Publicly available web-based resources are utilized to browse and retrieve data, and software, such as Haploview and Goldsurfer2, is applied to investigate LD and to select tagSNPs.
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Clarke GM, Carter KW, Palmer LJ, Morris AP, Cardon LR. Fine mapping versus replication in whole-genome association studies. Am J Hum Genet 2007; 81:995-1005. [PMID: 17924341 DOI: 10.1086/521952] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2007] [Accepted: 07/25/2007] [Indexed: 11/03/2022] Open
Abstract
Association replication studies have a poor track record and, even when successful, often claim association with different markers, alleles, and phenotypes than those reported in the primary study. It is unknown whether these outcomes reflect genuine associations or false-positive results. A greater understanding of these observations is essential for genomewide association (GWA) studies, since they have the potential to identify multiple new associations that that will require external validation. Theoretically, a repeat association with precisely the same variant in an independent sample is the gold standard for replication, but testing additional variants is commonplace in replication studies. Finding different associated SNPs within the same gene or region as that originally identified is often reported as confirmatory evidence. Here, we compare the probability of replicating a gene or region under two commonly used marker-selection strategies: an "exact" approach that involves only the originally significant markers and a "local" approach that involves both the originally significant markers and others in the same region. When a region of high intermarker linkage disequilibrium is tested to replicate an initial finding that is only weak association with disease, the local approach is a good strategy. Otherwise, the most powerful and efficient strategy for replication involves testing only the initially identified variants. Association with a marker other than that originally identified can occur frequently, even in the presence of real effects in a low-powered replication study, and instances of such association increase as the number of included variants increases. Our results provide a basis for the design and interpretation of GWA replication studies and point to the importance of a clear distinction between fine mapping and replication after GWA.
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Affiliation(s)
- Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, UK
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29
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Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, Goddard ME, Visscher PM. Recent human effective population size estimated from linkage disequilibrium. Genome Res 2007; 17:520-6. [PMID: 17351134 PMCID: PMC1832099 DOI: 10.1101/gr.6023607] [Citation(s) in RCA: 291] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Effective population size (N(e)) determines the amount of genetic variation, genetic drift, and linkage disequilibrium (LD) in populations. Here, we present the first genome-wide estimates of human effective population size from LD data. Chromosome-specific effective population size was estimated for all autosomes and the X chromosome from estimated LD between SNP pairs <100 kb apart. We account for variation in recombination rate by using coalescent-based estimates of fine-scale recombination rate from one sample and correlating these with LD in an independent sample. Phase I of the HapMap project produced between 18 and 22 million SNP pairs in samples from four populations: Yoruba from Ibadan (YRI), Nigeria; Japanese from Tokyo (JPT); Han Chinese from Beijing (HCB); and residents from Utah with ancestry from northern and western Europe (CEU). For CEU, JPT, and HCB, the estimate of effective population size, adjusted for SNP ascertainment bias, was approximately 3100, whereas the estimate for the YRI was approximately 7500, consistent with the out-of-Africa theory of ancestral human population expansion and concurrent bottlenecks. We show that the decay in LD over distance between SNPs is consistent with recent population growth. The estimates of N(e) are lower than previously published estimates based on heterozygosity, possibly because they represent one or more bottlenecks in human population size that occurred approximately 10,000 to 200,000 years ago.
