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Pascart T, Wasik KA, Preda C, Chune V, Torterat J, Prud'homme N, Nassih M, Martin A, Le Masson J, Rodière V, Frogier S, Canova G, Pescheux JP, Shan Sei Fan C, Jauffret C, Claeys P, von Baeyer SL, Castel SE, Emde AK, Yerges-Armstrong L, Fox K, Leask M, Vitagliano JJ, Graf S, Norberciak L, Raynal J, Dalbeth N, Merriman T, Bardin T, Oehler E. The gout epidemic in French Polynesia: a modelling study of data from the Ma'i u'u epidemiological survey. Lancet Glob Health 2024; 12:e685-e696. [PMID: 38485432 DOI: 10.1016/s2214-109x(24)00012-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 12/22/2023] [Accepted: 01/09/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND Gout is the most common cause of inflammatory arthritis worldwide, particularly in Pacific regions. We aimed to establish the prevalence of gout and hyperuricaemia in French Polynesia, their associations with dietary habits, their comorbidities, the prevalence of the HLA-B*58:01 allele, and current management of the disease. METHODS The Ma'i u'u survey was epidemiological, prospective, cross-sectional, and gout-focused and included a random sample of adults from the general adult population of French Polynesia. It was conducted and data were collected between April 13 and Aug 16, 2021. Participants were randomly selected to represent the general adult population of French Polynesia on the basis of housing data collected during the 2017 territorial census. Each selected household was visited by a research nurse from the Ma'i u'u survey who collected data via guided, 1-h interviews with participants. In each household, the participant was the individual older than 18 years with the closest upcoming birthday. To estimate the frequency of HLA-B*58:01, we estimated HLA-B haplotypes on individuals who had whole-genome sequencing to approximately 5× average coverage (mid-pass sequencing). A subset of individuals who self-reported Polynesian ancestry and not European, Chinese, or other ancestry were used to estimate Polynesian-ancestry specific allele frequencies. Bivariate associations were reported for weighted participants; effect sizes were estimated through the odds ratio (OR) of the association calculated on the basis of a logistic model fitted with weighted observations. FINDINGS Among the random sample of 2000 households, 896 participants were included, 140 individuals declined, and 964 households could not be contacted. 22 participants could not be weighted due to missing data, so the final weighted analysis included 874 participants (449 [51·4%] were female and 425 [48·6%] were male) representing the 196 630 adults living in French Polynesia. The estimated prevalence of gout was 14·5% (95% CI 9·9-19·2), representing 28 561 French Polynesian adults, that is 25·5% (18·2-32·8) of male individuals and 3·5% (1·0-6·0) of female individuals. The prevalence of hyperuricaemia was estimated at 71·6% (66·7-76·6), representing 128 687 French Polynesian adults. In multivariable analysis, age (OR 1·5, 95% CI 1·2-1·8 per year), male sex (10·3, 1·8-60·7), serum urate (1·6, 1·3-2·0 per 1 mg/dL), uraturia (0·8, 0·8-0·8 per 100 mg/L), type 2 diabetes (2·1, 1·4-3·1), BMI more than 30 kg/m2 (1·1, 1·0-1·2 per unit), and percentage of visceral fat (1·7, 1·1-2·7 per 1% increase) were associated with gout. There were seven heterozygous HLA-B*58:01 carriers in the full cohort of 833 individuals (seven [0·4%] of 1666 total alleles) and two heterozygous carriers in a subset of 696 individuals of Polynesian ancestry (two [0·1%]). INTERPRETATION French Polynesia has an estimated high prevalence of gout and hyperuricaemia, with gout affecting almost 15% of adults. Territorial measures that focus on increasing access to effective urate-lowering therapies are warranted to control this major public health problem. FUNDING Variant Bio, the French Polynesian Health Administration, Lille Catholic University Hospitals, French Society of Rheumatology, and Novartis.
