graph-GPA: A graphical model for prioritizing GWAS results and investigating pleiotropic architecture

PLoS Computational Biology
Dongjun ChungHongyu Zhao


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. However, identification of risk variants associated with complex diseases remains challenging as they are often affected by many genetic variants with small or moderate effects. There has been accumulating evidence suggesting that different complex traits share common risk basis, namely pleiotropy. Recently, several statistical methods have been developed to improve statistical power to identify risk variants for complex traits through a joint analysis of multiple GWAS datasets by leveraging pleiotropy. While these methods were shown to improve statistical power for association mapping compared to separate analyses, they are still limited in the number of phenotypes that can be integrated. In order to address this challenge, in this paper, we propose a novel statistical framework, graph-GPA, to integrate a large number of GWAS datasets for multiple phenotypes using a hidden Markov random field approach. Application of graph-GPA to a joint analysis of GWAS datasets for 12 phenot...Continue Reading


Sep 6, 2003·Arteriosclerosis, Thrombosis, and Vascular Biology·Kelly J HuntClicerio González Villalpando
Mar 6, 2008·Nature Reviews. Genetics·Peter M VisscherNaomi R Wray
May 7, 2009·Proceedings of the National Academy of Sciences of the United States of America·Laura J ScottMichael Boehnke
Oct 9, 2009·Nature·Teri ManolioPeter M Visscher
Jan 30, 2010·Clinical Journal of the American Society of Nephrology : CJASN·Jane C TanBryan D Myers
Jun 22, 2010·Nature Genetics·Jian YangPeter M Visscher
Jul 22, 2010·The New England Journal of Medicine·Teri Manolio
Aug 6, 2010·Nature·Tanya M TeslovichSekar Kathiresan
Jun 12, 2012·Molecular Autism·Paula S RamosStephen J Walker
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)
Dec 10, 2013·Nucleic Acids Research·Danielle WelterHelen Parkinson
Dec 18, 2013·Human Genetics·Cong LiHongyu Zhao
Nov 5, 2014·Nature·Kyle Kai-How FarhBradley E Bernstein
Jul 11, 2015·Clinics and Research in Hepatology and Gastroenterology·G F Mells, G M Hirschfield

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