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Affiliation(s)
- Albert Tenesa
- Colon Cancer Genetics Group, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
- MRC Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Pau Navarro
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
| | - Ben J. Hayes
- Victorian Institute of Animal Science, DPI, Attwood 3049, Australia
| | - David L. Duffy
- Queensland Institute of Medical Research, Royal Brisbane Hospital, Brisbane 4006, Australia
| | - Geraldine M. Clarke
- The Wellcome Trust Centre for Human Genetics, The University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Mike E. Goddard
- Victorian Institute of Animal Science, DPI, Attwood 3049, Australia
- Institute of Land and Food Resources, University of Melbourne, Parkville 3010, Australia
| | - Peter M. Visscher
- Institute of Evolutionary Biology, University of Edinburgh, Edinburgh EH9 3JT, United Kingdom
- Queensland Institute of Medical Research, Royal Brisbane Hospital, Brisbane 4006, Australia
- Corresponding author.E-mail ; fax +61-7-3362-0101
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Clarke GM, Eidt S, Sun L, Mawdsley G, Zubovits JT, Yaffe MJ. Whole-specimen histopathology: a method to produce whole-mount breast serial sections for 3-D digital histopathology imaging. Histopathology 2007; 50:232-42. [PMID: 17222252 DOI: 10.1111/j.1365-2559.2006.02561.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
AIMS To develop a method for preparing diagnostic-quality, whole-mount serial sections of breast specimens while preserving 3-D conformation. This required supporting the fresh specimen prior to breadloafing and refining the conventional tissue processing method. The overall goal is to use digital images of whole-specimen histopathology to improve the estimation of extent of disease. METHODS AND RESULTS To maintain a 3-D conformation, the specimen is suspended in 3.5% agar at 55 degrees C. The block is sliced at 5-mm intervals. Sectioning is performed after extended fixation in 4% formaldehyde from paraformaldehyde in 0.1 m Millonig's buffer, followed by paraffin processing using a non-routine schedule and extended paraffin infiltration. Whole-mount serial breast sections are produced with features of equal or superior quality to that which can be achieved using conventional methods. The method is compatible with some immunohistochemical stains but requires further optimization for others. CONCLUSIONS The technique is currently suitable for research applications. With the reduction in processing time achievable with microwave-assisted processing, there is the potential for its use as a routine clinical method. This tool may improve the accuracy of margin estimates and identification of multifocality in breast cancer; further evaluation is necessary.
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Affiliation(s)
- G M Clarke
- Imaging Research, Sunnybrook and Women's College Health Sciences Centre, Toronto, Ontario, Canada.
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Mikac KM, Clarke GM. Tracing the geographic origin of the cosmopolitan parthenogenetic insect pest Liposcelis bostrychophila (Psocoptera: Liposcelididae). Bull Entomol Res 2006; 96:523-30. [PMID: 17092363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The randomly amplified polymorphic DNA technique was used to trace the geographic origin of Liposcelis bostrychophila Badonnel populations in Australia from unknown geographic sources internationally. Haplotype (or clonal) diversity was high, with 474 unique haplotypes found from 616 individuals genotyped. Gene diversity estimates (0.10-0.28) and percent polymorphic loci (38.1-88.1%) were moderate to high for most populations. This resulted in genetic distance estimates that ranged from 0.04 to 0.26 and were significantly different for most pairwise population combinations. G ST values for all populations were also moderate (0.04-0.54) and again were significantly different for most pairwise population comparisons. Analysis of molecular variance revealed that the majority of variation was apportioned among individuals within populations regardless of the level at which they were grouped. Gene flow (Nm) was mostly low for all pairwise populations comparisons with an average Nm=1.8. A non-significant negative correlation between genetic distance and geographic distance was found for worldwide populations. In contrast, within Australian populations a significant positive correlation between genetic distance and geographic distance was detected. Genetic relationships explored using unweighted pair group method analysis and non-metric multidimensional scaling indicated a mixed pattern of genetic similarities among all populations. Multiple introductions, from a wide range of international source populations, have obscured the ability to accurately determine the geographic origin of L. bostrychophila in Australia.
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Affiliation(s)
- K M Mikac
- CSIRO Division of Entomology, GPO Box 1700, Acton, 2601 ACT, Australia.