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LeBaron von Baeyer S, Crocker R, Rakotoarivony R, Ranaivoarisoa JF, Spiral GJ, Castel S, Farnum A, Vance H, Collins N, Fox K, Wasik K. Why community consultation matters in genomic research benefit-sharing models. Genome Res 2024; 34:1-6. [PMID: 38296591 PMCID: PMC10904008 DOI: 10.1101/gr.278308.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 01/08/2024] [Indexed: 02/09/2024]
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Radhoe SP, Boersma E, Bertrand M, Remme W, Ferrari R, Fox K, MacMahon S, Chalmers J, Simoons ML, Brugts JJ. The Effects of a Perindopril-Based Regimen in Relation to Statin Use on the Outcomes of Patients with Vascular Disease: a Combined Analysis of the ADVANCE, EUROPA, and PROGRESS Trials. Cardiovasc Drugs Ther 2024; 38:131-139. [PMID: 36194352 PMCID: PMC10876738 DOI: 10.1007/s10557-022-07384-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/12/2022] [Indexed: 11/30/2022]
Abstract
PURPOSE To study the effects of a perindopril-based regimen on cardiovascular (CV) outcomes in patients with vascular disease in relation to background statin therapy. METHODS A pooled analysis of the randomized ADVANCE, EUROPA, and PROGRESS trials was performed to evaluate CV outcomes in 29,463 patients with vascular disease treated with perindopril-based regimens versus placebo. The primary endpoint was a composite of CV mortality, nonfatal myocardial infarction, and stroke. Multivariable Cox regression analyses were performed to assess the effects of a perindopril-based regimen versus placebo in relation to statin use. RESULTS At randomization, 39.5% of the overall combined study population used statins. After a mean follow-up of 4.0 years (SD 1.0), the cumulative event-free survival was highest in the statin/perindopril group and lowest in the no statin/placebo group (91.2% vs. 85.6%, respectively, log-rank p < 0.001). In statin users (adjusted hazard ratio [aHR] 0.87, 95% confidence interval [CI] 0.77-0.98) and non-statin users (aHR 0.80, 95% CI 0.74-0.87), a perindopril-based regimen was associated with a significantly lower risk of the primary endpoint when compared to placebo. The additional treatment effect appeared numerically greater in non-statin users, but the observed difference was statistically nonsignificant. CONCLUSION Our data suggest that the treatment benefits of a perindopril-based regimen in patients with vascular disease are independent of statin use.
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De La Vega FM, Barnes KC, Fox K, Ioannidis A, Kenny E, Mathias RA, Pasaniuc B. Session Introduction: Overcoming health disparities in precision medicine. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2024; 29:322-326. [PMID: 38160289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
The following sections are included:OverviewDealing with the lack of diversity in current research datasetsDevelopment of fair machine learning algorithmsRace, genetic ancestry, and population structureConclusionAcknowledgments.
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Lancaster JJ, Grijalva A, Fink J, Ref J, Daugherty S, Whitman S, Fox K, Gorman G, Lancaster LD, Avery R, Acharya T, McArthur A, Strom J, Pierce MK, Moukabary T, Borgstrom M, Benson D, Mangiola M, Pandey AC, Zile MR, Bradshaw A, Koevary JW, Goldman S. Biologically derived epicardial patch induces macrophage mediated pathophysiologic repair in chronically infarcted swine hearts. Commun Biol 2023; 6:1203. [PMID: 38007534 PMCID: PMC10676365 DOI: 10.1038/s42003-023-05564-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 11/09/2023] [Indexed: 11/27/2023] Open
Abstract
There are nearly 65 million people with chronic heart failure (CHF) globally, with no treatment directed at the pathologic cause of the disease, the loss of functioning cardiomyocytes. We have an allogeneic cardiac patch comprised of cardiomyocytes and human fibroblasts on a bioresorbable matrix. This patch increases blood flow to the damaged heart and improves left ventricular (LV) function in an immune competent rat model of ischemic CHF. After 6 months of treatment in an immune competent Yucatan mini swine ischemic CHF model, this patch restores LV contractility without constrictive physiology, partially reversing maladaptive LV and right ventricular remodeling, increases exercise tolerance, without inducing any cardiac arrhythmias or a change in myocardial oxygen consumption. Digital spatial profiling in mice with patch placement 3 weeks after a myocardial infarction shows that the patch induces a CD45pos immune cell response that results in an infiltration of dendritic cells and macrophages with high expression of macrophages polarization to the anti-inflammatory reparative M2 phenotype. Leveraging the host native immune system allows for the potential use of immunomodulatory therapies for treatment of chronic inflammatory diseases not limited to ischemic CHF.
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Handsley-Davis M, Anderson MZ, Bader AC, Ehau-Taumaunu H, Fox K, Kowal E, Weyrich LS. Microbiome ownership for Indigenous peoples. Nat Microbiol 2023; 8:1777-1786. [PMID: 37770744 DOI: 10.1038/s41564-023-01470-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 08/11/2023] [Indexed: 09/30/2023]
Abstract
Several studies have reported increased microbial diversity, or distinct microbial community compositions, in the microbiomes of Indigenous peoples around the world. However, there is a widespread failure to include Indigenous cultures and perspectives in microbiome research programmes, and ethical issues pertaining to microbiome research involving Indigenous participants have not received enough attention. We discuss the benefits and risks arising from microbiome research involving Indigenous peoples and analyse microbiome ownership as an ethical concept in this context. We argue that microbiome ownership represents an opportunity for Indigenous peoples to steward and protect their resident microbial communities at every stage of research.
