How accurate is the current picture of human genetic variation?
How accurate is the current picture of human genetic variation?
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DOI：
10.1038/hdy.2008.89
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发表时间：
2009-02-01
期刊：
影响因子：
3.8
通讯作者：
Balloux, F.
中科院分区：
文献类型：
--
作者：
Romero, I. G.;Manica, A.;Balloux, F.
近年来，由于来自短串联重复序列（STR）、插入缺失多态性（indels）和单核苷酸多态性（SNP）的大数据集的可用性，我们对全球人类基因组多样性分布的理解大大增加。然而，令人担忧的是，由于遗传标记选择过程中的偏差（所谓的“确定偏差”），目前全球人类基因组多样性的情况可能不准确。为了评估这个问题，我们首先比较了HGDP-CEPH面板中这三种类型的遗传标记在人群中的基因组多样性分布，以寻找偏倚或不一致的证据。在第二步中，使用一套非常宽松的标准来防止偏倚的侵入，我们开发了一套新的无偏倚STR标记，并将结果与现有面板的结果进行比较。与最近的声明不同，我们的研究结果表明STR标记没有明显的偏倚，因此可以用作人类遗传多样性和群体分化的基线参考。SNPs的偏见是温和的，相比，对一组的indels分析，我们建议应避免工作描述人类遗传多样性的分布或人类定居历史的推断。
Our understanding of the distribution of worldwide human genomic diversity has greatly increased over recent years thanks to the availability of large data sets derived from short tandem repeats (STRs), insertion deletion polymorphisms (indels) and single nucleotide polymorphisms (SNPs). A concern, however, is that the current picture of worldwide human genomic diversity may be inaccurate because of biases in the selection process of genetic markers (so-called 'ascertainment bias'). To evaluate this problem, we first compared the distribution of genomic diversity between these three types of genetic markers in the populations from the HGDP-CEPH panel for evidence of bias or incongruities. In a second step, using a very relaxed set of criteria to prevent the intrusion of bias, we developed a new set of unbiased STR markers and compared the results against those from available panels. Contrarily to recent claims, our results show that the STR markers suffer from no discernible bias, and can thus be used as a baseline reference for human genetic diversity and population differentiation. The bias on SNPs is moderate compared to that on the set of indels analysed, which we recommend should be avoided for work describing the distribution of human genetic diversity or making inference on human settlement history.