Unbiased Estimation of Gene Diversity in Samples Containing Related Individuals: Exact Variance and Arbitrary Ploidy
Unbiased Estimation of Gene Diversity in Samples Containing Related Individuals: Exact Variance and Arbitrary Ploidy
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DOI：
10.1534/genetics.110.121756
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发表时间：
2010-12-01
期刊：
影响因子：
3.3
通讯作者：
Rosenberg, Noah A.
中科院分区：
文献类型：
--
作者：
DeGiorgio, Michael;Jankovic, Ivana;Rosenberg, Noah A.
基因多样性是遗传变异的常用衡量标准，在哈迪-温伯格平衡的假设下评估群体中某个位点预期杂合个体的比例。当使用基因多样性的标准估计量时，样本中包含相关或近交个体会产生向下偏差。在这里，我们将最近开发的估计量扩展到任意倍性的一般情况，该估计量在包括已知相关或近交个体的二倍体常染色体样本中被证明是无偏的。我们推导了新估计量的方差的精确公式，(H) 与波形符，并提出了一个近似值，以便于在样本中每个个体最多与另一个个体相关时评估方差。当检查来自人类 X 染色体的样本（代表单倍体和二倍体个体的混合物）时，我们发现在均方误差的理论计算和数据分析中，与标准估计器相比，(H) 波浪线的表现更佳。因此，我们提出，(H) 波浪号是表征包含相关或近交个体的任意倍性样本中基因多样性的有用工具。
Gene diversity, a commonly used measure of genetic variation, evaluates the proportion of heterozygous individuals expected at a locus in a population, under the assumption of Hardy-Weinberg equilibrium. When using the standard estimator of gene diversity, the inclusion of related or inbred individuals in a sample produces a downward bias. Here, we extend a recently developed estimator shown to be unbiased in a diploid autosomal sample that includes known related or inbred individuals to the general case of arbitrary ploidy. We derive an exact formula for the variance of the new estimator, (H) over tilde, and present an approximation to facilitate evaluation of the variance when each individual is related to at most one other individual in a sample. When examining samples from the human X chromosome, which represent a mixture of haploid and diploid individuals, we find that (H) over tilde performs favorably compared to the standard estimator, both in theoretical computations of mean squared error and in data analysis. We thus propose that (H) over tilde is a useful tool in characterizing gene diversity in samples of arbitrary ploidy that contain related or inbred individuals.