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Fox K. Hawai'i, from ashes to sustainability. Science 2023; 381:815. [PMID: 37616353 DOI: 10.1126/science.adk4197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Driven by fierce winds and dry, hot conditions, the fire that consumed Maui's Lahaina-the deadliest US fire in more than a century-is a sad, stark reminder of the environmental pressures on the Hawaiian islands caused by overdevelopment and industrial tourism. As Maui emerges from the ashes, there is an opportunity to reimagine the governance of habitats through sustainable and equitable processes that preserve Hawai'i's natural beauty, with a less destructive, green economy that centers on ecotourism and Indigenous environmental management.
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Lasisi T, Claw KG, Fox K, Zaidi AA. Editorial: The ethics and challenges of studying the genetics of marginalized populations. Front Genet 2023; 14:1260457. [PMID: 37674477 PMCID: PMC10478705 DOI: 10.3389/fgene.2023.1260457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Accepted: 07/24/2023] [Indexed: 09/08/2023] Open
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Cowell K, Pang TY, Kwok JS, McCrowe C, Langenberg F, Easton D, Williams C, Davis SM, Donnan GA, De Aizpurua H, Balabanski A, Dos Santos A, Fox K. Can We Miniaturize CT Technology for a Successful Mobile Stroke Unit Roll-Out? ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2023; 2023:1-5. [PMID: 38083304 DOI: 10.1109/embc40787.2023.10340965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2023]
Abstract
Mortality from stroke remains high in Australia, especially for patients located outside the metropolitan cities. This is because they have limited access to specialized stroke facilities for optimal stroke treatment. Mobile stroke units have the capability to take CT scanners out to the patient however current CT commercial scanner designs are large and heavy. As such, this paper aims to design and develop a lightweight CT scanner for use in a mobile stroke unit (either road-based or air-based ambulance) to bring healthcare solution to patients in the rural and remote areas. We used the engineering design optimization approach to redesign and reduce the weight of the existing CT scanner with without compromised it structural performance. We managed to reduce the weight the CT scanner by three-fold while reducing design costs by allowing numerous simulations to be performed using computer software to achieve our design goals. The results are not only useful to optimize CT scanner structure to retrofit on a mobile stroke unit, but also bring the medical device solution to the market and support scalable solution to the larger community. Such an advance will allow for improved equity in healthcare whereby patients can be treated irrespective of location.
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Fernández Silva B, Jackson M, Fox K, Wynne BP. Tool for automatic macrozone characterization from EBSD data sets of titanium alloys. J Appl Crystallogr 2023; 56:737-749. [PMID: 37284269 PMCID: PMC10241041 DOI: 10.1107/s1600576723003862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 05/01/2023] [Indexed: 06/08/2023] Open
Abstract
Microtexture heterogeneities are commonly found in titanium forgings because of the thermomechanical processing. Also known as macrozones, these regions can reach millimetres in length, with grains sharing a similar crystallographic orientation leading to less resistance to crack propagation. Since the link between macrozones and the reduction of cold-dwell-fatigue performance on rotative components in gas turbine engines was established, efforts have been put into macrozone definition and characterization. The electron backscatter diffraction (EBSD) technique, widely used for texture analysis, allows for a qualitative macrozone characterization; however, further processing is required to define the boundaries and disorientation spread of each macrozone. Current approaches often use c-axis misorientation criteria, but this can sometimes lead to a large disorientation spread within a macrozone. This article describes the development and application of a computational tool implemented in MATLAB for automatic macrozone identification from EBSD data sets on the basis of a more conservative approach where both the c-axis tilting and rotation are considered. The tool allows for detection of macrozones according to the disorientation angle and density-fraction criteria. The clustering efficiency is validated by pole-figure plots, and the effects of the key parameters defining the macrozone clustering (disorientation and fraction) are discussed. In addition, this tool was successfully applied to both fully equiaxed and bimodal microstructures of titanium forgings.
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Boscarino N, Cartwright RA, Fox K, Tsosie KS. Federated learning and Indigenous genomic data sovereignty. NAT MACH INTELL 2022; 4:909-911. [PMID: 36504698 PMCID: PMC9731328 DOI: 10.1038/s42256-022-00551-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Indigenous peoples are under-represented in genomic datasets, which can lead to limited accuracy and utility of machine learning models in precision health. While open data sharing undermines rights of Indigenous communities to govern data decisions, federated learning may facilitate secure and community-consented data sharing.
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Pareek M, Bhatt DL, Zheng L, Lee JJ, Leiter LA, Simon T, Mehta SR, Harrington RA, Fox K, Himmelmann A, Vidal-Petiot E, Steg PG. Blood pressure and clinical outcomes in patients with diabetes and stable coronary artery disease in THEMIS. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.1226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
Various BP characteristics, e.g., systolic blood pressure (SBP), diastolic blood pressure (DBP), and pulse pressure (PP), as well as heart rate (HR) may affect the risk of both cardiovascular events and bleeding events. However, the exact way in which these characteristics and outcomes are associated among patients with diabetes and stable coronary artery disease (CAD) remains debated. Moreover, it is unknown whether the risks and benefits of intensified antiplatelet therapy in this patient population are affected by their baseline BP and HR.
