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Mortlock S, Lord A, Montgomery G, Zakrzewski M, Simms LA, Krishnaprasad K, Hanigan K, Doecke JD, Walsh A, Lawrance IC, Bampton PA, Andrews JM, Mahy G, Connor SJ, Sparrow MP, Bell S, Florin TH, Begun J, Gearry RB, Radford-Smith GL. An Extremes of Phenotype Approach Confirms Significant Genetic Heterogeneity in Patients with Ulcerative Colitis. J Crohns Colitis 2023; 17:277-288. [PMID: 36111848 PMCID: PMC10024548 DOI: 10.1093/ecco-jcc/jjac121] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND AND AIMS Ulcerative colitis [UC] is a major form of inflammatory bowel disease globally. Phenotypic heterogeneity is defined by several variables including age of onset and disease extent. The genetics of disease severity remains poorly understood. To further investigate this, we performed a genome wide association [GWA] study using an extremes of phenotype strategy. METHODS We conducted GWA analyses in 311 patients with medically refractory UC [MRUC], 287 with non-medically refractory UC [non-MRUC] and 583 controls. Odds ratios [ORs] were calculated for known risk variants comparing MRUC and non-MRUC, and controls. RESULTS MRUC-control analysis had the greatest yield of genome-wide significant single nucleotide polymorphisms [SNPs] [2018], including lead SNP = rs111838972 [OR = 1.82, p = 6.28 × 10-9] near MMEL1 and a locus in the human leukocyte antigen [HLA] region [lead SNP = rs144717024, OR = 12.23, p = 1.7 × 10-19]. ORs for the lead SNPs were significantly higher in MRUC compared to non-MRUC [p < 9.0 × 10-6]. No SNPs reached significance in the non-MRUC-control analysis (top SNP, rs7680780 [OR 2.70, p = 5.56 × 10-8). We replicate findings for rs4151651 in the Complement Factor B [CFB] gene and demonstrate significant changes in CFB gene expression in active UC. Detailed HLA analyses support the strong associations with MHC II genes, particularly HLA-DQA1, HLA-DQB1 and HLA-DRB1 in MRUC. CONCLUSIONS Our MRUC subgroup replicates multiple known UC risk variants in contrast to non-MRUC and demonstrates significant differences in effect sizes compared to those published. Non-MRUC cases demonstrate lower ORs similar to those published. Additional risk and prognostic loci may be identified by targeted recruitment of individuals with severe disease.
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Affiliation(s)
- Sally Mortlock
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Anton Lord
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
- Centre for Health Services Research, University of Queensland, Brisbane, QLD, Australia
| | - Grant Montgomery
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | | | - Lisa A Simms
- QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | | | | | - James D Doecke
- Australian eHealth Research Centre, CSIRO, Brisbane, QLD, Australia
| | - Alissa Walsh
- Department of Gastroenterology, John Radcliffe Hospital, Headington, Oxford, UK
| | - Ian C Lawrance
- Centre of Inflammatory Bowel Diseases, Saint John of God Hospital Subiaco, University of Western Australia, WA, Australia
| | | | - Jane M Andrews
- Department of Gastroenterology and Hepatology, Royal Adelaide Hospital & University of Adelaide, Adelaide, SA, Australia
| | - Gillian Mahy
- Department of Gastroenterology and Hepatology, Townsville University Hospital, Townsville, QLD, Australia
| | - Susan J Connor
- Department of Gastroenterology and Hepatology, Liverpool Hospital, Sydney, NSW, Australia
- South Western Sydney Clinical School, University of New South Wales, Sydney, NSW, Australia
| | - Miles P Sparrow
- Department of Gastroenterology, Alfred Health, Melbourne, VIC, Australia
| | - Sally Bell
- Department of Gastroenterology and Hepatology, Monash Health, Melbourne, VIC, Australia
| | - Timothy H Florin
- Inflammatory Bowel Diseases Group, Translational Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Jakob Begun
- Inflammatory Bowel Diseases Group, Translational Research Institute, Brisbane, QLD, Australia
- Inflammatory Disease Biology and Therapeutics Group, Translational Research Institute, Brisbane, QLD, Australia
- Faculty of Medicine, University of Queensland, Brisbane, QLD, Australia
| | - Richard B Gearry
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Graham L Radford-Smith
- Corresponding author: Graham Radford-Smith, Gut Health Lab, QIMR Berghofer Medical Research Institute, Brisbane, QLD, Australia. Tel: +617 3362 0499; Fax: +617 3009 0053;
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De Gregorio M, Lee T, Krishnaprasad K, Amos G, An YK, Bastian-Jordan M, Begun J, Borok N, Brown DJM, Cheung W, Connor SJ, Gerstenmaier J, Gilbert LE, Gilmore R, Gu B, Kutaiba N, Lee A, Mahy G, Srinivasan A, Thin L, Thompson AJ, Welman CJ, Yong EXZ, De Cruz P, van Langenberg D, Sparrow MP, Ding NS. Higher Anti-tumor Necrosis Factor-α Levels Correlate With Improved Radiologic Outcomes in Crohn's Perianal Fistulas. Clin Gastroenterol Hepatol 2022; 20:1306-1314. [PMID: 34389484 DOI: 10.1016/j.cgh.2021.07.053] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 07/08/2021] [Accepted: 07/28/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Higher anti-tumor necrosis factor-α (TNF) drug levels are associated with improved clinical healing of Crohn's perianal fistulas. It is unclear whether this leads to improved healing on radiologic assessment. We aimed to evaluate the association between anti-TNF drug levels and radiologic outcomes in perianal fistulising Crohn's disease. METHODS A cross-sectional retrospective multicenter study was undertaken. Patients with perianal fistulising Crohn's disease on maintenance infliximab or adalimumab, with drug levels within 6 months of perianal magnetic resonance imaging were included. Patients receiving dose changes or fistula surgery between drug level and imaging were excluded. Radiologic disease activity was scored using the Van Assche Index, with an inflammatory subscore calculated using indices: T2-weighted imaging hyperintensity, collections >3 mm diameter, rectal wall involvement. Primary endpoint was radiologic healing (inflammatory subscore ≤6). Secondary endpoint was radiologic remission (inflammatory subscore = 0). RESULTS Of 193 patients (infliximab, n = 117; adalimumab, n = 76), patients with radiologic healing had higher median drug levels compared with those with active disease (infliximab 6.0 vs 3.9 μg/mL; adalimumab 9.1 vs 6.2 μg/mL; both P < .05). Patients with radiologic remission also had higher median drug levels compared with those with active disease (infliximab 7.4 vs 3.9 μg/mL; P < .05; adalimumab 9.8 vs 6.2 μg/mL; P = .07). There was a significant incremental reduction in median inflammatory subscores with higher anti-TNF drug level tertiles. CONCLUSIONS Higher anti-TNF drug levels were associated with improved radiologic outcomes on magnetic resonance imaging in perianal fistulising Crohn's disease, with an incremental improvement at higher drug level tertiles for both infliximab and adalimumab.
