ShinyGPA: An interactive visualization toolkit for investigating pleiotropic architecture using GWAS datasets

PloS One
Emma KortemeierDongjun Chung

Abstract

In spite of accumulating evidence suggesting that different complex traits share a common risk basis, namely pleiotropy, effective investigation of pleiotropic architecture still remains challenging. In order to address this challenge, we developed ShinyGPA, an interactive and dynamic visualization toolkit to investigate pleiotropic structure. ShinyGPA requires only the summary statistics from genome-wide association studies (GWAS), which reduces the burden on researchers using this tool. ShinyGPA allows users to effectively investigate genetic relationships among phenotypes using a flexible low-dimensional visualization and an intuitive user interface. In addition, ShinyGPA provides joint association mapping functionality that can facilitate biological understanding of the pleiotropic architecture. We analyzed GWAS summary statistics for 12 phenotypes using ShinyGPA and obtained visualization results and joint association mapping results that are well supported by the literature. The visualization produced by ShinyGPA can also be used as a hypothesis generating tool for relationships between phenotypes, which might also be used to improve the design of future genetic studies. ShinyGPA is currently available at https://dongjunc...Continue Reading

References

Dec 21, 2019·Bioinformatics·Gittu GeorgeAlex S F Doney

Citations

Dec 23, 2000·Science·J B TenenbaumJ C Langford
Sep 6, 2003·Arteriosclerosis, Thrombosis, and Vascular Biology·Kelly J HuntClicerio González Villalpando
Dec 2, 2004·Nature Reviews. Genetics·Roger HortonStephan Beck
Apr 26, 2006·Diabetes, Obesity & Metabolism·Harold E Lebovitz
May 3, 2008·The Journal of Clinical Investigation·Teri A ManolioFrancis S Collins
Jul 9, 2008·Current Opinion in Lipidology·Mahamood Edavalath, Alan Rees
May 29, 2009·Proceedings of the National Academy of Sciences of the United States of America·Lucia A HindorffTeri A Manolio
Aug 6, 2010·Nature·Tanya M TeslovichSekar Kathiresan
Dec 17, 2011·PLoS Genetics·Paula S RamosInternational Consortium on the Genetics of Systemic Erythematosus
Aug 14, 2012·Nature Genetics·Andrew P MorrisDIAbetes Genetics Replication And Meta-analysis (DIAGRAM) Consortium
Mar 5, 2013·Lancet·Cross-Disorder Group of the Psychiatric Genomics Consortium
Aug 13, 2013·Nature Genetics·Cross-Disorder Group of the Psychiatric Genomics ConsortiumInternational Inflammatory Bowel Disease Genetics Consortium (IIBDGC)
Nov 5, 2014·Nature·Kyle Kai-How FarhBradley E Bernstein

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Genome-Wide Association Study
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Dysequilibrium Syndrome
GYPA

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