Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.
Human genomic regions with exceptionally high levels of population differentiation identified from 911 whole-genome sequences.
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DOI：
10.1186/gb-2014-15-6-r88
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发表时间：
2014-06-30
期刊：
影响因子：
12.3
通讯作者：
McVean GA
中科院分区：
文献类型：
--
作者：
Colonna V;Ayub Q;Chen Y;Pagani L;Luisi P;Pybus M;Garrison E;Xue Y;Tyler-Smith C;1000 Genomes Project Consortium;Abecasis GR;Auton A;Brooks LD;DePristo MA;Durbin RM;Handsaker RE;Kang HM;Marth GT;McVean GA
群体分化已被证明是有效的地理定位的积极选择下的基因座识别，并有可能识别基因座的平衡选择。我们之前研究了3680万个基因组变异的人群中的遗传分化模式，以确定基因组中显示高频率差异的位点。在这里，我们扩展了这个数据集，包括其他的变体，调查网站的分化水平低，并评估高度分化的网站可能导致选择性或其他过程的程度。我们表明，虽然低分化的网站代表采样效果，而不是平衡选择，网站显示极高的人口分化富集积极的选择事件，一半可能是经典的选择性扫描的结果。其中，我们重新发现了已知的例子，我们实际上确定了已建立的功能SNP，并发现了新的例子，包括基因ABCA12，CALD 1和ZNF 804，我们推测这些基因可能分别与皮肤，钙代谢和防御的适应有关。我们确定了已知的和许多新的候选地区的地理限制性积极选择，并提出了几个方向，为进一步的研究。
Population differentiation has proved to be effective for identifying loci under geographically localized positive selection, and has the potential to identify loci subject to balancing selection. We have previously investigated the pattern of genetic differentiation among human populations at 36.8 million genomic variants to identify sites in the genome showing high frequency differences. Here, we extend this dataset to include additional variants, survey sites with low levels of differentiation, and evaluate the extent to which highly differentiated sites are likely to result from selective or other processes. We demonstrate that while sites with low differentiation represent sampling effects rather than balancing selection, sites showing extremely high population differentiation are enriched for positive selection events and that one half may be the result of classic selective sweeps. Among these, we rediscover known examples, where we actually identify the established functional SNP, and discover novel examples including the genes ABCA12, CALD1 and ZNF804, which we speculate may be linked to adaptations in skin, calcium metabolism and defense, respectively. We identify known and many novel candidate regions for geographically restricted positive selection, and suggest several directions for further research.
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来自1,092个人基因组的遗传变异的综合图。
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
30.8
作者：
Enattah, NS;Sahi, T;Järvelä, I
通讯作者：
Järvelä, I
影响因子：
4.5
作者：
Engelken J;Carnero-Montoro E;Pybus M;Andrews GK;Lalueza-Fox C;Comas D;Sekler I;de la Rasilla M;Rosas A;Stoneking M;Valverde MA;Vicente R;Bosch E
通讯作者：
Bosch E
影响因子：
3.5
作者：
Abrams J;Davuluri G;Seiler C;Pack M
通讯作者：
Pack M
影响因子：
56.9
作者：
Grossman, Sharon R.;Shylakhter, Ilya;Sabeti, Pardis C.
通讯作者：
Sabeti, Pardis C.