JAG: A Computational Tool to Evaluate the Role of Gene-Sets in Complex Traits
AbstractGene-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
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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.
Lips ES, Kooyman M, de Leeuw C, Posthuma D. JAG: A Computational Tool to Evaluate the Role of Gene-Sets in Complex Traits. Genes. 2015; 6(2):238-251.Chicago/Turabian Style
Lips, Esther S.; Kooyman, Maarten; de Leeuw, Christiaan; Posthuma, Danielle. 2015. "JAG: A Computational Tool to Evaluate the Role of Gene-Sets in Complex Traits." Genes 6, no. 2: 238-251.