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Genes 2015, 6(2), 238-251;

JAG: A Computational Tool to Evaluate the Role of Gene-Sets in Complex Traits

Department of Complex Trait Genetics, Neuroscience Campus Amsterdam, VU University & VU Medical Center, Amsterdam 1081HV, The Netherlands
Netherlands Bioinformatics Centre, Geert de Grooteplein 28, Nijmegen 6525 GA, The Netherlands
Delft Bioinformatics Lab, Delft University of Technology, Delft 2600GA, The Netherlands
Radboud University Nijmegen, Nijmegen 6525EC, The Netherlands
Author to whom correspondence should be addressed.
Academic Editor: J. Peter W. Young
Received: 20 November 2014 / Accepted: 27 April 2015 / Published: 14 May 2015
(This article belongs to the Section Technologies and Resources for Genetics)
Full-Text   |   PDF [633 KB, uploaded 14 May 2015]   |  


Gene-set analysis has been proposed as a powerful tool to deal with the highly polygenic architecture of complex traits, as well as with the small effect sizes typically found in GWAS studies for complex traits. We developed a tool, Joint Association of Genetic variants (JAG), which can be applied to Genome Wide Association (GWA) data and tests for the joint effect of all single nucleotide polymorphisms (SNPs) located in a user-specified set of genes or biological pathway. JAG assigns SNPs to genes and incorporates self-contained and/or competitive tests for gene-set analysis. JAG uses permutation to evaluate gene-set significance, which implicitly controls for linkage disequilibrium, sample size, gene size, the number of SNPs per gene and the number of genes in the gene-set. We conducted a power analysis using the Wellcome Trust Case Control Consortium (WTCCC) Crohn’s disease data set and show that JAG correctly identifies validated gene-sets for Crohn’s disease and has more power than currently available tools for gene-set analysis. JAG is a powerful, novel tool for gene-set analysis, and can be freely downloaded from the CTG Lab website. View Full-Text
Keywords: gene-set analysis; pathway analysis; biological pathway; genetic association; GWAS gene-set analysis; pathway analysis; biological pathway; genetic association; GWAS

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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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Lips, E.S.; Kooyman, M.; de Leeuw, C.; Posthuma, D. JAG: A Computational Tool to Evaluate the Role of Gene-Sets in Complex Traits. Genes 2015, 6, 238-251.

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