A new permutation strategy of pathway-based approach for genome-wide association study

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A new permutation strategy of pathway-based approach for genome-wide association study

Please use this identifier to cite or link to this item: http://dx.doi.org/10.1186/1471-2105-10-429

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dc.contributor.author Guo, Yan-Fang
dc.contributor.author Li, Jian
dc.contributor.author Chen, Yuan
dc.contributor.author Zhang, Li-Shu
dc.contributor.author Deng, Hong-Wen
dc.date.accessioned 2012-08-29T15:23:39Z
dc.date.available 2012-08-29T15:23:39Z
dc.date.issued 2009-12-18
dc.identifier.citation BMC Bioinformatics. 2009 Dec 18;10(1):429
dc.identifier.uri http://dx.doi.org/10.1186/1471-2105-10-429
dc.identifier.uri http://hdl.handle.net/10355/15023
dc.description.abstract Abstract Background 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. Results 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. Conclusion Our findings indicate the improved performance of SNP permutation and thus render pathway-based analysis of GWAS more applicable and attractive.
dc.title A new permutation strategy of pathway-based approach for genome-wide association study
dc.type Journal Article
dc.date.updated 2012-08-29T15:23:40Z
dc.description.version Peer Reviewed
dc.language.rfc3066 en
dc.rights.holder Yan-Fang Guo et al.; licensee BioMed Central Ltd.


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