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Affiliation(s)
- Michael De Gregorio
- St Vincent's Hospital Melbourne, Department of Gastroenterology, Fitzroy, Australia; University of Melbourne, Medicine, Parkville, Australia.
| | - Tanya Lee
- St Vincent's Hospital Melbourne, Department of Gastroenterology, Fitzroy, Australia
| | - Krupa Krishnaprasad
- St Vincent's Hospital Melbourne, Department of Gastroenterology, Fitzroy, Australia; QIMR Berghofer Medical Research Institute, Gut Health Lab, Brisbane, Australia
| | - Gregory Amos
- University of Queensland, Medicine, St Lucia, Australia; Queensland X-ray, Medical Imaging, Brisbane, Australia
| | - Yoon-Kyo An
- University of Queensland, Medicine, St Lucia, Australia; Mater Hospital Brisbane, Gastroenterology, South Brisbane, Australia
| | - Matthew Bastian-Jordan
- University of Queensland, Medicine, St Lucia, Australia; Queensland X-ray, Medical Imaging, Brisbane, Australia
| | - Jakob Begun
- Mater Hospital Brisbane, Gastroenterology, South Brisbane, Australia; University of Queensland, Mater Research Institute, St Lucia, Australia
| | - Nira Borok
- Liverpool Hospital, Medical Imaging, Liverpool, Australia; South Western Sydney Local Health District, Medicine, Liverpool, Australia
| | - Dougal J M Brown
- Townsville University Hospital, Medical Imaging, Douglas, Australia
| | - Wa Cheung
- Alfred Health, Medical Imaging, Melbourne, Australia
| | - Susan J Connor
- Liverpool Hospital, Gastroenterology and Hepatology, Liverpool, Australia; Ingham Institute for Applied Medical Research, Medicine, Liverpool, Australia; University of New South Wales, South Western Sydney Clinical School, Sydney, Australia
| | | | | | | | - Bonita Gu
- Liverpool Hospital, Gastroenterology and Hepatology, Liverpool, Australia; University of New South Wales, South Western Sydney Clinical School, Sydney, Australia; Royal Prince Alfred Hospital, Gastroenterology and Hepatology, Camperdown, Australia
| | - Numan Kutaiba
- Austin Health, Radiology, Heidelberg, Australia; Eastern Health, Radiology, Box Hill, Australia
| | - Allan Lee
- Imaging Associates Eastern Health, Medical Imaging, Melbourne, Australia; Peter MacCallum Cancer Centre, Cancer Imaging, Melbourne, Australia
| | - Gillian Mahy
- Townsville University Hospital, Gastroenterology, Douglas, Australia
| | - Ashish Srinivasan
- Austin Health, Gastroenterology, Heidelberg, Australia; Eastern Health, Gastroenterology, Box Hill, Australia; Monash University, Medicine, Clayton, Australia
| | - Lena Thin
- Fiona Stanley Hospital, Gastroenterology, Murdoch, Australia; University of Western Australia, School of Medicine and Pharmacology, Crawley, Australia
| | - Alexander J Thompson
- St Vincent's Hospital Melbourne, Department of Gastroenterology, Fitzroy, Australia; University of Melbourne, Medicine, Parkville, Australia
| | | | - Eric X Z Yong
- St Vincent's Hospital Melbourne, Medical Imaging, Fitzroy, Australia
| | - Peter De Cruz
- University of Melbourne, Medicine, Parkville, Australia; Austin Health, Gastroenterology, Heidelberg, Australia
| | - Daniel van Langenberg
- Eastern Health, Gastroenterology, Box Hill, Australia; Monash University, Medicine, Clayton, Australia
| | - Miles P Sparrow
- Alfred Health, Gastroenterology, Melbourne, Australia; Monash University, Medicine, Clayton, Australia
| | - Nik S Ding
- St Vincent's Hospital Melbourne, Department of Gastroenterology, Fitzroy, Australia; University of Melbourne, Medicine, Parkville, Australia
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3
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de Tombeur F, Turner BL, Laliberté E, Lambers H, Mahy G, Faucon MP, Zemunik G, Cornelis JT. Plants sustain the terrestrial silicon cycle during ecosystem retrogression. Science 2020; 369:1245-1248. [DOI: 10.1126/science.abc0393] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/17/2020] [Indexed: 12/25/2022]
Affiliation(s)
- F. de Tombeur
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, 5030 Gembloux, Belgium
| | - B. L. Turner
- Smithsonian Tropical Research Institute, Balboa, Ancon, Panama
| | - E. Laliberté
- Institut de Recherche en Biologie Végétale, Département de Sciences Biologiques, Université de Montréal, Montréal, QC H1X 2B2, Canada
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - H. Lambers
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - G. Mahy
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, 5030 Gembloux, Belgium
| | | | - G. Zemunik
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia
| | - J.-T. Cornelis
- TERRA Teaching and Research Centre, Gembloux Agro-Bio Tech, University of Liege, 5030 Gembloux, Belgium
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Pulusu SSR, Srinivasan A, Krishnaprasad K, Cheng D, Begun J, Keung C, Van Langenberg D, Thin L, Mogilevski T, De Cruz P, Radford-Smith G, Flanagan E, Bell S, Kashkooli S, Sparrow M, Ghaly S, Bampton P, Sawyer E, Connor S, Rizvi QUA, Andrews JM, Mahy G, Chivers P, Travis S, Lawrance IC. Vedolizumab for ulcerative colitis: Real world outcomes from a multicenter observational cohort of Australia and Oxford. World J Gastroenterol 2020; 26:4428-4441. [PMID: 32874055 PMCID: PMC7438197 DOI: 10.3748/wjg.v26.i30.4428] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 07/18/2020] [Accepted: 07/30/2020] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Vedolizumab (VDZ), a humanised monoclonal antibody that selectively inhibits alpha4-beta7 integrins is approved for use in adult moderate to severe ulcerative colitis (UC) patients.
AIM To assess the efficacy and safety of VDZ in the real-world management of UC in a large multicenter cohort involving two countries and to identify predictors of achieving remission.
METHODS A retrospective review of Australian and Oxford, United Kingdom data for UC patients. Clinical response at 3 mo, endoscopic remission at 6 mo and clinical remission at 3, 6 and 12 mo were assessed. Cox regression models and Kaplan Meier curves were performed to assess the time to remission, time to failure and the covariates influencing them. Safety outcomes were recorded.
RESULTS Three hundred and three UC patients from 14 centres in Australia and United Kingdom, [60% n = 182, anti-TNF naïve] were included. The clinical response was 79% at 3 mo with more Australian patients achieving clinical response compared to Oxford (83% vs 70% P = 0.01). Clinical remission for all patients was 56%, 62% and 60% at 3, 6 and 12 mo respectively. Anti-TNF naive patients were more likely to achieve remission than exposed patients at all the time points (3 mo 66% vs 40% P < 0.001, 6 mo 73% vs 46% P < 0.001, 12 mo 66% vs 51% P = 0.03). More Australian patients achieved endoscopic remission at 6 mo compared to Oxford (69% vs 43% P = 0.01). On multi-variate analysis, anti-TNF naïve patients were 1.8 (95%CI: 1.3-2.3) times more likely to achieve remission than anti-TNF exposed (P < 0.001). 32 patients (11%) had colectomy by 12 mo.
CONCLUSION VDZ was safe and effective with 60% of UC patients achieving clinical remission at 12 mo and prior anti-TNF exposure influenced this outcome.
