在高标记密度基因分型的群体样本中的连锁不平衡和单倍型纯合性。
Linkage disequilibrium and haplotype homozygosity in population samples genotyped at a high marker density.
作者信息
Wang Hui, Lin Chia-Ho, Service Susan, Chen Yuguo, Freimer Nelson, Sabatti Chiara
机构信息
Department of Statistics, UCLA, Los Angeles, CA 90095, USA.
出版信息
Hum Hered. 2006;62(4):175-89. doi: 10.1159/000096599. Epub 2006 Oct 30.
OBJECTIVE
Analyze the information contained in homozygous haplotypes detected with high density genotyping.
METHODS
We analyze the genotypes of approximately 2,500 markers on chr 22 in 12 population samples, each including 200 individuals. We develop a measure of disequilibrium based on haplotype homozygosity and an algorithm to identify genomic segments characterized by non-random homozygosity (NRH), taking into account allele frequencies, missing data, genotyping error, and linkage disequilibrium.
RESULTS
We show how our measure of linkage disequilibrium based on homozygosity leads to results comparable to those of R(2), as well as the importance of correcting for small sample variation when evaluating D'. We observe that the regions that harbor NRH segments tend to be consistent across populations, are gene rich, and are characterized by lower recombination.
CONCLUSIONS
It is crucial to take into account LD patterns when interpreting long stretches of homozygous markers.
目的
分析通过高密度基因分型检测到的纯合单倍型中包含的信息。
方法
我们分析了12个群体样本中22号染色体上约2500个标记的基因型，每个样本包含200个个体。我们基于单倍型纯合性开发了一种不平衡度量方法以及一种算法，用于识别以非随机纯合性（NRH）为特征的基因组片段，同时考虑了等位基因频率、缺失数据、基因分型错误和连锁不平衡。
结果
我们展示了基于纯合性的连锁不平衡度量方法如何得出与R(2)相当的结果，以及在评估D'时校正小样本变异的重要性。我们观察到，含有NRH片段的区域在不同群体中往往是一致的，富含基因，并且具有较低的重组率。
结论
在解释长片段纯合标记时，考虑连锁不平衡模式至关重要。
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