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Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies

Recent advances in genome-wide association and sequencing studies have shown that the genetic architecture of complex traits and diseases involves a combination of rare and common genetic variants distributed throughout the genome. One way to better understand this architecture is to visualize genet...

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Autores principales: Corte, Lucia, Liou, Lathan, O’Reilly, Paul F., García-González, Judit
Formato: Online Artículo Texto
Lenguaje:English
Publicado: GigaScience Press 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498096/
https://www.ncbi.nlm.nih.gov/pubmed/37711278
http://dx.doi.org/10.46471/gigabyte.89
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author Corte, Lucia
Liou, Lathan
O’Reilly, Paul F.
García-González, Judit
author_facet Corte, Lucia
Liou, Lathan
O’Reilly, Paul F.
García-González, Judit
author_sort Corte, Lucia
collection PubMed
description Recent advances in genome-wide association and sequencing studies have shown that the genetic architecture of complex traits and diseases involves a combination of rare and common genetic variants distributed throughout the genome. One way to better understand this architecture is to visualize genetic associations across a wide range of allele frequencies. However, there is currently no standardized or consistent graphical representation for effectively illustrating these results. Here we propose a standardized approach for visualizing the effect size of risk variants across the allele frequency spectrum. The proposed plots have a distinctive trumpet shape: with the majority of variants having high frequency and small effects, and a small number of variants having lower frequency and larger effects. To demonstrate the utility of trumpet plots in illustrating the relationship between the number of variants, their frequency, and the magnitude of their effects in shaping the genetic architecture of complex traits and diseases, we generated trumpet plots for more than one hundred traits in the UK Biobank. To facilitate their broader use, we developed an R package, ‘TrumpetPlots’ (available at the Comprehensive R Archive Network) and R Shiny application, ‘Shiny Trumpets’ (available at https://juditgg.shinyapps.io/shinytrumpets/) that allows users to explore these results and submit their own data.
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spelling pubmed-104980962023-09-14 Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies Corte, Lucia Liou, Lathan O’Reilly, Paul F. García-González, Judit GigaByte Technical Release Recent advances in genome-wide association and sequencing studies have shown that the genetic architecture of complex traits and diseases involves a combination of rare and common genetic variants distributed throughout the genome. One way to better understand this architecture is to visualize genetic associations across a wide range of allele frequencies. However, there is currently no standardized or consistent graphical representation for effectively illustrating these results. Here we propose a standardized approach for visualizing the effect size of risk variants across the allele frequency spectrum. The proposed plots have a distinctive trumpet shape: with the majority of variants having high frequency and small effects, and a small number of variants having lower frequency and larger effects. To demonstrate the utility of trumpet plots in illustrating the relationship between the number of variants, their frequency, and the magnitude of their effects in shaping the genetic architecture of complex traits and diseases, we generated trumpet plots for more than one hundred traits in the UK Biobank. To facilitate their broader use, we developed an R package, ‘TrumpetPlots’ (available at the Comprehensive R Archive Network) and R Shiny application, ‘Shiny Trumpets’ (available at https://juditgg.shinyapps.io/shinytrumpets/) that allows users to explore these results and submit their own data. GigaScience Press 2023-09-01 /pmc/articles/PMC10498096/ /pubmed/37711278 http://dx.doi.org/10.46471/gigabyte.89 Text en © The Author(s) 2023. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Technical Release
Corte, Lucia
Liou, Lathan
O’Reilly, Paul F.
García-González, Judit
Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies
title Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies
title_full Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies
title_fullStr Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies
title_full_unstemmed Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies
title_short Trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies
title_sort trumpet plots: visualizing the relationship between allele frequency and effect size in genetic association studies
topic Technical Release
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10498096/
https://www.ncbi.nlm.nih.gov/pubmed/37711278
http://dx.doi.org/10.46471/gigabyte.89
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