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Affiliation(s)
- Samba Siva Reddy Pulusu
- Centre for Inflammatory Bowel Diseases, St John of God Hospital, Subiaco 6008, Western Australia, Australia
| | - Ashish Srinivasan
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Krupa Krishnaprasad
- Inflammatory Bowel Disease Research Group, Queensland institute of Medical Research, Herston 4006, Queensland, Australia
| | - Daniel Cheng
- Department of Gastroenterology, Mater Hospital, Brisbane 4101, Queensland, Australia
| | - Jakob Begun
- Department of Gastroenterology, Mater Hospital, South Brisbane 4101, Queensland, Australia
| | - Charlotte Keung
- Department of Gastroenterology, Eastern Health, Box Hill 3128, Victoria, Australia
| | | | - Lena Thin
- Department of Gastroenterology, Fiona Stanley Hospital, Murdoch 6150, Western Australia, Australia
| | - Tamara Mogilevski
- Department of Gastroenterology, Austin Health, Heidelberg 3084, Victoria, Australia
| | - Peter De Cruz
- Department of Gastroenterology, Austin Health, Heidelberg 3084, Victoria, Australia
| | - Graham Radford-Smith
- Department of Gastroenterology, Mater Hospital, South Brisbane 4101, Queensland, Australia
| | - Emma Flanagan
- Department of Gastroenterology, St Vincent’s Hospital, Fitzroy 3065, Victoria, Australia
| | - Sally Bell
- Department of Gastroenterology, St Vincent’s Hospital, Fitzroy 3065, Victoria, Australia
| | - Soleiman Kashkooli
- Department of Gastroenterology, Northern Health, Epping 3076, Victoria, Australia
| | - Miles Sparrow
- Department of Gastroenterology, The Alfred Hospital, Melbourne 3004, Victoria, Australia
| | - Simon Ghaly
- Department of Gastroenterology, St Vincent’s Hospital, Darlinghurst 2010, New South Wales, Australia
| | - Peter Bampton
- Department of Gastroenterology, Flinders Medical Centre, Bedford Park 5042, South Australia, Australia
| | - Elise Sawyer
- Department of Gastroenterology, Liverpool Hospital, Sydney 2170, New South Wales, Australia
| | - Susan Connor
- Department of Gastroenterology, Liverpool Hospital, Sydney 2170, New South Wales, Australia
| | - Quart-ul-ain Rizvi
- Department of Gastroenterology, Royal Adelaide Hospital & University of Adelaide, Adelaide 5000, South Australia, Australia
| | - Jane M Andrews
- Department of Gastroenterology, Royal Adelaide Hospital & University of Adelaide, Adelaide 5000, South Australia, Australia
| | - Gillian Mahy
- Department of Gastroenterology, Townsville Hospital, Douglas 4814, Queensland, Australia
| | - Paola Chivers
- Institute for Health Research, University of Notre Dame, Fremantle 6160, Western Australia, Australia
| | - Simon Travis
- Translational Gastroenterology Unit, NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, John Radcliffe Hospital, Oxford OX3 9DU, United Kingdom
| | - Ian Craig Lawrance
- Centre for Inflammatory Bowel Diseases, St John of God Hospital, Subiaco 6008, Western Australia, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley 6009, Western Australia, Australia
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5
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Chen GB, Lee SH, Montgomery GW, Wray NR, Visscher PM, Gearry RB, Lawrance IC, Andrews JM, Bampton P, Mahy G, Bell S, Walsh A, Connor S, Sparrow M, Bowdler LM, Simms LA, Krishnaprasad K, Radford-Smith GL, Moser G. Performance of risk prediction for inflammatory bowel disease based on genotyping platform and genomic risk score method. BMC Med Genet 2017; 18:94. [PMID: 28851283 PMCID: PMC5576242 DOI: 10.1186/s12881-017-0451-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2016] [Accepted: 08/14/2017] [Indexed: 12/11/2022]
Abstract
Background Predicting risk of disease from genotypes is being increasingly proposed for a variety of diagnostic and prognostic purposes. Genome-wide association studies (GWAS) have identified a large number of genome-wide significant susceptibility loci for Crohn’s disease (CD) and ulcerative colitis (UC), two subtypes of inflammatory bowel disease (IBD). Recent studies have demonstrated that including only loci that are significantly associated with disease in the prediction model has low predictive power and that power can substantially be improved using a polygenic approach. Methods We performed a comprehensive analysis of risk prediction models using large case-control cohorts genotyped for 909,763 GWAS SNPs or 123,437 SNPs on the custom designed Immunochip using four prediction methods (polygenic score, best linear genomic prediction, elastic-net regularization and a Bayesian mixture model). We used the area under the curve (AUC) to assess prediction performance for discovery populations with different sample sizes and number of SNPs within cross-validation. Results On average, the Bayesian mixture approach had the best prediction performance. Using cross-validation we found little differences in prediction performance between GWAS and Immunochip, despite the GWAS array providing a 10 times larger effective genome-wide coverage. The prediction performance using Immunochip is largely due to the power of the initial GWAS for its marker selection and its low cost that enabled larger sample sizes. The predictive ability of the genomic risk score based on Immunochip was replicated in external data, with AUC of 0.75 for CD and 0.70 for UC. CD patients with higher risk scores demonstrated clinical characteristics typically associated with a more severe disease course including ileal location and earlier age at diagnosis. Conclusions Our analyses demonstrate that the power of genomic risk prediction for IBD is mainly due to strongly associated SNPs with considerable effect sizes. Additional SNPs that are only tagged by high-density GWAS arrays and low or rare-variants over-represented in the high-density region on the Immunochip contribute little to prediction accuracy. Although a quantitative assessment of IBD risk for an individual is not currently possible, we show sufficient power of genomic risk scores to stratify IBD risk among individuals at diagnosis. Electronic supplementary material The online version of this article (doi:10.1186/s12881-017-0451-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guo-Bo Chen
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Sang Hong Lee
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia.,School of Environmental and Rural Science, The University of New England, Armidale, Australia
| | - Grant W Montgomery
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Naomi R Wray
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Peter M Visscher
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia.,University of Queensland Diamantina Institute, Translational Research Institute, The University of Queensland, Brisbane, Australia
| | - Richard B Gearry
- Department of Medicine, University of Otago, Christchurch, New Zealand.,Department of Gastroenterology, Christchurch Hospital, Christchurch, New Zealand
| | - Ian C Lawrance
- Harry Perkins Institute of Medical Research, School of Medicine and Pharmacology, University of Western Australia, Murdoch, Australia.,Centre for Inflammatory Bowel Diseases, Saint John of God Hospital, Subiaco, Australia
| | - Jane M Andrews
- Inflammatory Bowel Disease Service, Department of Gastroenterology and Hepatology, Royal Adelaide Hospital, School of Medicine, University of Adelaide, Adelaide, Australia
| | - Peter Bampton
- Department of Gastroenterology and Hepatology, Flinders Medical Centre, Adelaide, Australia
| | - Gillian Mahy
- Department of Gastroenterology, Townsville Hospital, Townsville, Australia
| | - Sally Bell
- Department of Gastroenterology, St Vincent's Hospital, Melbourne, Australia
| | - Alissa Walsh
- Department of Gastroenterology and Hepatology, St Vincent's Hospital, Sydney, Australia
| | - Susan Connor
- Department of Gastroenterology and Hepatology, Liverpool Hospital, Sydney, Australia.,University of NSW, Sydney, Australia
| | - Miles Sparrow
- Department of Gastroenterology, Alfred Health, Melbourne, Australia
| | - Lisa M Bowdler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Lisa A Simms
- Inflammatory Bowel Disease Research Group, Immunology Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Krupa Krishnaprasad
- Inflammatory Bowel Disease Research Group, Immunology Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | | | - Graham L Radford-Smith
- School of Medicine, The University of Queensland, Brisbane, Australia.,Inflammatory Bowel Disease Research Group, Immunology Division, QIMR Berghofer Medical Research Institute, Brisbane, Australia.,Department of Gastroenterology, Royal Brisbane and Women's Hospital, Brisbane, Australia
| | - Gerhard Moser
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia.