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Clarke GM. "You See but you do Not Observe, Watson". CRIT CARE RESUSC 2005; 7:158. [PMID: 16545036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Affiliation(s)
- G M Clarke
- Intensive Care Unit, Royal Perth Hospital, Perth, WA 6000, Australia
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Abstract
Parent-offspring trios are widely collected for disease gene-mapping studies and are being extensively genotyped as part of the International HapMap Project. With dense maps of markers on trios, the effects of LD and linkage can be separated, allowing estimation of recombination rates in a model-free setting. Here we define a model-free multipoint method on the basis of dense sequence polymorphism data from parent-offspring trios to estimate intermarker recombination rates. We use simulations to show that this method has up to 92% power to detect recombination hotspots of intensity 25 times background over a region of size 10 kb typed at density 1 marker per 2.5 kb and almost 100% power to detect large hotspots of intensity >125 times background over regions of size 10 kb typed with just 1 marker per 5 kb (alpha = 0.05). We found strong agreement at megabase scales between estimates from our method applied to HapMap trio data and estimates from the genetic map. At finer scales, using Centre d'Etude du Polymorphisme Humain (CEPH) pedigree data across a 10-Mb region of chromosome 20, a comparison of population recombination rate estimates obtained from our method with estimates obtained using a coalescent-based approximate-likelihood method implemented in PHASE 2.0 shows detection of the same coldspots and most hotspots: The Spearman rank correlation between the estimates from our method and those from PHASE is 0.58 (p < 2.2(-16)).
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Affiliation(s)
- Geraldine M Clarke
- Wellcome Trust Centre for Human Genetics, Oxford University, Roosevelt Drive, Oxford OX3 7BN, United Kingdom.
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Clarke GM, Yen JL, McKenzie JA. Wings and bristles: character specificity of the asymmetry phenotype in insecticide-resistant strains of Lucilia cuprina. Proc Biol Sci 2000; 267:1815-8. [PMID: 11052530 PMCID: PMC1690755 DOI: 10.1098/rspb.2000.1215] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We investigated the hypothesis that observed higher levels of asymmetry displayed by insecticide-resistance genotypes of Lucilia cuprina are restricted to bristle characters, due to the action of resistance genes in bristle cell development, rather than through the disruption of genomic coadaptation. We compared the level of asymmetry of three bristle characters and three wing characters in non-modified and modified-resistance genotypes. Consistent with previous studies, resistance genotypes displayed greater levels of bristle asymmetry than either susceptible or modified genotypes. However, there were no differences among genotypes for any of the wing characters. To confirm that this result is attributable to the action of the resistance and modifier genes themselves, we also examined the responses of both bristle and wing characters to the more general developmental stress of extreme temperature. Sub-optimal temperature was shown to increase both bristle and wing asymmetry, suggesting that there are no underlying differences between the two character types which could, of themselves, explain the differential response observed in the resistance genotypes.
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Affiliation(s)
- G M Clarke
- Commonwealth Scientific and Industrial Research Organization Entomology, Canberra, ACT, Australia.
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35
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Heath CH, Jaksic A, McKerracher D, Clarke GM. Disseminated Saccharomyces cerevisiae infection following polymicrobial hepatobiliary sepsis. Aust N Z J Med 2000; 30:521-2. [PMID: 10985529 DOI: 10.1111/j.1445-5994.2000.tb02070.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Clarke GM, Higgins TN. Laboratory investigation of hemoglobinopathies and thalassemias: review and update. Clin Chem 2000; 46:1284-90. [PMID: 10926923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
Structural hemoglobin (Hb) variants typically are based on a point mutation in a globin gene that produce a single amino acid substitution in a globin chain. Although most are of limited clinical significance, a few important subtypes have been identified with some frequency. Homozygous Hb C and Hb S (sickle cell disease) produce significant clinical manifestations, whereas Hb E and Hb D homozygotes may be mildly symptomatic. Although heterozygotes for these variants are typically asymptomatic, diagnosis may be important for genetic counseling. Thalassemia, in contrast, results from quantitative reductions in globin chain synthesis. Those with diminished beta-globin chains are termed beta-thalassemias, whereas those with decreased alpha-chain production are called alpha-thalassemias. Severity of clinical manifestations in these disorders relates to the amount of globin chain produced and the stability of residual chains present in excess. The thalassemia minor syndromes are characterized clinically by mild anemia with persistent microcytosis. Thalassemia intermedia (i.e., Hb H disease) is typified by a moderate, variably compensated hemolytic anemia that may present with clinical symptoms during a period of physiologic stress such as infection, pregnancy, or surgery. The thalassemia major syndromes produce severe, life-threatening anemia. alpha-Thalassemia major usually is incompatible with extrauterine life; beta-thalassemia major presents in infancy and requires life-long transfusion therapy and/or bone marrow transplantation for successful control of the disease. Double heterozygosity for certain structural variants and/or thalassemia syndromes may also lead to severe clinical disease. Several guidelines have been published that outline the required steps for hemoglobinopathy and thalassemia investigation. The availability of HPLC has streamlined many of these requirements, allowing an efficient stepwise diagnostic strategy for these complex disorders.
