PheGWAS: a new dimension to visualize GWAS across multiple phenotypes

Doney, Alex S F and Palmer, Colin N A and Mohan, V and Radha, V and Nar, A S and Appleby, P and Huang, Yu and Gan, Sushrima and George, Gittu and Schwartz, Russell (2020) PheGWAS: a new dimension to visualize GWAS across multiple phenotypes. Bioinformatics, 36 (8). p. 2500. ISSN 1367-4803



Motivation: PheGWAS was developed to enhance exploration of phenome-wide pleiotropy at the genome-wide level through the efficient generation of a dynamic visualization combining Manhattan plots from GWAS with PheWAS to create a 3D 'landscape'. Pleiotropy in sub-surface GWAS significance strata can be explored in a sectional view plotted within user defined levels. Further complexity reduction is achieved by confining to a single chromosomal section. Comprehensive genomic and phenomic coordinates can be displayed. Results: PheGWAS is demonstrated using summary data from Global Lipids Genetics Consortium GWAS across multiple lipid traits. For single and multiple traits PheGWAS highlighted all 88 and 69 loci, respectively. Further, the genes and SNPs reported in Global Lipids Genetics Consortium were identified using additional functions implemented within PheGWAS. Not only is PheGWAS capable of identifying independent signals but also provides insights to local genetic correlation (verified using HESS) and in identifying the potential regions that share causal variants across phenotypes (verified using colocalization tests). Availability and implementation: The PheGWAS software and code are freely available at (

Item Type:Article
Official URL/DOI:
Uncontrolled Keywords:PheGWAS
Subjects:Genetics and Diabetes
Divisions:Department of Epidemiology
Department of Diabetology
ID Code:1253
Deposited By:surendar radha
Deposited On:05 Aug 2021 13:51
Last Modified:05 Aug 2021 13:51
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