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6
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Doecke JD, Hartnell F, Bampton P, Bell S, Mahy G, Grover Z, Lewindon P, Jones LV, Sewell K, Krishnaprasad K, Prosser R, Marr D, Fischer J, R Thomas G, Tehan JV, Ding NS, Cooke SE, Moss K, Sechi A, De Cruz P, Grafton R, Connor SJ, Lawrance IC, Gearry RB, Andrews JM, Radford-Smith GL. Infliximab vs. adalimumab in Crohn's disease: results from 327 patients in an Australian and New Zealand observational cohort study. Aliment Pharmacol Ther 2017; 45:542-552. [PMID: 27995633 DOI: 10.1111/apt.13880] [Citation(s) in RCA: 19] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Revised: 06/19/2016] [Accepted: 11/06/2016] [Indexed: 12/14/2022]
Abstract
BACKGROUND Maintenance anti-tumour necrosis factor-α (anti-TNFα) treatment for Crohn's disease is the standard of care for patients with an inadequate response to corticosteroids and immunomodulators. AIM To compare the efficacy and safety of infliximab and adalimumab in clinical practice and assess the value of concomitant immunomodulator therapy. METHODS We performed an observational cohort study in consecutive patients with Crohn's disease qualifying for anti-TNFα treatment in Australia and New Zealand between 2007 and 2011. Demographic and clinical data were prospectively recorded to identify independent factors associated with induction and maintenance of response to infliximab or adalimumab, or to either anti-TNFα therapy. RESULTS Three hundred and twenty-seven patients (183 infliximab, 144 adalimumab) successfully applied for treatment. Eighty-nine percent responded in all groups and median maintenance of response was similar for the two agents. Concomitant immunomodulator with infliximab, but not adalimumab, demonstrated a significantly longer response overall (P = 0.002), and significantly fewer disease and treatment-related complications (P = 0.017). Corticosteroids at baseline, and/or in the preceding 12 months, were associated with a 9-13 times greater risk of disease flare during maintenance treatment as compared to no corticosteroids (P < 0.0001). Maintenance of response was similar in the anti-TNF naïve and anti-TNF experienced subgroups. CONCLUSIONS In this large, real-life study, we demonstrate infliximab and adalimumab to have similar response characteristics. However, infliximab requires concomitant immunomodulator to achieve optimal maintenance of response comparable to adalimumab monotherapy. The results of this study will assist clinicians in further optimising patient care in their day-to-day clinical practice.
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Affiliation(s)
- J D Doecke
- Parkville, Vic., Australia.,Brisbane, Qld, Australia
| | | | | | - S Bell
- Melbourne, Vic., Australia
| | - G Mahy
- Townsville, Qld, Australia
| | | | | | | | | | | | | | | | | | | | | | | | | | - K Moss
- Bedford Park, SA, Australia
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Bodea C, Neale B, Ripke S, Daly M, Devlin B, Roeder K, Barclay M, Peyrin-Biroulet L, Chamaillard M, Colombel JF, Cottone M, Croft A, D’Incà R, Halfvarson J, Hanigan K, Henderson P, Hugot JP, Karban A, Kennedy N, Khan M, Lémann M, Levine A, Massey D, Milla M, Montgomery G, Ng S, Oikonomou I, Peeters H, Proctor D, Rahier JF, Roberts R, Rutgeerts P, Seibold F, Stronati L, Taylor K, Törkvist L, Ublick K, Van Limbergen J, Van Gossum A, Vatn M, Zhang H, Zhang W, Andrews J, Bampton P, Barclay M, Florin T, Gearry R, Krishnaprasad K, Lawrance I, Mahy G, Montgomery G, Radford-Smith G, Roberts R, Simms L, Amininijad L, Cleynen I, Dewit O, Franchimont D, Georges M, Laukens D, Peeters H, Rahier JF, Rutgeerts P, Theatre E, Van Gossum A, Vermeire S, Aumais G, Baidoo L, Barrie A, Beck K, Bernard EJ, Binion D, Bitton A, Brant S, Cho J, Cohen A, Croitoru K, Daly M, Datta L, Deslandres C, Duerr R, Dutridge D, Ferguson J, Fultz J, Goyette P, Greenberg G, Haritunians T, Jobin G, Katz S, Lahaie R, McGovern D, Nelson L, Ng S, Ning K, Oikonomou I, Paré P, Proctor D, Regueiro M, Rioux J, Ruggiero E, Schumm L, Schwartz M, Scott R, Sharma Y, Silverberg M, Spears D, Steinhart A, Stempak J, Swoger J, Tsagarelis C, Zhang W, Zhang C, Zhao H, Aerts J, Ahmad T, Arbury H, Attwood A, Auton A, Ball S, Balmforth A, Barnes C, Barrett J, Barroso I, Barton A, Bennett A, Bhaskar S, Blaszczyk K, Bowes J, Brand O, Braund P, Bredin F, Breen G, Brown M, Bruce I, Bull J, Burren O, Burton J, Byrnes J, Caesar S, Cardin N, Clee C, Coffey A, Connell J, Conrad D, Cooper J, Dominiczak A, Downes K, Drummond H, Dudakia D, Dunham A, Ebbs B, Eccles D, Edkins S, Edwards C, Elliot A, Emery P, Evans D, Evans G, Eyre S, Farmer A, Ferrier N, Flynn E, Forbes A, Forty L, Franklyn J, Frayling T, Freathy R, Giannoulatou E, Gibbs P, Gilbert P, Gordon-Smith K, Gray E, Green E, Groves C, Grozeva D, Gwilliam R, Hall A, Hammond N, Hardy M, Harrison P, Hassanali N, Hebaishi H, Hines S, Hinks A, Hitman G, Hocking L, Holmes C, Howard E, Howard P, Howson J, Hughes D, Hunt S, Isaacs J, Jain M, Jewell D, Johnson T, Jolley J, Jones I, Jones L, Kirov G, Langford C, Lango-Allen H, Lathrop G, Lee J, Lee K, Lees C, Lewis K, Lindgren C, Maisuria-Armer M, Maller J, Mansfield J, Marchini J, Martin P, Massey D, McArdle W, McGuffin P, McLay K, McVean G, Mentzer A, Mimmack M, Morgan A, Morris A, Mowat C, Munroe P, Myers S, Newman W, Nimmo E, O’Donovan M, Onipinla A, Ovington N, Owen M, Palin K, Palotie A, Parnell K, Pearson R, Pernet D, Perry J, Phillips A, Plagnol V, Prescott N, Prokopenko I, Quail M, Rafelt S, Rayner N, Reid D, Renwick A, Ring S, Robertson N, Robson S, Russell E, St Clair D, Sambrook J, Sanderson J, Sawcer S, Schuilenburg H, Scott C, Scott R, Seal S, Shaw-Hawkins S, Shields B, Simmonds M, Smyth D, Somaskantharajah E, Spanova K, Steer S, Stephens J, Stevens H, Stirrups K, Stone M, Strachan D, Su Z, Symmons D, Thompson J, Thomson W, Tobin M, Travers M, Turnbull C, Vukcevic D, Wain L, Walker M, Walker N, Wallace C, Warren-Perry