将亲属的基因型纳入连锁不平衡测试中。
Incorporating genotypes of relatives into a test of linkage disequilibrium.
作者信息
Excoffier L, Slatkin M
机构信息
Department of Anthropology, University of Geneva, Geneva, Switzerland.
出版信息
Am J Hum Genet. 1998 Jan;62(1):171-80. doi: 10.1086/301674.
Abstract
Genetic data from autosomal loci in diploids generally consist of genotype data for which no phase information is available, making it difficult to implement a test of linkage disequilibrium. In this paper, we describe a test of linkage disequilibrium based on an empirical null distribution of the likelihood of a sample. Information on the genotypes of related individuals is explicitly used to help reconstruct the gametic phase of the independent individuals. Simulation studies show that the present approach improves on estimates of linkage disequilibrium gathered from samples of completely independent individuals but only if some offspring are sampled together with their parents. The failure to incorporate some parents sharply decreases the sensitivity and accuracy of the test. Simulations also show that for multiallelic data (more than two alleles) our testing procedure is not as powerful as an exact test based on known haplotype frequencies, owing to the interaction between departure from Hardy-Weinberg equilibrium and linkage disequilibrium.
摘要
二倍体常染色体位点的遗传数据通常由无相位信息的基因型数据组成，这使得实施连锁不平衡检验变得困难。在本文中，我们描述了一种基于样本似然性的经验性零分布的连锁不平衡检验方法。明确使用相关个体的基因型信息来帮助重建独立个体的配子相位。模拟研究表明，当前方法改进了从完全独立个体样本中收集的连锁不平衡估计，但前提是要与一些后代及其父母一起采样。不纳入一些父母会大幅降低检验的灵敏度和准确性。模拟还表明，对于多等位基因数据（超过两个等位基因），由于偏离哈迪 - 温伯格平衡与连锁不平衡之间的相互作用，我们的检验程序不如基于已知单倍型频率的精确检验有效。
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