Purpose
To assess the relationship between BP components (including HR) and cardiovascular and bleeding events, and to determine if the effects of ticagrelor vs. placebo varied across the BP and HR spectrum, in patients with diabetes and stable CAD.
Methods
THEMIS was a randomized, controlled trial in which 19,220 individuals ≥50 years of age with stable CAD and type 2 diabetes were randomized to receive either ticagrelor plus aspirin or placebo plus aspirin. Patients with a prior myocardial infarction or stroke, or already on dual antiplatelet therapy, were excluded. The primary efficacy outcome was a composite of cardiovascular death, myocardial infarction, or stroke. The primary safety outcome was TIMI major bleeding. We examined prognostic implications of BP components using 1) restricted cubic splines for the overall trends with outcomes; 2) Cox proportional-hazards regression models with predefined BP component intervals adjusted for demographic, clinical, and laboratory variables; and 3) Cox regression models for the effects of ticagrelor vs. placebo on outcomes across the spectrum of BP component values (test for interaction). THEMIS is registered at ClinicalTrials.gov (NCT01991795).
Results
Mean values of baseline BP components were similar between the two study groups. Median follow-up duration was 39.9 months (range 0–57), with 1554 primary efficacy events and 306 primary safety events occurring over the course of the study. All BP components (including HR) displayed various, independent relationships with the tested outcomes. For example, in adjusted spline models, SBP displayed non-linear relationships with the primary outcome, all-cause death, any bleeding, serious adverse events, and intracranial bleeding, and linear relationships with the remaining outcomes. Figure 1 shows the associations of each BP component with the primary efficacy outcome. BP components did not substantially modify the risks and benefits of ticagrelor vs. placebo for the tested outcomes.
Conclusions
BP components were independently associated with efficacy and safety outcomes in patients with stable CAD and type 2 diabetes. However, no important modification of BP components on the effect of ticagrelor vs. placebo was detected.
Funding Acknowledgement
Type of funding sources: Private company. Main funding source(s): AstraZeneca
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Barrowcliff A, Khan M, Fox K, Khatib R. Management of statin intolerance in a pharmacy led cardiology innovative medicines optimisation lipid clinic. Eur Heart J 2022. [DOI: 10.1093/eurheartj/ehac544.2759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Abstract
Background
Statins are cornerstone in the management of atherosclerotic cardiovascular disease. If a patient has experienced clinically significant adverse drug reactions (ADRs), representing an unacceptable risk or may result in adherence issues, we would consider them intolerant. The prevalence is lower in randomised trials than cohort observational studies, 5% vs. 17%.
Purpose
To assess how many people we reviewed in clinic were able to be re-challenged and successfully continued on a statin, free from side effects.
Methods
Over 6 months we reviewed all patients referred to our innovative clinic for lipid optimisation labelled as “statin intolerant”. Initially, as per our protocol, we adopted a person-centred approach and explored this label (actual vs. potential concerns, any previous issues, symptoms experienced and timings, statins tried (if any), and patient's feelings on re-challenge). A statin re-challenge was offered if not contraindicated. If agreed, based on shared-decision making, we offered patients a once weekly statin (usually rosuvastatin 5mg) with a clear self-management plan to up/down-titrate frequency and dose, until they identify a tolerated regimen. We measured LDL-C at baseline and every 3 months thereafter until satisfactory.
Results
Of 207 patients referred 152 (73%) were labelled as “statin intolerant”. Average age was 62 (±11), 51% females. 78% for secondary prevention and 37% had familial hypercholesterolaemia. The average baseline LDL-C was 4.4mmol/L. 108 (71%) qualified for PCSK9 inhibitors therapy (PCSK9i) as per UK NICE guidance.
The top 3 reported ADRs were musculoskeletal side effects (48%), GI upsets (13%) and deranged LFTs (7%).
25 (58%) of those “intolerant” who did not qualify for PCSK9i attempted a re-challenge with statins vs. 44 (41%) among those who qualified.
Of the 69 patients, who accepted a re-challenge, 43 (62%) were successfully restarted on a statin. At an average of 14 months post re-challenge, LDL-C (available for >80% of the sample) was reduced by an average of 31% in those not on PCSK9i, compared to a 62% reduction (sustained over an average of 40 months) in those on combination therapy with PCSK9i.
The top 3 rosuvastatin regimens established were 5mg OD (29%), 5mg weekly (24%) and 10mg OD (15%). Approximately 80% of patients were on rosuvastatin, and the rest accepted atorvastatin, pravastatin or simvastatin.
