Post genome-wide association analysis: dissecting computational pathway/network-based approaches.

Journal: Briefings in bioinformatics

Volume: 20

Issue: 2

Year of Publication: 2020

Affiliated Institutions:  Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Level , Wernher and Beit North, Private Bag, Rondebosch, , Anzio road, Observatory Cape Town, South Africa. Department of Psychiatry and Mental Health, University of Cape Town, Observatory, , Cape Town, South Africa. Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, , Cape Town, South Africa. Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Private Bag, Rondebosch, , Cape Town, South Africa; African Institute for Mathematical Sciences, Muizenberg, Cape Town, South Africa and Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Medical School, Anzio Road, Observatory, , Cape Town, South Africa.

Abstract summary 

Over thousands of genetic associations to diseases have been identified by genome-wide association studies (GWASs), which conceptually is a single-marker-based approach. There are potentially many uses of these identified variants, including a better understanding of the pathogenesis of diseases, new leads for studying underlying risk prediction and clinical prediction of treatment. However, because of inadequate power, GWAS might miss disease genes and/or pathways with weak genetic or strong epistatic effects. Driven by the need to extract useful information from GWAS summary statistics, post-GWAS approaches (PGAs) were introduced. Here, we dissect and discuss advances made in pathway/network-based PGAs, with a particular focus on protein-protein interaction networks that leverage GWAS summary statistics by combining effects of multiple loci, subnetworks or pathways to detect genetic signals associated with complex diseases. We conclude with a discussion of research areas where further work on summary statistic-based methods is needed.

Authors & Co-authors:  Chimusa Emile R ER Dalvie Shareefa S Dandara Collet C Wonkam Ambroise A Mazandu Gaston K GK

Study Outcome 

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Statistics
Citations :  Li MJ, Liu Z, Wang P.. GWASdb v2: an update database for human genetic variants identified by genome-wide association studies. Nucleic Acids Res 2016;44(D1):D869–76.
Authors :  5
Identifiers
Doi : 10.1093/bib/bby035
SSN : 1477-4054
Study Population
Male,Female
Mesh Terms
Computational Biology
Other Terms
biological network;genome-wide association;pathways;post-GWAS;protein–protein interaction;subnetwork
Study Design
Cross Sectional Study
Study Approach
Country of Study
Publication Country
England