Characterizing allelic associations from unphased diploid data by graphical modeling
Characterizing allelic associations from unphased diploid data by graphical modeling
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DOI：
10.1002/gepi.20076
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发表时间：
2005-07-01
影响因子：
2.1
通讯作者：
Thomas, A
中科院分区：
文献类型：
--
作者：
Thomas, A
一种用于估计描述遗传位点之间等位基因关联的图形模型的方法被扩展到使用二倍体基因型而不是单倍体数据。它还提供单倍型频率估计、采样个体的相位估计、允许缺失或部分信息、基因型错误和任意外显率函数。一个数据集的688个无关的个人基因分型的25个遗传基因座被用来说明单倍型频率估计。所获得的频率被证明是类似的那些获得的相位程序。我们还说明了如何推定的性状位点可以包括在分析中，以检测等位基因表型协会。单倍型重建说明了一组标准的40个男性X染色体单倍型，随机配对，以模拟二倍体基因型数据。新的方法被证明是可比的大多数现有的，虽然相位方法在这个问题上始终更好。图形模型的方法被证明有一些优势，在易处理性方面，可用于选择信息的基因座子集，并映射影响表型的基因座。(c)2005 Wiley-Liss，Inc.
A method for estimating a graphical model to describe allelic associations between genetic loci is extended to use diploid genotypes rather than haploid data. It also provides haplotype frequency estimates, estimates of phase for sampled individuals, allows for missing or partial information, genotyping errors, and arbitrary penetrance functions. A data set of 688 unrelated individuals genotyped on 25 genetic loci is used to illustrate haplotype frequency estimation. The frequencies obtained are shown to be similar to those obtained by the PHASE program. We also illustrate how putative loci for traits can be included in the analysis in order to detect allele-phenotype associations. Haplotype reconstruction is illustrated on a standard set of 40 male X-chromosome haplotypes, randomly paired to simulate diploid genotype data. The novel method is shown to be comparable to most existing ones, though the PHASE method does consistently better on this problem. The graphical model approach is shown to have some advantages in terms of tractability and can be used to select informative subsets of loci and to map loci influencing phenotypes. (c) 2005 Wiley-Liss, Inc.