A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis.
A haplotype-based algorithm for multilocus linkage disequilibrium mapping of quantitative trait loci with epistasis.
复制标题
一种基于单倍型的算法，用于具有上位性的数量性状基因座的多基因座连锁不平衡作图。
DOI：
10.1093/genetics/163.4.1533
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发表时间：
2003
期刊：
影响因子：
3.3
通讯作者：
Wu,Rongling
中科院分区：
文献类型：
--
作者：
Lou,Xiang-Yang;Casella,George;Littell,RamonC;Yang,MarkCK;Johnson,JulieA;Wu,Rongling
For tightly linked loci, cosegregation may lead to nonrandom associations between alleles in a population. Because of its evolutionary relationship with linkage, this phenomenon is called linkage disequilibrium. Today, linkage disequilibrium-based mapping has become a major focus of recent genome research into mapping complex traits. In this article, we present a new statistical method for mapping quantitative trait loci (QTL) of additive, dominant, and epistatic effects in equilibrium natural populations. Our method is based on haplotype analysis of multilocus linkage disequilibrium and exhibits two significant advantages over current disequilibrium mapping methods. First, we have derived closed-form solutions for estimating the marker-QTL haplotype frequencies within the maximum-likelihood framework implemented by the EM algorithm. The allele frequencies of putative QTL and their linkage disequilibria with the markers are estimated by solving a system of regular equations. This procedure has significantly improved the computational efficiency and the precision of parameter estimation. Second, our method can detect marker-QTL disequilibria of different orders and QTL epistatic interactions of various kinds on the basis of a multilocus analysis. This can not only enhance the precision of parameter estimation, but also make it possible to perform whole-genome association studies. We carried out extensive simulation studies to examine the robustness and statistical performance of our method. The application of the new method was validated using a case study from humans, in which we successfully detected significant QTL affecting human body heights. Finally, we discuss the implications of our method for genome projects and its extension to a broader circumstance. The computer program for the method proposed in this article is available at the webpage http://www.ifasstat.ufl.edu/genome/~LD.
