GPA-MDS: A Visualization Approach to Investigate Genetic Architecture among Phenotypes Using GWAS Results

International Journal of Genomics
Wei WeiDongjun Chung

Abstract

Genome-wide association studies (GWAS) have identified tens of thousands of genetic variants associated with hundreds of phenotypes and diseases, which have provided clinical and medical benefits to patients with novel biomarkers and therapeutic targets. Recently, there has been accumulating evidence suggesting that different complex traits share a common risk basis, namely, pleiotropy. Previously, a statistical method, namely, GPA (Genetic analysis incorporating Pleiotropy and Annotation), was developed to improve identification of risk variants and to investigate pleiotropic structure through a joint analysis of multiple GWAS datasets. While GPA provides a statistically rigorous framework to evaluate pleiotropy between phenotypes, it is still not trivial to investigate genetic relationships among a large number of phenotypes using the GPA framework. In order to address this challenge, in this paper, we propose a novel approach, GPA-MDS, to visualize genetic relationships among phenotypes using the GPA algorithm and multidimensional scaling (MDS). This tool will help researchers to investigate common etiology among diseases, which can potentially lead to development of common treatments across diseases. We evaluate the propose...Continue Reading

References

Nov 3, 2017·Open Biology·Sophie Hackinger, Eleftheria Zeggini

Citations

Sep 6, 2003·Arteriosclerosis, Thrombosis, and Vascular Biology·Kelly J HuntClicerio González Villalpando
May 29, 2009·Proceedings of the National Academy of Sciences of the United States of America·Lucia A HindorffTeri A Manolio
Mar 5, 2013·Lancet·Cross-Disorder Group of the Psychiatric Genomics Consortium
Mar 29, 2013·Nature Genetics·Lori C SakodaJohn S Witte
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

Related Concepts

Biological Markers
Genome-Wide Association Study
TNS3
Acquired Ichthyosis
Genetic Analysis
Genetic Screening Method
GYPA
Research Personnel
Genetic Pleiotropy
Etiology

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