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Affiliation(s)
- G M Clarke
- Dynacare Kasper Medical Laboratories, 14940 123rd Ave., Edmonton, Alberta T5V 1B4, Canada
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Affiliation(s)
- H L Berendt
- Dynacare Kasper Medical Laboratories, 14940-123 Avenue, Edmonton, Alberta, Canada
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Clarke GM. Pulmonary artery catheter versus new technology. CRIT CARE RESUSC 2000; 2:103-4. [PMID: 16597292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
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Schneider M, Valentine S, Clarke GM, Newman MA, Peacock J. Acute renal failure in cardiac surgical patients, potentiated by gentamicin and calcium. Anaesth Intensive Care 1996; 24:647-50. [PMID: 8971310 DOI: 10.1177/0310057x9602400602] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
A retrospective study in coronary artery bypass graft patients was undertaken to assess the effect of gentamicin and a bypass prime with a high calcium on the incidence of renal failure. Patients who received both Haemaccel (polygeline, Hoechst Marion Roussel) (calcium concentration 6.25 mmol/l) in the bypass prime and gentamicin perioperatively had a higher incidence of renal failure compared with those who received only Haemaccel (P = 0.005), only gentamicin (P = 0.002) or neither (P = 0.0001). We suggest that the combination be avoided in this group of patients.
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Affiliation(s)
- M Schneider
- Department of Anaesthesia, Royal Perth Hospital, W.A
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Leslie GD, Jacobs IG, Clarke GM. Proximally delivered dilute heparin does not improve circuit life in continuous venovenous haemodiafiltration. Intensive Care Med 1996; 22:1261-4. [PMID: 9120123 DOI: 10.1007/bf01709346] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE To assess the effect on circuit life in continuous venovenous haemodiafiltration (CVVHD) by manipulating heparin dilution and point of administration. DESIGN Repeated crossover design. Cases were randomised for first circuit and heparin dilution, after which crossovers occurred until treatment was stopped. SETTING A 24-bed combined general and surgical intensive care unit admitting 1900 patients a year. On average, 54 cases a year receive CVVHD. PATIENTS 26 critically ill adult patients requiring CVVHD were enrolled, 18 of whom used at least one standard circuit and one modified circuit. INTERVENTIONS Two circuit configurations and heparin dilutions were compared. In combination A, standard CVVHD blood lines and heparin concentration (100 units/ml) were used. In combination B, heparin was delivered in a more dilute volume (10 units/ml) via a modified circuit design with an administration port immediately adjacent to the venous access. MEASUREMENTS AND RESULTS 18 randomised crossovers of circuits A and B occurred. Mean/median circuit life for the standard heparin/circuit combination A was 20.1/17.5 (SD 14.6) and for the modified combination B 21.4/15.4 (SD 19.2). There was no significant difference between circuits (paired t-test, p = 0.8175). To identify other factors which could have influenced circuit life (platelet count, heparin dose and pre- and post-filter activated partial thromboplastin time, APTT) all circuits terminated for the reasons identified (n = 105) were analysed using linear modelling. Survival analysis was used to determine the survival function of the circuit. Pre-heparin APTT was the only factor associated with an increase in filter life (p = 0.035). The hazard rate for filter failure was 0.049/h (95% confidence interval 0.04 to 0.06), the range of time until filters failed was 1.8 to 78.5 h. CONCLUSIONS Proximally administered dilute heparin is not associated with a significant increase in circuit life.
