Protocol for detecting introgressed archaic variants with SPrime.
Protocol for detecting introgressed archaic variants with SPrime.
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DOI：
10.1016/j.xpro.2021.100550
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发表时间：
2021-06-18
期刊：
影响因子：
--
通讯作者：
Browning SR
中科院分区：
文献类型：
--
作者：
Zhou Y;Browning SR
SPrime程序可以检测到当前种群中的变异，这些变异是从过去的古老来源中渗入的。它被优化用于检测现代人类中尼安德特人和丹尼索瓦人的基因渗入。我们提供了一个检测尼安德特人和丹尼索瓦人基因渗入1000个基因组计划数据的协议，特别关注CHB（北京汉族）人口。有关本方案使用和执行的完整详细信息，请参阅。该方案描述了如何运行和解释SPrime的结果SPrime识别从古代来源群体渐渗的变体，并提供了用于将SPrime结果与古代基因组进行比较的方法SPrime程序检测过去从古代来源渐渗的当前群体中的变体。它被优化用于检测现代人类中尼安德特人和丹尼索瓦人的基因渗入。我们提供了一个检测尼安德特人和丹尼索瓦人基因渗入1000个基因组计划数据的协议，特别关注CHB（北京汉族）人口。
The SPrime program detects the variants in current-day populations that were introgressed from an archaic source in the past. It is optimized for detecting introgression from Neanderthals and Denisovans in modern humans. We provide a protocol for detecting Neanderthal and Denisovan introgression in 1000 Genomes Project data, specifically focusing on the CHB (Han Chinese in Beijing) population. For complete details on the use and execution of this protocol, please refer to. This protocol describes how to run and interpret the results of SPrime SPrime identifies variants that are introgressed from an archaic source population Scripts for comparing the SPrime results to archaic genomes are provided The SPrime program detects the variants in current-day populations that were introgressed from an archaic source in the past. It is optimized for detecting introgression from Neanderthals and Denisovans in modern humans. We provide a protocol for detecting Neanderthal and Denisovan introgression in 1000 Genomes Project data, specifically focusing on the CHB (Han Chinese in Beijing) population.
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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
影响因子：
64.5
作者：
Browning SR;Browning BL;Zhou Y;Tucci S;Akey JM
通讯作者：
Akey JM
克罗地亚文迪亚洞穴的高覆盖率尼安德特人基因组
DOI：
10.1126/science.aao1887
发表时间：
2017-11-03
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Prüfer K;de Filippo C;Grote S;Mafessoni F;Korlević P;Hajdinjak M;Vernot B;Skov L;Hsieh P;Peyrégne S;Reher D;Hopfe C;Nagel S;Maricic T;Fu Q;Theunert C;Rogers R;Skoglund P;Chintalapati M;Dannemann M;Nelson BJ;Key FM;Rudan P;Kućan Ž;Gušić I;Golovanova LV;Doronichev VB;Patterson N;Reich D;Eichler EE;Slatkin M;Schierup MH;Andrés AM;Kelso J;Meyer M;Pääbo S
通讯作者：
Pääbo S
影响因子：
5.8
作者：
Danecek, Petr;Auton, Adam;Durbin, Richard
通讯作者：
Durbin, Richard
影响因子：
64.8
作者：
1000 Genomes Project Consortium;Auton A;Brooks LD;Durbin RM;Garrison EP;Kang HM;Korbel JO;Marchini JL;McCarthy S;McVean GA;Abecasis GR
通讯作者：
Abecasis GR