ALDsuite: Dense marker MALD using principal components of ancestral linkage disequilibrium.
ALDsuite: Dense marker MALD using principal components of ancestral linkage disequilibrium.
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DOI：
10.1186/s12863-015-0179-y
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发表时间：
2015-03-07
期刊：
影响因子：
2.9
通讯作者：
Winkler CA
中科院分区：
文献类型：
--
作者：
Johnson RC;Nelson GW;Zagury JF;Winkler CA
混合连锁不平衡定位（MALD）是一种全基因组基因定位方法，它利用来自混合个体亲本群体遗传的扩展祖先块的LD来绘制人类群体中患病率不同的疾病的关联。与标准的全基因组关联研究相比，查询标记与祖先关联的扩展LD大大减少了比较数量。由于祖先种群LD容易混淆混合LD的分析，早期的MALD算法要求标记集足够稀疏，从而使标记间缺乏显著的祖先LD。然而，目前的基因分型技术通常提供密集的SNP数据，如果这些信息可以有效地利用，它们比稀疏集传递更多的信息。目前还没有软件解决方案可以同时提供使用密集标记数据和疾病关联统计的本地祖先推断。我们在这里介绍了一个R软件包，ALDsuite，它使用来自代祖先群体数据的单倍型的主要成分来计算本地LD，并包括数据质量控制，MALD，结果下游分析和可视化图形的工具。ALDsuite提供快速、准确的全球和本地祖先估计，并与MALD所需的工具捆绑在一起，从数据质量控制到疾病基因的映射和可视化。
Mapping by admixture linkage disequilibrium (MALD) is a whole genome gene mapping method that uses LD from extended blocks of ancestry inherited from parental populations among admixed individuals to map associations for diseases, that vary in prevalence among human populations. The extended LD queried for marker association with ancestry results in a greatly reduced number of comparisons compared to standard genome wide association studies. As ancestral population LD tends to confound the analysis of admixture LD, the earliest algorithms for MALD required marker sets sufficiently sparse to lack significant ancestral LD between markers. However current genotyping technologies routinely provide dense SNP data, which convey more information than sparse sets, if this information can be efficiently used. There are currently no software solutions that offer both local ancestry inference using dense marker data and disease association statistics. We present here an R package, ALDsuite, which accounts for local LD using principal components of haplotypes from surrogate ancestral population data, and includes tools for quality control of data, MALD, downstream analysis of results and visualization graphics. ALDsuite offers a fast, accurate estimation of global and local ancestry and comes bundled with the tools needed for MALD, from data quality control through mapping of and visualization of disease genes.
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影响因子：
30.8
作者：
Kopp, Jeffrey B.;Smith, Michael W.;Nelson, George W.;Johnson, Randall C.;Freedman, Barry I.;Bowden, Donald W.;Oleksyk, Taras;McKenzie, Louise M.;Kajiyama, Hiroshi;Ahuja, Tejinder S.;Berns, Jeffrey S.;Briggs, William;Cho, Monique E.;Dart, Richard A.;Kimmel, Paul L.;Korbet, Stephen M.;Michel, Donna M.;Mokrzycki, Michele H.;Schelling, Jeffrey R.;Simon, Eric;Trachtman, Howard;Vlahov, David;Winkler, Cheryl A.
通讯作者：
Winkler, Cheryl A.
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：
9.8
作者：
Parra, EJ;Marcini, A;Shriver, MD
通讯作者：
Shriver, MD
影响因子：
2.1
作者：
Churchhouse, Claire;Marchini, Jonathan
通讯作者：
Marchini, Jonathan
影响因子：
9.8
作者：
Nalls, Michael A.;Wilson, James G.;Ziv, Elad
通讯作者：
Ziv, Elad