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Affiliation(s)
- G D Leslie
- Critical Care Division, Royal Perth Hospital, Western Australia
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Clarke GM. Specialist training and examinations in anaesthesia and intensive care in Australia and New Zealand. Ann Acad Med Singap 1994; 23:149. [PMID: 7710227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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Harrison GA, Clarke GM. The Training/Examination Programme in Intensive Care, Australian and New Zealand College of Anaesthetists: 2. Examination. Anaesth Intensive Care 1993; 21:854-60. [PMID: 8122747 DOI: 10.1177/0310057x9302100619] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The structure of the Final Examination in Intensive Care for the award of Diploma of Fellow of the Australian and New Zealand College of Anaesthetists is based on a model explicated in the College's Objectives of Training in Intensive Care. There are five sections in the examination: short answer questions, essay questions, investigations, orals and a clinical. The first examination was held in October 1979. Up to and including the examination of October 1992, 94 of the 136 attempts by 107 candidates had been successful. Eighty-three per cent of the candidates passed at the first attempt. The failure rate has been highest in the clinical section. The examination is regarded as a hard examination but one which is helpful in training and subsequent practice.
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Affiliation(s)
- G A Harrison
- Cardiothoracic Critical Care Unit, St Vincent's Hospital, Sydney, N.S.W
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Clarke GM, Harrison GA. The Training/Examination Programme in Intensive Care, Australian and New Zealand College of Anaesthetists. 1. Training. Anaesth Intensive Care 1993; 21:848-53. [PMID: 8122746 DOI: 10.1177/0310057x9302100618] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Unlike training for programmes in other countries which have published details of training programmes for Intensive Care Medicine, the training programme of the Australian and New Zealand College of Anaesthetists does not require certification in a primary specialty, although it is possible to combine training in Intensive Care and Anaesthetics. The lynchpin of the programme is the requirement that training can be undertaken in recognised posts in intensive care units which are approved by the College. Approval of the Unit requires evidence of appropriate supervision and teaching of trainees, sufficient number of admissions with a casemix suitable for the trainees' learning needs and an adequate level of staff and equipment. The Units are assessed by physical inspection by assessors appointed by the College. The programme includes a Final Examination in Intensive Care.
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Affiliation(s)
- G M Clarke
- Intensive Care Unit, Royal Perth Hospital, W.A
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Watkins DN, Jenkins IR, Rankin JM, Clarke GM. Inhaled nitric oxide in severe acute respiratory failure--its use in intensive care and description of a delivery system. Anaesth Intensive Care 1993; 21:861-6. [PMID: 7993404 DOI: 10.1177/0310057x9302100620] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- D N Watkins
- Intensive Care Unit, Royal Perth Hospital, Western Australia
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Clarke GM. Fluctuating asymmetry of invertebrate populations as a biological indicator of environmental quality. Environ Pollut 1993; 82:207-211. [PMID: 15091791 DOI: 10.1016/0269-7491(93)90119-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/1992] [Accepted: 08/19/1992] [Indexed: 05/24/2023]
Abstract
Fluctuating asymmetry (FA) of populations of the shrimp, Palaemon elegans, and the blood worm, Chironomus salinarius, was used to assess the environmental impact of a fertilizer manufacturing facility on the surrounding marine and freshwater ecosystems, respectively. Populations of both species were found to have elevated levels of asymmetry compared with control populations, indicating that the facility was having a significant impact on organism development. The use of FA of invertebrate populations as a simple, sensitive and cost-effective biomonitoring system for the detection of environmental stress is discussed.