M, Watkins N, Webster J, Weedon M, Wilson A, Woodburn M, Wordsworth B, Yau C, Young A, Zeggini E, Brown M, Burton P, Caulfield M, Compston A, Farrall M, Gough S, Hall A, Hattersley A, Hill A, Mathew C, Pembrey M, Satsangi J, Stratton M, Worthington J, Hurles M, Duncanson A, Ouwehand W, Parkes M, Rahman N, Todd J, Samani N, Kwiatkowski D, McCarthy M, Craddock N, Deloukas P, Donnelly P, Blackwell J, Bramon E, Casas J, Corvin A, Jankowski J, Markus H, Palmer C, Plomin R, Rautanen A, Trembath R, Viswanathan A, Wood N, Spencer C, Band G, Bellenguez C, Freeman C, Hellenthal G, Giannoulatou E, Pirinen M, Pearson R, Strange A, Blackburn H, Bumpstead S, Dronov S, Gillman M, Jayakumar A, McCann O, Liddle J, Potter S, Ravindrarajah R, Ricketts M, Waller M, Weston P, Widaa S, Whittaker P. A Method to Exploit the Structure of Genetic Ancestry Space to Enhance Case-Control Studies. Am J Hum Genet 2016; 98:857-868. [PMID: 27087321 DOI: 10.1016/j.ajhg.2016.02.025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2015] [Accepted: 02/29/2016] [Indexed: 02/08/2023] Open
Abstract
One goal of human genetics is to understand the genetic basis of disease, a challenge for diseases of complex inheritance because risk alleles are few relative to the vast set of benign variants. Risk variants are often sought by association studies in which allele frequencies in case subjects are contrasted with those from population-based samples used as control subjects. In an ideal world we would know population-level allele frequencies, releasing researchers to focus on case subjects. We argue this ideal is possible, at least theoretically, and we outline a path to achieving it in reality. If such a resource were to exist, it would yield ample savings and would facilitate the effective use of data repositories by removing administrative and technical barriers. We call this concept the Universal Control Repository Network (UNICORN), a means to perform association analyses without necessitating direct access to individual-level control data. Our approach to UNICORN uses existing genetic resources and various statistical tools to analyze these data, including hierarchical clustering with spectral analysis of ancestry; and empirical Bayesian analysis along with Gaussian spatial processes to estimate ancestry-specific allele frequencies. We demonstrate our approach using tens of thousands of control subjects from studies of Crohn disease, showing how it controls false positives, provides power similar to that achieved when all control data are directly accessible, and enhances power when control data are limiting or even imperfectly matched ancestrally. These results highlight how UNICORN can enable reliable, powerful, and convenient genetic association analyses without access to the individual-level data.
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Shah S, Mahy G, Roche E. Rare case of sclerosing mesenteritis and low grade follicular lymphoma. World J Clin Cases 2016; 4:108-111. [PMID: 27099861 PMCID: PMC4832116 DOI: 10.12998/wjcc.v4.i4.108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 12/06/2015] [Accepted: 01/11/2016] [Indexed: 02/05/2023] Open
Abstract
An unusual case of long standing sclerosing mesenteritis; initially presented with recurrent abdominal pain and a mesenteric mass with surrounding fat oedema and stranding with a pseudocapsule and fat ring sign were clearly visualised on the initial computed tomography scan. Laparotomy showed diffuse thickening at the root of the mesentery and histology from this specimen revealed fat necrosis and reactive lymphoid tissue consistent with sclerosing mesenteritis. Initial treatment with steroids and tamoxifen relieved the symptoms and the mass. He was maintained on tamoxifen. Three years later he developed a recurrence of his symptoms and abdominal mass that responded to a course of steroids. Two years following this, he developed a follicular Hodgkin’s lymphoma.
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Halford M, Heemers L, van Wesemael D, Mathys C, Wallens S, Branquart E, Vanderhoeven S, Monty A, Mahy G. The voluntary Code of conduct on invasive alien plants in Belgium: results and lessons learned from the AlterIAS LIFE+ project. ACTA ACUST UNITED AC 2014. [DOI: 10.1111/epp.12111] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. Halford
- Biodiversity and Landscape Unit; University of Liège Gembloux Agro-Bio Tech; Passage des Déportés, 2 B-5030 Gembloux Belgium
| | - L. Heemers
- Proefcentrum voor Sierteelt; Schaessestraat, 18 B-9070 Destelbergen Belgium
| | - D. van Wesemael
- Proefcentrum voor Sierteelt; Schaessestraat, 18 B-9070 Destelbergen Belgium
| | - C. Mathys
- Centre Technique Horticole; Chemin de la Sibérie, 4 B-5030 Gembloux Belgium
| | - S. Wallens
- Federal Public Service, Health, Food Chain Safety and Environment; Place Victor Horta, 40 B-1060 Brussels Belgium
| | - E. Branquart
- Service Public de Wallonie; Département d'Etude du Milieu Naturel et Agricole; Avenue Maréchal Juin, 23 B-5030 Gembloux Belgium
| | - S. Vanderhoeven
- Belgian Biodiversity Platform; Avenue Louise 231 B-1050 Brussels Belgium
| | - A. Monty
- Biodiversity and Landscape Unit; University of Liège Gembloux Agro-Bio Tech; Passage des Déportés, 2 B-5030 Gembloux Belgium
| | - G. Mahy
- Biodiversity and Landscape Unit; University of Liège Gembloux Agro-Bio Tech; Passage des Déportés, 2 B-5030 Gembloux Belgium
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Daïnou K, Mahy G, Duminil J, Dick CW, Doucet JL, Donkpégan ASL, Pluijgers M, Sinsin B, Lejeune P, Hardy OJ. Speciation slowing down in widespread and long-living tree taxa: insights from the tropical timber tree genus Milicia (Moraceae). Heredity (Edinb) 2014; 113:74-85. [PMID: 24549110 DOI: 10.1038/hdy.2014.5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Revised: 12/18/2013] [Accepted: 12/19/2013] [Indexed: 11/09/2022] Open
Abstract
The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically.
