Background

Determining the ages of polymorphic sites in human genomes needs to be carried out in a careful balance between the degree of complexity of the approach and the desired accuracy.

Objective

We provide evidence that a simpler approach where age determination is based upon the degree to which the alternative allele is spread among the population can be competitive with more complex methods.

Methods

The information contained in the vcf files of Phase 1 of the 1000 Genomes Project combined with the genomic sequences of seven non-human primate species was analyzed. The analyses were supplemented by a computer simulation of the mutational changes in 10,000 model chromosomes with a length of 10,000 nucleotides over a period of 16 million years. The list of the birth dates of the derived alleles of homozygous and heterozygous components of the derived alleles served as a yardstick to estimate the ages of human alternative alleles.

Results

The age of the derived alleles born in Africa before the “Out of Africa” event and not brought to other continents are estimated to be 0.17 Ma, the derived alleles present simultaneously on all continents are estimated to be 1.3 Ma old and the age of alleles arising in Europe or Asia is 0.06 Ma.

Conclusion

Our approach functions with polymorphisms that respect the “more frequent means older” principle. However, this shortcoming only leads to disagreement with the Atlas of Variant Age in about 20% of cases.

中文翻译：

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估计人类单核苷酸多态性位点的年龄

背景

确定人类基因组中多态位点的年龄需要在方法的复杂程度和所需的准确性之间进行仔细的平衡。

客观的

我们提供的证据表明，年龄确定基于替代等位基因在人群中传播的程度的更简单方法可以与更复杂的方法竞争。

方法

分析了千人基因组计划第一阶段 vcf 文件中包含的信息，并结合了七种非人类灵长类动物的基因组序列。计算机模拟了 10,000 条长度为 10,000 个核苷酸的模型染色体在 1600 万年期间的突变变化，对这些分析进行了补充。衍生等位基因的纯合和杂合成分的衍生等位基因的出生日期列表作为估计人类替代等位基因年龄的标准。

结果

“走出非洲”事件之前在非洲出生且未带到其他大陆的衍生等位基因的年龄估计为0.17 Ma，所有大陆同时存在的衍生等位基因的年龄估计为1.3 Ma，等位基因的年龄在欧洲或亚洲出现的是 0.06 Ma。

结论

我们的方法适用于尊重“更频繁意味着更旧”原则的多态性。然而，这个缺点只导致在大约 20% 的情况下与变异年龄图谱存在分歧。