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Affiliation(s)
- G M Clarke
- CSIRO Division of Entomology, GPO Box 1700, Canberra, ACT 2601, Australia
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Donovan KD, Dobb GJ, Coombs LJ, Lee KY, Weekes JN, Murdock CJ, Clarke GM. Efficacy of flecainide for the reversion of acute onset atrial fibrillation. Am J Cardiol 1992; 70:50A-54A; discussion 54A-55A. [PMID: 1509999 DOI: 10.1016/0002-9149(92)91078-i] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The efficacy and safety of intravenous flecainide to convert recent-onset atrial fibrillation (AF) (present for greater than or equal to 30 minutes and less than or equal to 72 hours and a ventricular response greater than or equal to 120 beats/min) was investigated. A total of 102 patients without severe heart or circulatory failure were randomized to receive either intravenous flecainide (2 mg/kg, maximum dose 150 mg; 51 patients) or placebo (51 patients) in a double-blind trial. Digoxin (500 micrograms intravenously) was administered to all patients who had not previously been receiving digoxin. The electrocardiogram was monitored continuously during the study. In 29 (57%) patients stable sinus rhythm was restored within 1 hour after flecainide and in only 7 (14%) given placebo (chi square 18.9; p = 0.000013; odds ratio 8.3; 95% confidence interval 2.9-24.8). Reversion to sinus rhythm within 1 hour after starting the trial medication was considered a pretrial end point and likely to be due to a drug effect. At the end of the 6-hour monitoring period, 34 patients (67%) in the flecainide group were in sinus rhythm whereas only 18 (35%) in the placebo group had reverted (chi square 8.83, p = 0.003; odds ratio 3.67; 95% confidence interval 1.5-9.1). Significant hypotension, although short lived, was more common in the flecainide group. One patient given flecainide developed torsades de pointes and was successfully electrically cardioverted. Flecainide is useful for the management of recent-onset AF both for control of the ventricular response and conversion to sinus rhythm.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- K D Donovan
- Intensive Care Unit, Royal Perth Hospital, Western Australia
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Foster GG, Weller GL, Clarke GM. Male crossing over and genetic sexing systems in the Australian sheep blowfly Lucilia cuprina. Heredity (Edinb) 1991; 67 ( Pt 3):365-71. [PMID: 1774192 DOI: 10.1038/hdy.1991.100] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Field-female killing (FK) systems based on deleterious mutations and Y-autosome translocations are being evaluated for genetic control of the Australian sheep blowfly, Lucilia cuprina. Experience during field trials has shown that mass-reared colonies of FK strains are subject to genetic deterioration, caused mainly by genetic recombination in males. A previous study found higher male recombination frequencies in two Y-linked translocation strains than in chromosomally normal males. However, the results of the present study indicate that breakage of the Y chromosome is neither sufficient nor necessary for increased levels of male recombination. The frequency of male recombination appears to be unrelated to the presence of specific chromosome rearrangements.
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Affiliation(s)
- G G Foster
- CSIRO Division of Entomology, Canberra, Australia
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Clarke GM. Testing of an electrocutor trap for screw-worm fly Chrysomya bezziana. Aust Vet J 1991; 68:276-7. [PMID: 1953552 DOI: 10.1111/j.1751-0813.1991.tb03242.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- G M Clarke
- DPIE/CSIRO Screw-worm Fly Unit, Boroko, Papua New Guinea
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Affiliation(s)
- G M Clarke
- DPIE/CSIRO Screw-Worm Fly Unit, Boroko, Papua New Guinea
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Abstract
Spontaneous reversion to sinus rhythm is a frequent occurrence in recent-onset atrial fibrillation (AF). In a randomized, double-blind, controlled study, intravenous flecainide (2 mg/kg, maximum dose 150 mg) was compared with placebo in the treatment of recent-onset AF (present for greater than or equal to 30 minutes and less than or equal to 72 hours' duration and a ventricular response greater than or equal to 120 beats/min). Intravenous digoxin (500 micrograms) was administered concurrently to all patients in both groups who had not previously taken digoxin. The trial medication was administered over 30 minutes. Exclusion criteria included hemodynamic instability, severe heart failure, recent antiarrhythmic therapy, hypokalemia and pacemaker dependence. One hundred two consecutive patients with recent-onset AF were enrolled in the study. All patients underwent continuous electrocardiographic monitoring in the intensive care or coronary care unit. Twenty-nine (57%) patients given flecainide and digoxin, but only 7 (14%) given placebo and digoxin, reverted to sinus rhythm in less than or equal to 1 hour after starting the trial medication infusion and remained in stable sinus rhythm (chi-square 18.9, p = 0.000013; odds ratio 8.3, 95% confidence interval 2.9 to 24.8). At the end of the 6-hour monitoring period, 34 patients (67%) in the flecainide-digoxin group were in stable sinus rhythm, whereas only 18 patients (35%) in the placebo-digoxin group had reverted (chi-square 8.83, p = 0.003; odds ratio 3.67, 95% confidence interval 1.5 to 9.1).(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- K D Donovan
- Intensive Care Unit, Royal Perth Hospital, Western Australia
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