Spatial localization of recent ancestors for admixed individuals.
Spatial localization of recent ancestors for admixed individuals.
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DOI：
10.1534/g3.114.014274
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发表时间：
2014-11-03
期刊：
影响因子：
--
通讯作者：
Pasaniuc B
中科院分区：
文献类型：
--
作者：
Yang WY;Platt A;Chiang CW;Eskin E;Novembre J;Pasaniuc B
遗传数据的遗传学分析在人类疾病和进化的研究中起着至关重要的作用。最近的工作已经引入了明确的遗传变异的地理分布模型，并已表明，这种明确的模型产生上级准确性的祖先推断非模型为基础的方法。在这里，我们扩展了此类工作，引入了一种对地理连续体中多个来源的祖先之间的混合进行建模的方法。我们设计了基于隐马尔可夫模型的有效算法，以在地图上定位最近的祖先（例如，祖父母）的混合个体，联合分配祖先在基因组中的每个位点。我们验证了我们的方法，通过使用来自人口参考样本研究的混合欧洲血统的个人的经验数据，并表明我们的方法能够将他们最近的祖先定位在他们祖父母报告的位置的平均470公里内。此外，模拟从真实的人口参考样本基因型数据表明，我们的方法达到了很高的准确性在本地化最近的祖先在欧洲的混合个体（平均550公里，从他们的真实位置在欧洲的两个祖先，四代前的本地化）。我们探讨了我们的方法下的祖先本地化的限制，并发现性能下降的不同的祖先和世代的数量，因为混合物的增加。最后，我们建立了一个地图的预期定位精度在混合个人根据其祖先的起源在欧洲的位置。
Ancestry analysis from genetic data plays a critical role in studies of human disease and evolution. Recent work has introduced explicit models for the geographic distribution of genetic variation and has shown that such explicit models yield superior accuracy in ancestry inference over nonmodel-based methods. Here we extend such work to introduce a method that models admixture between ancestors from multiple sources across a geographic continuum. We devise efficient algorithms based on hidden Markov models to localize on a map the recent ancestors (e.g., grandparents) of admixed individuals, joint with assigning ancestry at each locus in the genome. We validate our methods by using empirical data from individuals with mixed European ancestry from the Population Reference Sample study and show that our approach is able to localize their recent ancestors within an average of 470 km of the reported locations of their grandparents. Furthermore, simulations from real Population Reference Sample genotype data show that our method attains high accuracy in localizing recent ancestors of admixed individuals in Europe (an average of 550 km from their true location for localization of two ancestries in Europe, four generations ago). We explore the limits of ancestry localization under our approach and find that performance decreases as the number of distinct ancestries and generations since admixture increases. Finally, we build a map of expected localization accuracy across admixed individuals according to the location of origin within Europe of their ancestors.
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影响因子：
4.5
作者：
Paschou, Peristera;Ziv, Elad;Burchard, Esteban G.;Choudhry, Shweta;Rodriguez-Cintron, William;Mahoney, Michael W.;Drineas, Petros
通讯作者：
Drineas, Petros
影响因子：
3.7
作者：
Drineas, Petros;Lewis, Jamey;Paschou, Peristera
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4.5
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Moreno-Estrada A;Gravel S;Zakharia F;McCauley JL;Byrnes JK;Gignoux CR;Ortiz-Tello PA;Martínez RJ;Hedges DJ;Morris RW;Eng C;Sandoval K;Acevedo-Acevedo S;Norman PJ;Layrisse Z;Parham P;Martínez-Cruzado JC;Burchard EG;Cuccaro ML;Martin ER;Bustamante CD
通讯作者：
Bustamante CD
影响因子：
5.3
作者：
Basu A;Tang H;Zhu X;Gu CC;Hanis C;Boerwinkle E;Risch N
通讯作者：
Risch N
影响因子：
4.5
作者：
Johnson NA;Coram MA;Shriver MD;Romieu I;Barsh GS;London SJ;Tang H
通讯作者：
Tang H