ArticleEvolution, medicine, and public health2013
How effectively can HIV phylogenies be used to measure heritability?
Article in Evolution, medicine, and public health, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
12 citing papers in PubMed.
- Long-term evolution of quantitative traits in the Drosophila melanogaster species subgroup.Genetica · 2022Article
- Heritability of the HIV-1 reservoir size and decay under long-term suppressive ART.Nature communications · 2020Article
- Automatic generation of evolutionary hypotheses using mixed Gaussian phylogenetic models.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Article
- A Practical Guide to Estimating the Heritability of Pathogen Traits.Molecular biology and evolution · 2018Article
- Dissecting HIV Virulence: Heritability of Setpoint Viral Load, CD4+ T-Cell Decline, and Per-Parasite Pathogenicity.Molecular biology and evolution · 2018Article
- Viral genetic variation accounts for a third of variability in HIV-1 set-point viral load in Europe.PLoS biology · 2017Article
- Parent-offspring regression to estimate the heritability of an HIV-1 trait in a realistic setup.Retrovirology · 2017Article
- Estimating the Respective Contributions of Human and Viral Genetic Variation to HIV Control.PLoS computational biology · 2017Article
- Simultaneously estimating evolutionary history and repeated traits phylogenetic signal: applications to viral and host phenotypic evolution.Methods in ecology and evolution · 2015Article
- Evidence that hepatitis C virus genome partly controls infection outcome.Evolutionary applications · 2014Article
- Virulence and pathogenesis of HIV-1 infection: an evolutionary perspective.Science (New York, N.Y.) · 2014Review
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Authors and funding
8 authors.
Funding
Abstract
BACKGROUND AND
objectivesThe 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.
resultsHeritability 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.
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