STATEMENT OF NEED Visualizations are powerful tools that have helped the field of genetics to better understand and communicate complex findings. By using visual aids like Manhattan and Volcano plots, genetic variants identified through genome-wide association studies can be more easily pinpointed. With the advancement of genome-wide association and sequencing studies, a mounting number of significant genetic variants, both common and rare, are being discovered. To better understand the relationship between these variants, combining these findings into single visualizations help to observe the relationship between effect size and allele frequency, providing a clearer picture of the genetic architecture of different traits and diseases. However, there is currently no consistent method for illustrating these results. In this paper, we propose a standardized approach for visualizing the effect size of risk variants across the allele frequency spectrum, generate plots for over a hundred traits in the UK Biobank, and provide to the field a R package and R Shiny application to explore their own results.
This work presents a new standardized graphical approach for visualizing genetic associations across a wide range of allele frequencies. These proposed TrumpetPlots have a distinctive trumpet shape, hence the proposed name. With the majority of variants having low frequency and small effects, while a small number of variants have higher frequency and larger effects, this view can help to provide new and valuable insights into the genetic basis of traits and diseases, and also help prioritize efforts to discover new risk variants. The tool is provided as a novel R package and R Shiny application and to demonstrate its use the article illustrates the distribution of variant effect sizes across the allele frequency range for over 100 continuous traits available in the UK Biobank. After some problems in testing the package is now available and easy to deploy via CRAN.
*This assessment refers to version 1 of this preprint.