Determination of probability distribution of diplotype configuration (diplotype distribution) for each subject from genotypic data using the EM algorithm
Determination of probability distribution of diplotype configuration (diplotype distribution) for each subject from genotypic data using the EM algorithm
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DOI：
10.1017/s0003480002001124
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发表时间：
2002-05-01
影响因子：
1.9
通讯作者：
Kamatani, N
中科院分区：
文献类型：
--
作者：
Kitamura, Y;Moriguchi, M;Kamatani, N
单倍型分析对性状定位具有重要意义。近年来，基于期望最大化（EM）算法的无亲缘关系个体基因型单倍型频率估计方法得到了发展。我们的程序估计种群中的单倍型频率，并根据估计的单倍型频率确定每个受试者的二倍型配置（二倍型分布）的后验概率分布。分析了3个民族的平滑蛋白基因（SMTN）和3个日本人的血清淀粉样蛋白A基因（SAA@）样本。在大多数情况下，每个个体的估计双倍型分布集中在单个双倍型配置中。由此确定的双倍型配置与体外实验中确定的相同，但有一个例外。因此，利用估算的非亲缘个体单倍型频率确定的双倍型配置是可靠的。使用这种方法，当表型与二倍型配置相关时，可以从二倍型分布估计受试者发生表型的风险。
Haplotype analysis is important for mapping traits. Recently, methods for estimating haplotype frequencies from genotypes of unrelated individuals based on the expectation-maximization (EM) algorithm have been developed. Our program estimates haplotype frequencies in the population and determines the posterior probability distribution of diplotype configuration (diplotype distribution) for each subject based on the estimated haplotype frequencies. Samples from three ethnic groups for the smoothelin gene (SMTN) and those from three Japanese groups for serum amyloid A genes (SAA@) were analyzed. The estimated diplotype distribution for each individual was concentrated, in most cases, in a single diplotype configuration. The diplotype configuration thus determined was the same as that determined in in vitro experiments, with one exception. Thus, the diplotype configurations determined using the estimated haplotype frequencies from unrelated individuals are reliable. Using this method, the risk of a subject developing a phenotype may be estimated from the diplotype distribution when the phenotype is associated with diplotype configurations.