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

Author:

Corte Lucia12ORCID,Liou Lathan1ORCID,O’Reilly Paul F.1ORCID,García-González Judit1ORCID

Affiliation:

1. Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA

2. Center for Excellence in Youth Education, Icahn School of Medicine at Mount Sinai, New York City, NY 10029, USA

Abstract

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.

Funder

National Institutes of Health

Brain & Behavior Research Foundation

Scientific Computing and the Data Ark

Publisher

GigaScience Press

Subject

General Agricultural and Biological Sciences

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