A new permutation strategy of pathway-based approach for genome-wide association study.
A new permutation strategy of pathway-based approach for genome-wide association study.
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DOI：
10.1186/1471-2105-10-429
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发表时间：
2009-12-18
影响因子：
3
通讯作者：
Deng HW
中科院分区：
文献类型：
--
作者：
Guo YF;Li J;Chen Y;Zhang LS;Deng HW
最近引入的基于路径的方法是有前途的和有利的，以提高分析全基因组关联扫描（GWAS）数据的效率，以确定疾病的变异，共同考虑属于同一生物学途径的基因的变体。然而，目前可用的路径为基础的方法来分析GWAS有有限的权力和效率。我们提出了一种新的和有效的置换策略的基础上SNP随机化确定显着性的途径分析GWAS。通过模拟研究和对真实的数据集的研究，对所开发的置换策略进行了评估，并与两种先前可用的方法，即样本置换和基因置换进行了比较。实验结果表明，该置换策略在降低计算复杂度的同时，具有更强的性能和更高的效率。我们的研究结果表明SNP置换的性能得到了改善，从而使基于通路的GWAS分析更具适用性和吸引力。
Recently introduced pathway-based approach is promising and advantageous to improve the efficiency of analyzing genome-wide association scan (GWAS) data to identify disease variants by jointly considering variants of the genes that belong to the same biological pathway. However, the current available pathway-based approaches for analyzing GWAS have limited power and efficiency. We proposed a new and efficient permutation strategy based on SNP randomization for determining significance in pathway analysis of GWAS. The developed permutation strategy was evaluated and compared to two previously available methods, i.e. sample permutation and gene permutation, through simulation studies and a study on a real dataset. Results showed that the proposed permutation strategy is more powerful and efficient with greatly reducing the computational complexity. Our findings indicate the improved performance of SNP permutation and thus render pathway-based analysis of GWAS more applicable and attractive.
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