There was no attempt to re-challenge in 77 (51%) patients, mostly due to choice (45%) or statins re-challenged prior to referral (44%). We stopped statins in 6 cases due to intolerable ADRs.
Conclusion(s)
By using a person-centred approach, and a variety of strategies to tackle “statin intolerance” we have successfully re-established over 60% of patients with very high CVD risk on statins. While patients who qualified for PCSK9i therapy were less likely to consider re-challenge with statins (41% v 58%), combination lipid-lowering therapies produced better reduction in LDL-C.
Funding Acknowledgement
Type of funding sources: None.
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Reyburn R, Tuivaga E, Ratu F, Dunne E, Nand D, Kado J, Jenkins K, Tikoduadua L, Jenney A, Howden B, Ballard S, Fox K, Devi R, Satzke C, Rafai E, Kama M, Flasche S, Mulholland E, Russell F. The impact of 10-valent pneumococcal vaccine introduction on invasive disease in Fiji. THE LANCET REGIONAL HEALTH. WESTERN PACIFIC 2022; 20:100352. [PMID: 35028629 PMCID: PMC8741523 DOI: 10.1016/j.lanwpc.2021.100352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
BACKGROUND In 2012, Fiji introduced the 10-valent pneumococcal conjugate vaccine (PCV10). We assessed the impact of PCV10 on invasive pneumococcal disease (IPD), probable bacterial or pneumococcal meningitis (PBPM), meningitis and sepsis 3-5 years post-introduction. METHODS Laboratory-confirmed IPD and PBPM cases were extracted from national laboratory records. ICD-10-AM coded all-cause meningitis and sepsis cases were extracted from national hospitalisation records. Incidence rate ratios were used to compare outcomes pre/post-PCV10, stratified by age groups: 1-23m, 2-4y, 5-9y, 10-19y, 20-54y, ≥55y. To account for different detection and serotyping methods in the pre-and post-PCV10 period, a Bayesian inference model estimated serotype-specific changes in IPD, using pneumococcal carriage and surveillance data. FINDINGS There were 423 IPD, 1,029 PBPM, 1,391 all-cause meningitis and 7,611 all-cause sepsis cases. Five years post-PCV10 introduction, IPD declined by 60% (95%CI: 37%, 76%) in children 1-23m months old, and in age groups 2-4y, 5-9y, 10-19y although confidence intervals spanned zero. PBPM declined by 36% (95%CI: 21%, 48%) among children 1-23 months old, and in all other age groups, although some confidence intervals spanned zero. Among children <5y of age, PCV10-type IPD declined by 83% (95%CI; 70%, 90%) and with no evidence of change in non-PCV10-type IPD (9%, 95%CI; -69, 43%). There was no change in all-cause meningitis or sepsis. Post-PCV10, the most common serotypes in vaccine age-eligible and non-age eligible people were serotypes 8 and 23B, and 3 and 7F, respectively. INTERPRETATIONS Our study demonstrates the effectiveness of PCV10 against IPD in a country in the Asia-Pacific of which there is a paucity of data. FUNDING This study was support by the Department of Foreign Affairs and Trade of the Australian Government and Fiji Health Sector Support Program (FHSSP). FHSSP is implemented by Abt JTA on behalf of the Australian Government.
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Claw K, Lippert D, Bardill J, Cordova A, Fox K, Yracheta J, Bader A, Bolnick D, Malhi R, TallBear K, Garrison N. Chaco Canyon Dig Unearths Ethical Concerns. Hum Biol 2022. [DOI: 10.1353/hub.2017.0012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Villanea FA, Huerta-Sanchez E, Fox K. Corrigendum to: ABO Genetic Variation in Neanderthals and Denisovans. Mol Biol Evol 2021; 38:5835. [PMID: 34622284 PMCID: PMC8662607 DOI: 10.1093/molbev/msab261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Emde AK, Phipps-Green A, Cadzow M, Gallagher CS, Major TJ, Merriman ME, Topless RK, Takei R, Dalbeth N, Murphy R, Stamp LK, de Zoysa J, Wilcox PL, Fox K, Wasik KA, Merriman TR, Castel SE. Mid-pass whole genome sequencing enables biomedical genetic studies of diverse populations. BMC Genomics 2021; 22:666. [PMID: 34719381 PMCID: PMC8559369 DOI: 10.1186/s12864-021-07949-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Historically, geneticists have relied on genotyping arrays and imputation to study human genetic variation. However, an underrepresentation of diverse populations has resulted in arrays that poorly capture global genetic variation, and a lack of reference panels. This has contributed to deepening global health disparities. Whole genome sequencing (WGS) better captures genetic variation but remains prohibitively expensive. Thus, we explored WGS at "mid-pass" 1-7x coverage. RESULTS Here, we developed and benchmarked methods for mid-pass sequencing. When applied to a population without an existing genomic reference panel, 4x mid-pass performed consistently well across ethnicities, with high recall (98%) and precision (97.5%). CONCLUSION Compared to array data imputed into 1000 Genomes, mid-pass performed better across all metrics and identified novel population-specific variants with potential disease relevance. We hope our work will reduce financial barriers for geneticists from underrepresented populations to characterize their genomes prior to biomedical genetic applications.
