A Ground Truth Based Comparative Study on Detecting Epistatic SNPs.
A Ground Truth Based Comparative Study on Detecting Epistatic SNPs.
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DOI：
10.1109/bibmw.2009.5332132
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发表时间：
2009-11-01
期刊：
影响因子：
--
通讯作者：
Wang Y
中科院分区：
文献类型：
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作者：
Chen L;Yu G;Miller DJ;Song L;Langefeld C;Herrington D;Liu Y;Wang Y
全基因组关联研究（GWAS）已被广泛应用于识别与常见和复杂疾病相关的信息SNP。除了单SNP分析外，由于遗传调控的复杂网络，SNP之间的相互作用被认为在疾病风险中起重要作用。虽然已经提出了许多方法来检测SNP相互作用，但这些方法在实践中的相对性能和优点在很大程度上尚不清楚。在本文中，一个基于地面实况的比较研究报告涉及9个流行的SNP检测方法，使用现实的模拟数据集。这些结果提供了这些方法的一般特征和指南，可能对生物学研究者提供信息。
Genome-wide association studies (GWAS) have been widely applied to identify informative SNPs associated with common and complex diseases. Besides single-SNP analysis, the interaction between SNPs is believed to play an important role in disease risk due to the complex networking of genetic regulations. While many approaches have been proposed for detecting SNP interactions, the relative performance and merits of these methods in practice are largely unclear. In this paper, a ground-truth based comparative study is reported involving 9 popular SNP detection methods using realistic simulation datasets. The results provide general characteristics and guidelines on these methods that may be informative to the biological investigators.