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Affiliation(s)
- K Daïnou
- 1] Laboratory of Tropical and Subtropical Forestry, Unit of Forest and Nature Management, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium [2] Laboratory of Applied Ecology, Faculty of Agronomic Science, University of Abomey-Calavi, Cotonou, Benin
| | - G Mahy
- Biodiversity and Landscape Unit, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - J Duminil
- 1] Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium [2] Bioversity International, Forest Genetic Resources Programme, Sub-Regional Office for Central Africa, Yaoundé, Cameroon
| | - C W Dick
- 1] Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA [2] Smithsonian Tropical Research Institute, Gamboa, Republic of Panama
| | - J-L Doucet
- Laboratory of Tropical and Subtropical Forestry, Unit of Forest and Nature Management, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - A S L Donkpégan
- Laboratory of Tropical and Subtropical Forestry, Unit of Forest and Nature Management, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - M Pluijgers
- Laboratory of Tropical and Subtropical Forestry, Unit of Forest and Nature Management, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - B Sinsin
- Laboratory of Applied Ecology, Faculty of Agronomic Science, University of Abomey-Calavi, Cotonou, Benin
| | - P Lejeune
- Unit of Forest and Nature Management, Gembloux Agro-Bio Tech, University of Liege, Gembloux, Belgium
| | - O J Hardy
- Evolutionary Biology and Ecology, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium
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Lawrance IC, Murray K, Batman B, Gearry RB, Grafton R, Krishnaprasad K, Andrews JM, Prosser R, Bampton PA, Cooke SE, Mahy G, Radford-Smith G, Croft A, Hanigan K. Crohn's disease and smoking: is it ever too late to quit? J Crohns Colitis 2013; 7:e665-71. [PMID: 23790611 DOI: 10.1016/j.crohns.2013.05.007] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [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: 04/11/2013] [Revised: 05/22/2013] [Accepted: 05/22/2013] [Indexed: 01/05/2023]
Abstract
BACKGROUND Smoking increases CD risk. The aim was to determine if smoking cessation at, prior to, or following, CD diagnosis affects medication use, disease phenotypic progression and/or surgery. METHODS Data on CD patients with disease for ≥5 yrs were collected retrospectively including the Montreal classification, smoking history, CD-related abdominal surgeries, family history, medication use and disease behaviour at diagnosis and the time when the disease behaviour changed. RESULTS 1115 patients were included across six sites (mean follow-up-16.6 yrs). More non-smokers were male (p=0.047) with A1 (p<0.0001), L4 (p=0.028) and perianal (p=0.03) disease. Non-smokers more frequently received anti-TNF agents (p=0.049). (p=0.017: OR 2.5 95%CI 1.18-5.16) and those who ceased smoking prior to diagnosis (p=0.045: OR 2.3 95%CI 1.02-5.21) progressed to complicated (B2/B3) disease as compared to those quitting at diagnosis. Patients with uncomplicated terminal ileal disease at diagnosis more frequently developed B2/B3 disease than isolated colonic CD (p<0.0001). B2/B3 disease was more frequent with perianal disease (p<0.0001) and if i.v. steroids (p=0.004) or immunosuppressants (p<0.0001) were used. 49.3% (558/1115) of patients required at least one intestinal surgery. More smokers had a 2nd surgical resection than patients who quit at, or before, the 1st resection and non-smokers (p=0.044: HR=1.39 95%CI 1.01-1.91). Patients smoking >3 cigarettes/day had an increased risk of developing B2/B3 disease (p=0.012: OR 3.8 95%CI 1.27-11.17). CONCLUSION Progression to B2/B3 disease and surgery is reduced by smoking cessation. All CD patients regardless of when they were diagnosed, or how many surgeries, should be strongly encouraged to cease smoking.
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Affiliation(s)
- Ian C Lawrance
- Centre for Inflammatory Bowel Diseases, Fremantle Hospital, WA, Australia; University Department of Medicine and Pharmacology, University of Western Australia, Fremantle Hospital, WA, Australia.
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Jaunard D, Monty A, Henriet F, De Proft M, Mahy G, Bodson B. Integrated management of wild chamomile (Matricaria chamomilla L.) populations by tillage. Commun Agric Appl Biol Sci 2013; 78:657-663. [PMID: 25151843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Nowadays, environmental, health and economic concerns encourage reviewing our weed management in agriculture. Integrated pest management is one key element in the development of weed management strategies less dependent from herbicides. To reach this goal, impact of different methods of tillage (Combinations of stubble cultivator and moldboard plow) on biology and dynamic of wild chamomile populations was studied in experimental plots of experimental farm of Gembloux Agro-Bio Tech. In summer 2012, wild chamomile densities were significantly lower in plots tilled with a moldboard plow. The use of a stubble cultivator did not significantly affect M. chamomilla density. In addition, we found higher wheat yields in plowed plots, indicating that the decrease in M. chamomilla densities reduces competition for wheat. These results show well long run impact of plowing and his effect on densities of wild chamomile and the seedbank.
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Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, Essers J, Mitrovic M, Ning K, Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z, Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan AN, Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A, Boucher G, Brand S, Büning C, Cohain A, Cichon S, D'Amato M, De Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson LR, Franchimont D, Fransen K, Gearry R, Georges M, Gieger C, Glas J, Haritunians T, Hart A, Hawkey C, Hedl M, Hu X, Karlsen TH, Kupcinskas L, Kugathasan S, Latiano A, Laukens D, Lawrance IC, Lees CW, Louis E, Mahy G, Mansfield J, Morgan AR, Mowat C, Newman W, Palmieri O, Ponsioen CY, Potocnik U, Prescott NJ, Regueiro M, Rotter JI, Russell RK, Sanderson JD, Sans M, Satsangi J, Schreiber S, Simms LA, Sventoraityte J, Targan SR, Taylor KD, Tremelling M, Verspaget HW, De Vos M, Wijmenga C, Wilson DC, Winkelmann J, Xavier RJ, Zeissig S, Zhang B, Zhang CK, Zhao H, Silverberg MS, Annese V, Hakonarson H, Brant SR, Radford-Smith G, Mathew CG, Rioux JD, Schadt EE, Daly MJ, Franke A, Parkes M, Vermeire S, Barrett JC, Cho JH. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature 2012; 491:119-24. [PMID: 23128233 PMCID: PMC3491803 DOI: 10.1038/nature11582] [Citation(s) in RCA: 3322] [Impact Index Per Article: 276.8] [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: 05/17/2012] [Accepted: 09/12/2012] [Indexed: 02/06/2023]
Abstract
Crohn’s disease (CD) and ulcerative colitis (UC), the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry with rising prevalence in other populations1. Genome-wide association studies (GWAS) and subsequent meta-analyses of CD and UC2,3 as separate phenotypes implicated previously unsuspected mechanisms, such as autophagy4, in pathogenesis and showed that some IBD loci are shared with other inflammatory diseases5. Here we expand knowledge of relevant pathways by undertaking a meta-analysis of CD and UC genome-wide association scans, with validation of significant findings in more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional and balancing selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe striking overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.
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Affiliation(s)
- Luke Jostins
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
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Krishnaprasad K, Andrews JM, Lawrance IC, Florin T, Gearry RB, Leong RWL, Mahy G, Bampton P, Prosser R, Leach P, Chitti L, Cock C, Grafton R, Croft AR, Cooke S, Doecke JD, Radford-Smith GL. Inter-observer agreement for Crohn's disease sub-phenotypes using the Montreal Classification: How good are we? A multi-centre Australasian study. J Crohns Colitis 2012; 6:287-93. [PMID: 22405164 DOI: 10.1016/j.crohns.2011.08.016] [Citation(s) in RCA: 13] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2011] [Revised: 08/21/2011] [Accepted: 08/21/2011] [Indexed: 12/13/2022]
Abstract
BACKGROUND Crohn's disease (CD) exhibits significant clinical heterogeneity. Classification systems attempt to describe this; however, their utility and reliability depends on inter-observer agreement (IOA). We therefore sought to evaluate IOA using the Montreal Classification (MC). METHODS De-identified clinical records of 35 CD patients from 6 Australian IBD centres were presented to 13 expert practitioners from 8 Australia and New Zealand Inflammatory Bowel Disease Consortium (ANZIBDC) centres. Practitioners classified the cases using MC and forwarded data for central blinded analysis. IOA on smoking and medications was also tested. Kappa statistics, with pre-specified outcomes of κ>0.8 excellent; 0.61-0.8 good; 0.41-0.6 moderate and ≤0.4 poor, were used. RESULTS 97% of study cases had colonoscopy reports, however, only 31% had undergone a complete set of diagnostic investigations (colonoscopy, histology, SB imaging). At diagnosis, IOA was excellent for age, κ=0.84; good for disease location, κ=0.73; only moderate for upper GI disease (κ=0.57) and disease behaviour, κ=0.54; and good for the presence of perianal disease, κ=0.6. At last follow-up, IOA was good for location, κ=0.68; only moderate for upper GI disease (κ=0.43) and disease behaviour, κ=0.46; but excellent for the presence/absence of perianal disease, κ=0.88. IOA for immunosuppressant use ever and presence of stricture were both good (κ=0.79 and 0.64 respectively). CONCLUSION IOA using MC is generally good; however some areas are less consistent than others. Omissions and inaccuracies reduce the value of clinical data when comparing cohorts across different centres, and may impair the ability to translate genetic discoveries into clinical practice.