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Graham C, Tan M, Chew D, Gale C, Fox K, Bagai A, Henderson M, Quraishi A, Dery J, Cheema A, Fisher H, Brieger D, Lutchmedial S, Lavi S, Wong B, Cieza T, Mehta S, Goodman S, Yan A. USE AND OUTCOME OF DUAL ANTIPLATELET THERAPY FOR ACUTE CORONARY SYNDROME IN PATIENTS WITH CHRONIC KIDNEY DISEASE: INSIGHTS FROM THE CANADIAN OBSERVATIONAL ANTIPLATELET STUDY (COAPT), A MULTICENTRE PROSPECTIVE COHORT STUDY. Can J Cardiol 2021. [DOI: 10.1016/j.cjca.2021.07.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Ioannidis AG, Blanco-Portillo J, Sandoval K, Hagelberg E, Barberena-Jonas C, Hill AVS, Rodríguez-Rodríguez JE, Fox K, Robson K, Haoa-Cardinali S, Quinto-Cortés CD, Miquel-Poblete JF, Auckland K, Parks T, Sofro ASM, Ávila-Arcos MC, Sockell A, Homburger JR, Eng C, Huntsman S, Burchard EG, Gignoux CR, Verdugo RA, Moraga M, Bustamante CD, Mentzer AJ, Moreno-Estrada A. Paths and timings of the peopling of Polynesia inferred from genomic networks. Nature 2021; 597:522-526. [PMID: 34552258 PMCID: PMC9710236 DOI: 10.1038/s41586-021-03902-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
Polynesia was settled in a series of extraordinary voyages across an ocean spanning one third of the Earth1, but the sequences of islands settled remain unknown and their timings disputed. Currently, several centuries separate the dates suggested by different archaeological surveys2-4. Here, using genome-wide data from merely 430 modern individuals from 21 key Pacific island populations and novel ancestry-specific computational analyses, we unravel the detailed genetic history of this vast, dispersed island network. Our reconstruction of the branching Polynesian migration sequence reveals a serial founder expansion, characterized by directional loss of variants, that originated in Samoa and spread first through the Cook Islands (Rarotonga), then to the Society (Tōtaiete mā) Islands (11th century), the western Austral (Tuha'a Pae) Islands and Tuāmotu Archipelago (12th century), and finally to the widely separated, but genetically connected, megalithic statue-building cultures of the Marquesas (Te Henua 'Enana) Islands in the north, Raivavae in the south, and Easter Island (Rapa Nui), the easternmost of the Polynesian islands, settled in approximately AD 1200 via Mangareva.
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Corroenne R, Yepez M, Pyarali M, Fox K, Mastrobattista JM, Mack LM, Lee W, Whitehead WE, Castillo HA, Castillo J, Mehollin-Ray AR, Espinoza J, Shamshirsaz AA, Nassr AA, Belfort MA, Sanz Cortes M. Longitudinal evaluation of motor function in patients who underwent prenatal or postnatal neural tube defect repair. ULTRASOUND IN OBSTETRICS & GYNECOLOGY : THE OFFICIAL JOURNAL OF THE INTERNATIONAL SOCIETY OF ULTRASOUND IN OBSTETRICS AND GYNECOLOGY 2021; 58:221-229. [PMID: 32730648 DOI: 10.1002/uog.22165] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 06/10/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
OBJECTIVE To compare the evolution of motor function from mid-gestation to 12 months of age between prenatally and postnatally repaired cases of open neural tube defect (ONTD). METHODS This was a retrospective cohort study of all fetuses that underwent prenatal (fetoscopic or open hysterotomy) or postnatal ONTD repair at a single institution between November 2011 and December 2018. The anatomical level of the lesion was defined as the upper bony spinal defect at initial magnetic resonance imaging assessment. Prenatal motor function of the lower extremities was evaluated by ultrasound according to the metameric level of the neurological lesion, based on the methodology of Carreras et al. Fetal motor function was assessed at referral, at 6 weeks after surgery in prenatally repaired cases or 6 weeks after referral in postnatally repaired cases (6-week follow-up) and at the last scan before delivery. In addition, motor function was assessed by a detailed neurological examination at birth and 12 months of age. First sacral (S1) neurological level of the lesion was considered as intact motor function. For statistical comparisons, we attributed numerical scores to each neurological level and motor function was expressed as median (range) neurological level. Motor function (as numerical score) and the proportion of cases with intact motor function and with motor function two or more levels better than expected based on the anatomical level of the lesion were compared between the prenatal- and postnatal-repair groups. Fetal motor function was compared to the anatomical level of the lesion at referral and a better motor function was defined when it was two or more levels better than the anatomical level of the lesion. To assess the evolution of motor function, we compared motor function at referral with