{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,1,31]],"date-time":"2025-01-31T00:40:27Z","timestamp":1738284027374,"version":"3.35.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"18","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":3007,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,9,15]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Large-scale genetic association studies are carried out with the hope of discovering single nucleotide polymorphisms involved in the etiology of complex diseases. There are several existing methods in the literature for performing this kind of analysis for case-control studies, but less work has been done for prospective cohort studies. We present a Bayesian method for linking markers to censored survival outcome by clustering haplotypes using gene trees. Coalescent-based approaches are promising for LD mapping, as the coalescent offers a good approximation to the evolutionary history of mutations.<\/jats:p><jats:p>Results: We compare the performance of the proposed method in simulation studies to the univariate Cox regression and to dimension reduction methods, and we observe that it performs similarly in localizing the causal site, while offering a clear advantage in terms of false positive associations. Moreover, it offers computational advantages. Applying our method to a real prospective study, we observe potential association between candidate ABC transporter genes and epilepsy treatment outcomes.<\/jats:p><jats:p>Availability: R codes are available upon request.<\/jats:p><jats:p>Contact: \u00a0ioanna.tachmazidou@imperial.ac.uk<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btn351","type":"journal-article","created":{"date-parts":[[2008,7,11]],"date-time":"2008-07-11T00:25:11Z","timestamp":1215735911000},"page":"2030-2036","source":"Crossref","is-referenced-by-count":6,"title":["Bayesian survival analysis in genetic association studies"],"prefix":"10.1093","volume":"24","author":[{"given":"Ioanna","family":"Tachmazidou","sequence":"first","affiliation":[{"name":"1 Department of Epidemiology and Public Health, Imperial College, London W2 1PG, 2Twin Research Unit, King's College, London SE1 7 EH, 3Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT and 4Division of Neurosciences and Mental Health, Imperial College, London SW7 2AZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Toby","family":"Andrew","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Public Health, Imperial College, London W2 1PG, 2Twin Research Unit, King's College, London SE1 7 EH, 3Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT and 4Division of Neurosciences and Mental Health, Imperial College, London SW7 2AZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudio J.","family":"Verzilli","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Public Health, Imperial College, London W2 1PG, 2Twin Research Unit, King's College, London SE1 7 EH, 3Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT and 4Division of Neurosciences and Mental Health, Imperial College, London SW7 2AZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael R.","family":"Johnson","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Public Health, Imperial College, London W2 1PG, 2Twin Research Unit, King's College, London SE1 7 EH, 3Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT and 4Division of Neurosciences and Mental Health, Imperial College, London SW7 2AZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Maria","family":"De Iorio","sequence":"additional","affiliation":[{"name":"1 Department of Epidemiology and Public Health, Imperial College, London W2 1PG, 2Twin Research Unit, King's College, London SE1 7 EH, 3Department of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT and 4Division of Neurosciences and Mental Health, Imperial College, London SW7 2AZ, UK"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2008,7,9]]},"reference":[{"key":"2023020211112164500_B1","doi-asserted-by":"crossref","first-page":"7468","DOI":"10.1038\/sj.onc.1206948","article-title":"P-glycoprotein: from genomics to mechanism","volume":"22","author":"Ambudkar","year":"2003","journal-title":"Oncogene"},{"key":"2023020211112164500_B2","doi-asserted-by":"crossref","first-page":"511","DOI":"10.1371\/journal.pbio.0020108","article-title":"Semi-supervised methods for predicting patient survival from gene expression data","volume":"2","author":"Bair","year":"2004","journal-title":"PLoS Biol."},{"key":"2023020211112164500_B3","doi-asserted-by":"crossref","first-page":"119","DOI":"10.1198\/016214505000000628","article-title":"Prediction by supervised principal components","volume":"101","author":"Bair","year":"2006","journal-title":"JASA"},{"key":"2023020211112164500_B4","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1111\/j.2517-6161.1972.tb00899.x","article-title":"Regression models and life tables","volume":"34","author":"Cox","year":"1972","journal-title":"J. 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