期刊
GENES
卷 6, 期 2, 页码 238-251出版社
MDPI AG
DOI: 10.3390/genes6020238
关键词
gene-set analysis; pathway analysis; biological pathway; genetic association; GWAS
资金
- Netherlands Scientific Organization [NWO 40-00812-98-07-032, NWO 645-000-003 NWO 016-140-052, NWO 480-05-003]
- European Union [HEALTHF2-2009-242167]
- Netherlands Genomics Initiative (NGI)
- Wellcome Trust [076113, 085475]
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.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据