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Affiliation(s)
- Krupa Krishnaprasad
- Inflammatory Bowel Disease Research Group, Queensland Institute of Medical Research, Brisbane, Australia.
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Jaunard D, Bizoux JP, Monty A, Henriet F, De Proft M, Vancutsem F, Mahy G, Bodson B. Effect of mechanical weeding on wild chamomile (Matricaria chamomilla L.) populations in winter wheat crop (Triticum aestivum L.). Commun Agric Appl Biol Sci 2012; 77:363-368. [PMID: 23878991] [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: 06/02/2023]
Abstract
Currently, economic, agronomic and environmental concerns lead to reduce the use of herbicides. Mechanical weeding can help to reach this objective. Dynamics and biology of wild chamomile (Matricaria chamomilla L.) populations were assessed as well as dynamic of winter wheat (Triticum aestivum L.) for four level of application of a weeder-harrow (0, 1, 2, 3 treatment(s)). After each treatment, an effect of mechanical weeding on wild chamomile density was observed. Density of wild chamomile decreased significantly with intensification of mechanical weeding. A third treatment allowed eliminating late emerged plants.
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Affiliation(s)
- D Jaunard
- Unit of Crop Management, University of Liège, Gembloux Agro-Bio Tech, Belgium.
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Bizoux JP, Cristofoli. S, Piqueray J, Mahy G. Conservation of an endemic metallophyte species: Effect of population history and vegetative density on the reproductive success of Viola calaminaria. J Nat Conserv 2011. [DOI: 10.1016/j.jnc.2010.06.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Vandersteen J, Jaunard D, Mahy G, Bizoux JP, Monty A, De Proft M, Henriet F, Vancutsem F, Bodson B. Dynamic of black-grass populations depending on the sowing time of winter wheat. Commun Agric Appl Biol Sci 2011; 76:485-490. [PMID: 22696956] [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: 06/01/2023]
Abstract
Currently, economic, agronomic and environmental concerns, lead to reduce use of herbicides. This reduction can be help by cultural measures like delay of the sowing date. Four sowing dates of winter wheat from 15th of October to 26th of November were tested. Dynamic of black-grass (Alopecurus myosuroides Huds.) populations and their reproduction rate were assessed as well as dynamic of winter wheat for each date. Delay of sowing could significantly reduce reproduction rate of black-grass. It was shown that the emergence rate (pl/m2), but also number of ears per plant and number of seeds per ear of black-grass decreased significantly with the sowing date. This reduction of seeds production already is from sixty per cent for a delay of two weeks sowing.
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Affiliation(s)
- J Vandersteen
- Unit of Crop management, Gembloux Agro Bio-Tech, University of Liège, Gembloux Agro Bio-Tec, Belgium
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Krebs C, Mahy G, Matthies D, Schaffner U, Tiébré MS, Bizoux JP. Taxa distribution and RAPD markers indicate different origin and regional differentiation of hybrids in the invasive Fallopia complex in central-western Europe. Plant Biol (Stuttg) 2010; 12:215-223. [PMID: 20653904 DOI: 10.1111/j.1438-8677.2009.00219.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Interspecific hybridization can be a driving force for evolutionary processes during plant invasions, by increasing genetic variation and creating novel gene combinations, thereby promoting genetic differentiation among populations of invasive species in the introduced range. We examined regional genetic structure in the invasive Fallopia complex, consisting of F. japonica var. japonica, F. sachalinensis and their hybrid F. x bohemica, in seven regions in Germany and Switzerland using RAPD analysis and flow cytometry. All individuals identified as F. japonica var. japonica had the same RAPD phenotype, while F. sachalinensis (11 RAPD phenotypes for 11 sampled individuals) and F. x bohemica (24 RAPD phenotypes for 32 sampled individuals) showed high genotypic diversity. Bayesian cluster analysis revealed three distinct genetic clusters. The majority of F. x bohemica individuals were assigned to a unique genetic cluster that differed from those of the parental species, while the other F. x bohemica individuals had different degrees of admixture to the three genetic clusters. At the regional scale, the occurrence of male-fertile F. sachalinensis coincided with the distribution of F. x bohemica plants showing a high percentage of assignment to both parental species, suggesting that they originated from hybridization between the parental species. In contrast, in regions where male-fertile F. sachalinensis were absent, F. x bohemica belonged to the non-admixed genetic group, indicating multiple introductions of hybrids or sexual reproduction among hybrids. We also found regional differentiation in the gene pool of F. x bohemica, with individuals within the same region more similar to each other than to individuals from different regions.
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Affiliation(s)
- C Krebs
- Faculty of Biology, Department of Ecology, Philipps-University Marburg, Marburg, Germany.
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Bizoux JP, Daïnou K, Raspé O, Lutts S, Mahy G. Fitness and genetic variation of Viola calaminaria, an endemic metallophyte: implications of population structure and history. Plant Biol (Stuttg) 2008; 10:684-693. [PMID: 18950425 DOI: 10.1111/j.1438-8677.2008.00077.x] [Citation(s) in RCA: 10] [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] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
We investigated variations in genetic diversity and plant fitness in a rare endemic metallophyte of calamine soils, Viola calaminaria, in relation to population size, population connectivity and population history in order to evaluate and discuss potential conservation strategies for the species. Mean population genetic diversity (H(s) = 0.25) of V. calaminaria was similar to endemic non-metallophyte taxa. Twenty-one per cent of the genetic variation was partitioned among populations and a low (9%) but significant differentiation was found among geographical regions. Our results did not support the hypothesis that the acquisition of metal tolerance may result in reduced genetic diversity, and suggested that strict metallophytes do not exhibit higher inter-population differentiation resulting from scattered habitats. There were no relationships between population genetic diversity and population size. Significant correlations were found between plant fitness and (i) population size and (ii) connectivity index. Recently-founded populations exhibited the same level of genetic diversity as ancient populations and also possessed higher plant fitness. There was no indication of strong founder effects in recently-established populations. The results suggest that the creation of habitats through human activities could provide new opportunities for conservation of this species.
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Affiliation(s)
- J-P Bizoux
- Laboratory of Ecology, Gembloux Agricultural University, Passage des Déportés 2, Gembloux, Belgium.