that at each follow-up assessment using paired t-tests. RESULTS We included 127 patients with ONTD, of whom 93 underwent prenatal (51 fetoscopic and 42 open hysterotomy) and 34 postnatal repair. At the time of referral, cases in the prenatal- and postnatal-repair groups presented with a similar anatomical level of lesion (L3 (T9-S1) vs L3 (T7-S1); P = 0.52), similar motor function (S1 (L1-S1) vs S1 (L1-S1); P = 0.52) and a similar proportion of cases with intact motor function (81% vs 79%; P = 0.88) and with motor function two or more levels better than expected based on the anatomical level of the lesion (62% vs 74%; P = 0.24). When compared with prenatally repaired cases, postnatally repaired cases showed worse motor function at birth (S1 (L1-S1) vs L4 (L1-S1); P < 0.01) and at 12 months of age (S1 (L1-S1) vs L4 (L1-S1); P < 0.01). In the prenatal-repair group, motor function remained stable from the time of referral to 12 months of age (P = 0.26). Furthermore, the proportion of patients with intact motor function at referral (81% (75/93)) was similar to that at the 6-week follow-up (74% (64/87)), at the last scan before birth (74% (42/57)), at birth (68% (63/93)) and at 12 months of age (67% (39/58)) in the prenatal-repair group. In the postnatal-repair group, worse motor function, starting from the third trimester to 12 months of age, was observed. The proportion of patients with intact motor function at referral (79% (27/34)) was similar to that at 6-week follow-up (80% (12/15); P = 0.92), but was lower at the last assessment before birth (25% (2/8); P < 0.01), at birth (24% (8/34); P < 0.01) and at 12 months of age (28% (7/25); P < 0.01). Similar findings were noted when assessing the evolution of the proportion of cases with motor function two or more levels better than expected based on the anatomical level of the lesion in each group. CONCLUSIONS Infants with ONTD that underwent postnatal repair had worse motor function at birth and at 12 months of age than at mid-gestation and when compared with infants that underwent prenatal ONTD repair. Prenatal motor function assessment by ultrasound is an adequate tool to identify those infants who should have a good clinical motor function after delivery. Information obtained by fetal motor function assessment can have an important role for patient counseling and case selection for surgery. © 2020 International Society of Ultrasound in Obstetrics and Gynecology.
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Mudd-Martin G, Cirino AL, Barcelona V, Fox K, Hudson M, Sun YV, Taylor JY, Cameron VA. Considerations for Cardiovascular Genetic and Genomic Research With Marginalized Racial and Ethnic Groups and Indigenous Peoples: A Scientific Statement From the American Heart Association. CIRCULATION-GENOMIC AND PRECISION MEDICINE 2021; 14:e000084. [PMID: 34304578 DOI: 10.1161/hcg.0000000000000084] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Historically marginalized racial and ethnic groups and Indigenous peoples are burdened by significant health inequities that are compounded by their underrepresentation in genetic and genomic research. Of all genome-wide association study participants, ≈79% are of European descent, despite this group constituting only 16% of the global population. For underrepresented populations, polygenic risk scores derived from these studies are less accurate in predicting disease phenotypes, novel population-specific genetic variations may be misclassified as potentially pathogenic, and there is a lack of understanding of how different populations metabolize drugs. Although inclusion of marginalized racial and ethnic groups and Indigenous peoples in genetic and genomic research is crucial, scientific studies must be guided by ethical principles of respect, honesty, justice, reciprocity, and care for individuals and communities. Special considerations are needed to support research that benefits the scientific community as well as Indigenous peoples and marginalized groups. Before a project begins, collaboration with community leaders and agencies can lead to successful implementation of the study. Throughout the study, consideration must be given to issues such as implications of informed consent for individuals and communities, dissemination of findings through scientific and community avenues, and implications of community identity for data governance and sharing. Attention to these issues is critical, given historical harms in biomedical research that marginalized groups and Indigenous peoples have suffered. Conducting genetic and genomic research in partnership with Indigenous peoples and marginalized groups guided by ethical principles provides a pathway for scientific advances that will enhance prevention and treatment of cardiovascular disease for everyone.
