How effectively can HIV phylogenies be used to measure heritability?
| العنوان: | How effectively can HIV phylogenies be used to measure heritability? |
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| المؤلفون: | Daniela Bezemer, Anne Cori, Huldrych F. Günthard, Oliver Laeyendecker, Ard van Sighem, George Shirreff, Christophe Fraser, Samuel Alizon |
| المساهمون: | Department of Infectious Disease Epidemiology [London] (DIDE), Imperial College London, Institute for Integrative Biology [Zürich] (IBZ), Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Evolution Théorique et Expérimentale (MIVEGEC-ETE), Perturbations, Evolution, Virulence (PEV), Génétique et évolution des maladies infectieuses (GEMI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Génétique et évolution des maladies infectieuses (GEMI), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Division of Infectious Diseases and Hospital Epidemiology [Zürich, Switzerland], Universität Zürich [Zürich] = University of Zurich (UZH)-University hospital of Zurich [Zurich], Department of Medicine [Baltimore, MD, USA], The Johns Hopkins University School of Medicine-Division of Infectious Diseases, National Institute of Allergy and Infectious Diseases [Baltimore, MD, USA], National Institutes of Health [Bethesda] (NIH), Stichting HIV Monitoring [Amsterdam], Universiteit van Amsterdam (UvA), The authors were funded by the European Research Council (ERC), Imperial College London, the Medical Research Council (MRC) Centre for Outbreak Research and Modelling, le Centre National de la Recherche Scientifique (CNRS), l’Institute National de la Santé et de la Recherche Médicale (INSERM), l’Institut de Recherche pour le Développement (IRD), Division of Intramural Research of the National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), the Dutch Ministry of Health, and the Royal Society., Alizon, Samuel, University of Zurich, Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud])-Maladies infectieuses et vecteurs : écologie, génétique, évolution et contrôle (MIVEGEC) |
| المصدر: | Evolution, Medicine, and Public Health Evolution, Medicine, and Public Health, 2013, 2013 (1), pp.209-24. ⟨10.1093/emph/eot019⟩ Evolution Medicine and Public Health Evolution, Medicine, and Public Health, Oxford : Oxford University Press, 2013, 2013 (1), pp.209-24. ⟨10.1093/emph/eot019⟩ |
| بيانات النشر: | HAL CCSD, 2013. |
| سنة النشر: | 2013 |
| مصطلحات موضوعية: | phylogenetic comparative analysis, Health, Toxicology and Mutagenesis, Human immunodeficiency virus (HIV), Medicine (miscellaneous), 610 Medicine & health, Biology, heritability, medicine.disease_cause, [SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, 10234 Clinic for Infectious Diseases, 03 medical and health sciences, 0302 clinical medicine, Disease severity, Phylogenetics, Genotype, Statistics, [SDV.BID.SPT] Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy, medicine, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], 030212 general & internal medicine, Original Research Article, set-point viral load, [SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Genetics, 0303 health sciences, Measure (data warehouse), Phylogenetic tree, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], phylogenetic signal, Variance (accounting), Heritability, [INFO.INFO-MO]Computer Science [cs]/Modeling and Simulation, 3. Good health, virulence, [SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology, HIV-1, [INFO.INFO-MO] Computer Science [cs]/Modeling and Simulation |
| الوصف: | International audience; BACKGROUND AND OBJECTIVES:The severity of HIV-1 infection, measured by set-point viral load (SPVL), is highly variable between individuals. Its heritability between infections quantifies the control the pathogen genotype has over disease severity. Heritability estimates vary widely between studies, but differences in methods make comparison difficult. Phylogenetic comparative analysis offers measures of phylogenetic signal, but it is unclear how to interpret them in terms of the fraction of variance in SPVL controlled by the virus genotype.METHODOLOGY:We present computational methods which link statistics summarizing phylogenetic signal to heritability, h(2) in order to test for and quantify it. We re-analyse data from Switzerland and Uganda, and apply it to new data from the Netherlands. We systematically compare established and new (e.g. phylogenetic pairs, PP) phylogenetic signal statistics.RESULTS:Heritability estimates varied by method and dataset. Several methods were consistently able to detect simulated heritability above , but none below. Pagel's λ was the most robust and sensitive. The PP method found no heritability in the Netherlands data, whereas Pagel's λ found significant heritability only in a narrow subdivision (P = 0.038). Heritability was estimated at h(2) = 0.52 (95% confidence interval 0.00-0.63).CONCLUSIONS AND IMPLICATIONS:This standardized measure, h(2), allows comparability of heritability between cohorts. We confirm high heritability in Swiss data, but neither in Ugandan data nor in the Netherlands, where it is barely significant or undetectable. Existing phylogenetic methods are ill-suited for detecting heritability below , which may nonetheless be biologically important. |
| وصف الملف: | application/pdf; Shirreff_et_al_HIV_phylogenies.pdf - application/pdf |
| اللغة: | English |
| تدمد: | 2050-6201 |
| DOI: | 10.1093/emph/eot019⟩ |
| URL الوصول: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e6e61e7b3c794c8b277d8f15ee18c5d1 https://hal.science/hal-01567924/document |
| Rights: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....e6e61e7b3c794c8b277d8f15ee18c5d1 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 20506201 |
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| DOI: | 10.1093/emph/eot019⟩ |