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Mahmood A, Needham J, Prosser J, Mainwaring J, Trebble T, Mahy G, Ramage J. Prevalence of hyperhomocysteinaemia, activated protein C resistance and prothrombin gene mutation in inflammatory bowel disease. Eur J Gastroenterol Hepatol 2005; 17:739-44. [PMID: 15947551 DOI: 10.1097/00042737-200507000-00008] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [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: 12/20/2022]
Abstract
BACKGROUND Thromboembolic disease is a significant cause of morbidity and mortality in patients with inflammatory bowel disease (IBD). A hypercoagulable state exists in IBD that may involve many components of haemostasis and is closely linked to the disease pathogenesis. It has been proposed that microvascular thrombosis and infarction may trigger the underlying inflammatory process. AIM To determine the prevalence of prothrombotic factors including hyperhomocysteinaemia, activated protein C (APC) resistance and prothrombin gene mutations as well as vitamin levels in the local IBD population. METHOD A total of 68 patients (37 men and 31 women) attending the IBD clinic were enrolled into the study. Citrated and ethylenediamine tetraacetic acid blood samples were collected from all patients as well as from 30 controls. Homocysteine levels were measured using the IMX immunoassay. APC resistance was measured using an unmodified activated partial thromboplastin time-based clotting assay. Prothrombin mutations were determined using polymerase chain reaction with the HB-gene factor II detection system. RESULTS Mean homocysteine levels were significantly higher and APC resistance ratios significantly lower in IBD patients compared with controls. No significant difference was detected between patients with ulcerative colitis or Crohn's disease. There was no significant increase in the incidence of prothrombin mutation in IBD patients. IBD patients had lower vitamin B12 and higher serum folate levels than controls. CONCLUSION High homocysteine and high serum folate may be associated with low vitamin B12 levels in IBD patients. We did not find any association between a low APC ratio and the factor V Leiden mutation or high factor VIII levels. Both hyperhomocysteinaemia and a low APC ratio may contribute to an increased risk of thromboembolic disease in IBD patients.
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Mahy G, Bruederle LP, Connors B, Van Hofwegen M, Vorsa N. Allozyme evidence for genetic autopolyploidy and high genetic diversity in tetraploid cranberry, Vaccinium oxycoccos (Ericaceae). Am J Bot 2000. [PMID: 11118425 DOI: 10.2307/2656840] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Polyploidy has been important in the evolution of angiosperms and may significantly affect population genetic diversity and structure. Nineteen isoenzyme loci were studied in diploid and tetraploid populations of Vaccinium oxycoccos (Ericaceae), and the results are compared with data previously reported for the related V. macrocarpon. Diploid V. oxycoccos and V. macrocarpon were readily discriminated based on their allozymic variation. No evidence for fixed heterozygosity was found in tetraploid V. oxycoccos. In contrast, all polymorphic loci exhibited both balanced and unbalanced heterozygotes, with some individuals exhibiting a pattern consistent with the presence of three alleles. These results support an autopolyploid origin for tetraploid V. oxycoccos. However, tetraploid V. oxycoccos possessed a suite of alleles not found in diploid V. oxycoccos; half of these alleles were shared with V. macrocarpon. This suggests that autotetraploid V. oxycoccos may have undergone hybridization with V. macrocarpon or that the autotetraploid retained the genetic variation present in an ancestral diploid species. Following theoretical expectations, proportion of polymorphic loci, mean number of alleles, and observed heterozygosity were significantly higher for the autotetraploid than for the diploid. Mean inbreeding (F(IS)) was similar for diploid and tetraploid V. oxycoccos. The latter exhibited population differentiation (F(ST)) exceeding both diploid species.
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Affiliation(s)
- G Mahy
- Unité d'Ecologie et de Biogéographie, Université catholique de Louvain, place Croix du Sud-5, B-1348 Louvain-la-Neuve, Belgium
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Mahy G, Ennos RA, Jacquemart AL. Allozyme variation and genetic structure of calluna vulgaris (heather) populations in scotland: the effect of postglacial recolonization. Heredity (Edinb) 1999; 82 (Pt 6):654-60. [PMID: 10383687 DOI: 10.1046/j.1365-2540.1999.00506.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent fragmentation of populations as well as historical postglacial recolonization may have significantly affected the population genetic diversity of temperate plant species. Regional allozymic variability was measured at seven loci within and among 12 populations of Calluna vulgaris in the previously glaciated region of Scotland. These results were compared with existing data on south-western continental populations. Low genetic differentiation (FST = 0.024) and lack of consistent geographical pattern were found at the regional level among Scottish populations, implying a high rate of gene flow (Nm = 10.2), probably favoured by the nearly continuous range of C. vulgaris across Scotland and characteristics of the Scottish environment. Scottish populations possessed lower mean allozymic diversity (PLP = 40.48, A = 1.95, He = 0.133) than populations from all the continental regions investigated previously. Belgian populations were genetically more closely related to Scottish than to other continental populations. These last two findings are interpreted with regard to the evolutionary history of the species revealed by palynological data.
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Affiliation(s)
- G Mahy
- Unite D'Ecologie et de Biogeographie, Universite catholique de Louvain, Place Croix du Sud, 5, B-1348 Louvain-la-Neuve, Belgium
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Mahy G, Vekemans X, Jacquemart AL, DE Sloover JR. Allozyme diversity and genetic structure in South-Western populations of heather, Calluna vulgaris. New Phytol 1997; 137:325-334. [PMID: 33863188 DOI: 10.1046/j.1469-8137.1997.00811.x] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Genetic diversity, population genetic structure and gene flow in Calluna vulgaris (L.) Hull were assessed by means of seven allozyme loci scored in 18 populations from the South-Western area of the species' range. Genetic diversity was lower (HT = 0.20) than reported for long-lived widespread species but was characterized by a high number of alleles per locus (5.60 at the species level) of which more than 70% were rare. More than 95% of genetic variation was found at the intrapopulation level (GST = 0.047). High levels of past gene flow were inferred, based on the allozyme data (Nm = 5.2 from GST . Nm = 10.2 from the 'private allele' method). Calluna vulgaris exhibited several geographic patterns of genetic variation. Both cluster analysis, constructed with various genetic distances and principal components analysis showed that Spanish and Pyrenean populations were clearly different from those collected in the Massif Central and Belgium. Also, a trend for decreasing genetic diversity towards Northern populations was detected. These patterns might be related to the post-glacial history of Calluna. In addition, it is shown that isolation by distance has played a role in the geographic shaping of genetic variation in this species.
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Affiliation(s)
- G Mahy
- Unité d'Ecologie et de Biogéographie, Université catholique de Louvain, Place Croix du Sud 5, B-1348 Louvain-la-Neuve, Belgium
| | - X Vekemans
- Laboratoire de Génétique et d'Ecologie Végétales, Université Libre de Bruxelles, Chausée de Wavre 1850, B-1160 Bruxelles, Belgium
| | - A L Jacquemart
- Unité d'Ecologie et de Biogéographie, Université catholique de Louvain, Place Croix du Sud 5, B-1348 Louvain-la-Neuve, Belgium
| | - J R DE Sloover
- Unité d'Ecologie et de Biogéographie, Université catholique de Louvain, Place Croix du Sud 5, B-1348 Louvain-la-Neuve, Belgium
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Mahy G. Completed suicide in Barbados. W INDIAN MED J 1987; 36:91-4. [PMID: 3673060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Mahy G. Attempted suicide in Barbados. W INDIAN MED J 1987; 36:31-4. [PMID: 3590748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Mahy G, Griffith EE. Suicide and parasuicide in Barbados, 1974-1978. J Natl Med Assoc 1980; 72:773-8. [PMID: 7401186 PMCID: PMC2552492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
This paper examines all the cases of suicide and parasuicide (non-fatal self-destructive acts) which took place on the Caribbean island of Barbados between 1974 and 1978. There were two females and 18 males who committed suicide in that period, and 14 of them were below age 44. There were 250 individuals who had attempted suicide for the first time, with a male to female ratio of 1:2.33. Most of the parasuicides were young and female, and the phenomenon is increasing. Health care officials on the island would seem to be legitimately unconcerned about the low suicide rates. However, the increasing parasuicide numbers may require more organized psychiatric care to meet the needs of this subgroup of the island's population.
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