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Curzen N, Nicholas Z, Stuart B, Wilding S, Hill K, Shambrook J, Eminton Z, Ball D, Barrett C, Johnson L, Nuttall J, Fox K, Connolly D, O'Kane P, Hobson A, Chauhan A, Uren N, Mccann GP, Berry C, Carter J, Roobottom C, Mamas M, Rajani R, Ford I, Douglas P, Hlatky MA. Fractional flow reserve derived from computed tomography coronary angiography in the assessment and management of stable chest pain: the FORECAST randomized trial. Eur Heart J 2021; 42:3844-3852. [PMID: 34269376 PMCID: PMC8648068 DOI: 10.1093/eurheartj/ehab444] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/10/2021] [Accepted: 06/25/2021] [Indexed: 11/25/2022] Open
Abstract
Aims Fractional flow reserve (FFRCT) using computed tomography coronary angiography (CTCA) determines both the presence of coronary artery disease and vessel-specific ischaemia. We tested whether an evaluation strategy based on FFRCT would improve economic and clinical outcomes compared with standard care. Methods and results Overall, 1400 patients with stable chest pain in 11 centres were randomized to initial testing with CTCA with selective FFRCT (experimental group) or standard clinical care pathways (standard group). The primary endpoint was total cardiac costs at 9 months. Secondary endpoints were angina status, quality of life, major adverse cardiac and cerebrovascular events, and use of invasive coronary angiography. Randomized groups were similar at baseline. Most patients had an initial CTCA: 439 (63%) in the standard group vs. 674 (96%) in the experimental group, 254 of whom (38%) underwent FFRCT. Mean total cardiac costs were higher by £114 (+8%) in the experimental group, with a 95% confidence interval from −£112 (−8%) to +£337 (+23%), though the difference was not significant (P = 0.10). Major adverse cardiac and cerebrovascular events did not differ significantly (10.2% in the experimental group vs. 10.6% in the standard group) and angina and quality of life improved to a similar degree over follow-up in both randomized groups. Invasive angiography was reduced significantly in the experimental group (19% vs. 25%, P = 0.01). Conclusion A strategy of CTCA with selective FFRCT in patients with stable angina did not differ significantly from standard clinical care pathways in cost or clinical outcomes, but did reduce the use of invasive coronary angiography.
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Fox K, Fox J, Bexfield N, Freeman P. Computerised decision support in veterinary medicine, exemplified in a canine idiopathic epilepsy care pathway. J Small Anim Pract 2021; 62:911-917. [PMID: 34155645 DOI: 10.1111/jsap.13345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/23/2021] [Accepted: 04/07/2021] [Indexed: 12/01/2022]
Abstract
Computerised decision support is of emerging and increasing importance in human medicine, but as yet has not been thoroughly applied or evaluated in veterinary medicine. In this essay, the authors report on the first example of a veterinary care pathway, a specific form of computerised decision support, which guides clinicians through a clinical workflow and incorporates individual patient data to inform patient-specific decision recommendations. The veterinary care pathway was designed using consensus statements and specialist neurologist opinion to create a decision support tool concerning canine idiopathic epilepsy. The authors evaluated the care pathway by comparing 35 clinical decisions made by referral clinicians in historical cases of idiopathic epilepsy to decisions recommended by the care pathway when presented with the same clinical case. Their results show that in 77.1% (95% confidence interval [59.9, 89.6]) of cases the care pathway recommended a decision that was the same or similar to a specialist neurologist's decision. Whilst further studies are needed to explore the potential use of such technology in clinical practice, the authors believe this first application provides great promise of a new and alternative method of clinical decision support.
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Villanea FA, Huerta-Sanchez E, Fox K. ABO Genetic Variation in Neanderthals and Denisovans. Mol Biol Evol 2021; 38:3373-3382. [PMID: 33892510 PMCID: PMC8321519 DOI: 10.1093/molbev/msab109] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Variation at the ABO locus was one of the earliest sources of data in the study of human population identity and history, and to this day remains widely genotyped due to its importance in blood and tissue transfusions. Here, we look at ABO blood type variants in our archaic relatives: Neanderthals and Denisovans. Our goal is to understand the genetic landscape of the ABO gene in archaic humans, and how it relates to modern human ABO variation. We found two Neanderthal variants of the O allele in the Siberian Neanderthals (O1 and O2), one of these variants is shared with an European Neanderthal, who is a heterozygote for this O1 variant and a rare cis-AB variant. The Denisovan individual is heterozygous for two variants of the O1 allele, functionally similar to variants found widely in modern humans. Perhaps more surprisingly, the O2 allele variant found in Siberian Neanderthals can be found at low frequencies in modern Europeans and Southeast Asians, and the O1 allele variant found in Siberian and European Neanderthal is also found at very low frequency in modern East Asians. Our genetic distance analyses suggest both alleles survive in modern humans due to inbreeding with Neanderthals. We find that the sequence backgrounds of the surviving Neanderthal-like O alleles in modern humans retain a higher sequence divergence than other surviving Neanderthal genome fragments, supporting a view of balancing selection operating in the Neanderthal ABO alleles by retaining highly diverse haplotypes compared with portions of the genome evolving neutrally.
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