对处于连锁不平衡状态的单核苷酸多态性进行多重检验的一种简单校正方法。
A simple correction for multiple testing for single-nucleotide polymorphisms in linkage disequilibrium with each other.
作者信息
Nyholt Dale R
机构信息
Genetic Epidemiology Laboratory, Queensland Institute of Medical Research, Brisbane, Queensland, Australia.
出版信息
Am J Hum Genet. 2004 Apr;74(4):765-9. doi: 10.1086/383251. Epub 2004 Mar 2.
Abstract
In this report, we describe a simple correction for multiple testing of single-nucleotide polymorphisms (SNPs) in linkage disequilibrium (LD) with each other, on the basis of the spectral decomposition (SpD) of matrices of pairwise LD between SNPs. This method provides a useful alternative to more computationally intensive permutation tests. A user-friendly interface (SNPSpD) for performing this correction is available online (http://genepi.qimr.edu.au/general/daleN/SNPSpD/). Additionally, output from SNPSpD includes eigenvalues, principal-component coefficients, and factor "loadings" after varimax rotation, enabling the selection of a subset of SNPs that optimize the information in a genomic region.
摘要
在本报告中，我们描述了一种基于单核苷酸多态性（SNP）之间成对连锁不平衡（LD）矩阵的谱分解（SpD），对处于LD状态的SNP进行多重检验的简单校正方法。该方法为计算量更大的置换检验提供了一种有用的替代方法。用于执行此校正的用户友好界面（SNPSpD）可在线获取（http://genepi.qimr.edu.au/general/daleN/SNPSpD/）。此外，SNPSpD的输出包括特征值、主成分系数以及方差最大化旋转后的因子“载荷”，从而能够选择一组SNP子集，以优化基因组区域中的信息。
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