近交个体间和染色体间变异的基因组检测
Genomic tests of variation in inbreeding among individuals and among chromosomes
摘要：
我们研究了9个欧洲人和9个约鲁班人的杂合位点的分布，他们的基因组序列是由完整基因组学公开提供的。我们表明，它是可能的，以获得有关近亲繁殖的详细信息时，一组相对较小的全基因组序列。而不是专注于测试偏离哈代-温伯格基因型频率在每个站点，我们分析了整个分布的杂合子的衍生（非黑猩猩）等位基因的拷贝数的条件。使用Levene的精确检验，我们拒绝Hardy-Weinberg在这两个群体。我们推广了Levene分布，得到了在每个个体具有相同的近交系数F的情况下，杂合子个体数的精确分布。我们估计欧洲人的F值为0.0026，约鲁巴人为0.0005，但我们也可以拒绝每个人的F值都相同的假设。我们使用复合似然方法来估计每个个体和每个染色体内的F。个体内染色体间F的变异太大，与单独的采样效应不一致。此外，在不同的人群中，每个染色体的F的估计是不相关的。我们的研究结果显示了如何详细比较人口基因组数据的理论预测。将这些方法应用于完整基因组学数据集表明，明显的近亲繁殖程度在染色体和个体之间存在差异，近亲繁殖系数的估计会受到意想不到的变异水平的影响，这可能部分是由选择造成的。
英文摘要：
We examine the distribution of heterozygous sites in nine European and nine Yoruban individuals whose genomic sequences were made publicly available by Complete Genomics. We show that it is possible to obtain detailed information about inbreeding when a relatively small set of whole-genome sequences is available. Rather than focus on testing for deviations from Hardy-Weinberg genotype frequencies at each site, we analyze the entire distribution of heterozygotes conditioned on the number of copies of the derived (non-chimpanzee) allele. Using Levene's exact test, we reject Hardy-Weinberg in both populations. We generalized Levene's distribution to obtain the exact distribution of the number of heterozygous individuals given that every individual has the same inbreeding coefficient, F. We estimated F to be 0.0026 in Europeans and 0.0005 in Yorubans, but we could also reject the hypothesis that F was the same in each individual. We used a composite likelihood method to estimate F in each individual and within each chromosome. Variation in F across chromosomes within individuals was too large to be consistent with sampling effects alone. Furthermore, estimates of F for each chromosome in different populations were not correlated. Our results show how detailed comparisons of population genomic data can be made to theoretical predictions. The application of methods to the Complete Genomics data set shows that the extent of apparent inbreeding varies across chromosomes and across individuals, and estimates of inbreeding coefficients are subject to unexpected levels of variation which might be partly accounted for by selection.
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