Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas.
Development of a panel of genome-wide ancestry informative markers to study admixture throughout the Americas.
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DOI：
10.1371/journal.pgen.1002554
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发表时间：
2012
期刊：
影响因子：
4.5
通讯作者：
LACE Consortium
中科院分区：
文献类型：
--
作者：
Galanter JM;Fernandez-Lopez JC;Gignoux CR;Barnholtz-Sloan J;Fernandez-Rozadilla C;Via M;Hidalgo-Miranda A;Contreras AV;Figueroa LU;Raska P;Jimenez-Sanchez G;Zolezzi IS;Torres M;Ponte CR;Ruiz Y;Salas A;Nguyen E;Eng C;Borjas L;Zabala W;Barreto G;González FR;Ibarra A;Taboada P;Porras L;Moreno F;Bigham A;Gutierrez G;Brutsaert T;León-Velarde F;Moore LG;Vargas E;Cruz M;Escobedo J;Rodriguez-Santana J;Rodriguez-Cintrón W;Chapela R;Ford JG;Bustamante C;Seminara D;Shriver M;Ziv E;Burchard EG;Haile R;Parra E;Carracedo A;LACE Consortium
美洲的大多数个体都是美洲原住民、欧洲人和非洲人祖先的混合后代。复杂的历史因素造成了族裔群体内部和族裔群体之间个人之间祖先贡献的比例不同。我们开发了一个由446个血统信息标记（AIM）组成的小组，经过优化以估计整个拉丁美洲个人和群体的祖先比例。我们使用了来自不同非洲，欧洲和美洲原住民群体的953个个体的全基因组数据，以选择为构成现代拉丁美洲人口基础的三个主要大陆人群中的每一个优化的AIM。我们根据基因座特异性分支长度选择标记，这些标记信息丰富，在整个基因组中分布良好，能够在广泛可用的商业平台上进行基因分型，并通过最大限度地减少大陆内异质性而适用于整个美洲。然后，我们通过比较基于AIMs面板的祖先估计值与基于全基因组关联研究（GWAS）数据的估计值，在来自四个混合人群的样本中验证了面板。该小组在三个祖先群体之间提供了平衡的判别力，并准确估计了个体祖先比例（对于具有显著受试者间方差的祖先组分，R2>0.9）。最后，我们使用AIMs面板对来自拉丁美洲的18个人群的样本进行基因分型，并估计这些人群内和人群之间的祖先变异性。这个面板和它的参考基因型信息将是有用的资源，以探索人口历史的混合在拉丁美洲和纠正潜在的影响，人口分层的混合样本在该地区。来自拉丁美洲的个体是多个祖先群体的后代，主要是美洲原住民，欧洲人和非洲人的祖先。这些祖先的相对比例可以使用遗传标记来估计，称为祖先信息标记（AIM），其等位基因频率在祖先群体之间变化。一旦确定，这些祖先比例可以与正常表型相关，可以与疾病相关，可以用于控制由于群体分层引起的混淆，或者可以告知群体中的混合物历史。在这项研究中，我们确定了一组与拉丁美洲人群相关的AIM，通过将使用该小组的祖先估计值与从全基因组数据确定的祖先进行比较来验证该小组，并在来自美洲的一组不同人群中测试该小组。AIM小组产生的祖先估计是高度准确的，并适当控制人口分层，它被用来对来自整个拉丁美洲的18个人口进行基因分型。我们已经向任何有兴趣估计美洲人口祖先比例的研究人员提供了AIM小组。
Most individuals throughout the Americas are admixed descendants of Native American, European, and African ancestors. Complex historical factors have resulted in varying proportions of ancestral contributions between individuals within and among ethnic groups. We developed a panel of 446 ancestry informative markers (AIMs) optimized to estimate ancestral proportions in individuals and populations throughout Latin America. We used genome-wide data from 953 individuals from diverse African, European, and Native American populations to select AIMs optimized for each of the three main continental populations that form the basis of modern Latin American populations. We selected markers on the basis of locus-specific branch length to be informative, well distributed throughout the genome, capable of being genotyped on widely available commercial platforms, and applicable throughout the Americas by minimizing within-continent heterogeneity. We then validated the panel in samples from four admixed populations by comparing ancestry estimates based on the AIMs panel to estimates based on genome-wide association study (GWAS) data. The panel provided balanced discriminatory power among the three ancestral populations and accurate estimates of individual ancestry proportions (R2>0.9 for ancestral components with significant between-subject variance). Finally, we genotyped samples from 18 populations from Latin America using the AIMs panel and estimated variability in ancestry within and between these populations. This panel and its reference genotype information will be useful resources to explore population history of admixture in Latin America and to correct for the potential effects of population stratification in admixed samples in the region. Individuals from Latin America are descendants of multiple ancestral populations, primarily Native American, European, and African ancestors. The relative proportions of these ancestries can be estimated using genetic markers, known as ancestry informative markers (AIMs), whose allele frequency varies between the ancestral groups. Once determined, these ancestral proportions can be correlated with normal phenotypes, can be associated with disease, can be used to control for confounding due to population stratification, or can inform on the history of admixture in a population. In this study, we identified a panel of AIMs relevant to Latin American populations, validated the panel by comparing estimates of ancestry using the panel to ancestry determined from genome-wide data, and tested the panel in a diverse set of populations from the Americas. The panel of AIMs produces ancestry estimates that are highly accurate and appropriately controlled for population stratification, and it was used to genotype 18 populations from throughout Latin America. We have made the panel of AIMs available to any researcher interested in estimating ancestral proportions for populations from the Americas.
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影响因子：
8.2
作者：
Below, J. E.;Gamazon, E. R.;Morrison, J. V.;Konkashbaev, A.;Pluzhnikov, A.;McKeigue, P. M.;Parra, E. J.;Elbein, S. C.;Hallman, D. M.;Nicolae, D. L.;Bell, G. I.;Cruz, M.;Cox, N. J.;Hanis, C. L.
通讯作者：
Hanis, C. L.
影响因子：
64.8
作者：
Frazer, Kelly A.;Ballinger, Dennis G.;Cox, David R.;Hinds, David A.;Stuve, Laura L.;Gibbs, Richard A.;Belmont, John W.;Boudreau, Andrew;Hardenbol, Paul;Leal, Suzanne M.;Pasternak, Shiran;Wheeler, David A.;Willis, Thomas D.;Yu, Fuli;Yang, Huanming;Zeng, Changqing;Gao, Yang;Hu, Haoran;Hu, Weitao;Li, Chaohua;Lin, Wei;Liu, Siqi;Pan, Hao;Tang, Xiaoli;Wang, Jian;Wang, Wei;Yu, Jun;Zhang, Bo;Zhang, Qingrun;Zhao, Hongbin;Zhao, Hui;Zhou, Jun;Gabriel, Stacey B.;Barry, Rachel;Blumenstiel, Brendan;Camargo, Amy;Defelice, Matthew;Faggart, Maura;Goyette, Mary;Gupta, Supriya;Moore, Jamie;Nguyen, Huy;Onofrio, Robert C.;Parkin, Melissa;Roy, Jessica;Stahl, Erich;Winchester, Ellen;Ziaugra, Liuda;Altshuler, David;Shen, Yan;Yao, Zhijian;Huang, Wei;Chu, Xun;He, Yungang;Jin, Li;Liu, Yangfan;Shen, Yayun;Sun, Weiwei;Wang, Haifeng;Wang, Yi;Wang, Ying;Xiong, Xiaoyan;Xu, Liang;Waye, Mary M. Y.;Tsui, Stephen K. W.;Wong, J. Tze-Fei;Galver, Luana M.;Fan, Jian-Bing;Gunderson, Kevin;Murray, Sarah S.;Oliphant, Arnold R.;Chee, Mark S.;Montpetit, Alexandre;Chagnon, Fanny;Ferretti, Vincent;Leboeuf, Martin;Olivier, Jean-Franccois;Phillips, Michael S.;Roumy, Stephanie;Sallee, Clementine;Verner, Andrei;Hudson, Thomas J.;Kwok, Pui-Yan;Cai, Dongmei;Koboldt, Daniel C.;Miller, Raymond D.;Pawlikowska, Ludmila;Taillon-Miller, Patricia;Xiao, Ming;Tsui, Lap-Chee;Mak, William;Song, You Qiang;Tam, Paul K. H.;Nakamura, Yusuke;Kawaguchi, Takahisa;Kitamoto, Takuya;Morizono, Takashi;Nagashima, Atsushi;Ohnishi, Yozo;Sekine, Akihiro;Tanaka, Toshihiro;Tsunoda, Tatsuhiko;Deloukas, Panos;Bird, Christine P.;Delgado, Marcos;Dermitzakis, Emmanouil T.;Gwilliam, Rhian;Hunt, Sarah;Morrison, Jonathan;Powell, Don;Stranger, Barbara E.;Whittaker, Pamela;Bentley, David R.;Daly, Mark J.;de Bakker, Paul I. W.;Barrett, Jeff;Chretien, Yves R.;Maller, Julian;McCarroll, Steve;Patterson, Nick;Pe'er, Itsik;Price, Alkes;Purcell, Shaun;Richter, Daniel J.;Sabeti, Pardis;Saxena, Richa;Schaffner, Stephen F.;Sham, Pak C.;Varilly, Patrick;Altshuler, David;Stein, Lincoln D.;Krishnan, Lalitha;Smith, Albert Vernon;Tello-Ruiz, Marcela K.;Thorisson, Gudmundur A.;Chakravarti, Aravinda;Chen, Peter E.;Cutler, David J.;Kashuk, Carl S.;Lin, Shin;Abecasis, Goncalo R.;Guan, Weihua;Li, Yun;Munro, Heather M.;Qin, Zhaohui Steve;Thomas, Daryl J.;McVean, Gilean;Auton, Adam;Bottolo, Leonardo;Cardin, Niall;Eyheramendy, Susana;Freeman, Colin;Marchini, Jonathan;Myers, Simon;Spencer, Chris;Stephens, Matthew;Donnelly, Peter;Cardon, Lon R.;Clarke, Geraldine;Evans, David M.;Morris, Andrew P.;Weir, Bruce S.;Tsunoda, Tatsuhiko;Johnson, Todd A.;Mullikin, James C.;Sherry, Stephen T.;Feolo, Michael;Skol, Andrew
通讯作者：
Skol, Andrew
DOI：
10.1164/rccm.200309-1293oc
发表时间：
2004-02-01
影响因子：
24.7
作者：
Burchard, EG;Avila, PC;Silverman, EK
通讯作者：
Silverman, EK
影响因子：
4.4
作者：
Chen, Guanjie;Shriner, Daniel;Adeyemo, Adebowale
通讯作者：
Adeyemo, Adebowale
影响因子：
2.8
作者：
Fenner, JN
通讯作者：
Fenner, JN