Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing.
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DOI：
10.1038/nbt.1523
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发表时间：
2009-02
影响因子：
46.9
通讯作者：
Nusbaum C
中科院分区：
文献类型：
--
作者：
Gnirke A;Melnikov A;Maguire J;Rogov P;LeProust EM;Brockman W;Fennell T;Giannoukos G;Fisher S;Russ C;Gabriel S;Jaffe DB;Lander ES;Nusbaum C
通过大规模平行测序来定位基因组位点，需要新的方法来丰富待测序模板。我们开发了一种捕获方法，使用生物素化的RNA“诱饵”从DNA片段的“池塘”中“钓”出目标。RNA是从pcr扩增的寡脱氧核苷酸转录而来，最初是在微阵列上合成的，在足够高的浓度下产生足够的诱饵进行多次捕获，以驱动杂交。我们使用Illumina测序作为读出，用170-mer的诱饵测试了该方法，该诱饵针对bbb15000个编码外显子（2.5 Mb）和4个区域（总计1.7 Mb）。约90%的独特对准碱基落在诱饵序列上或附近；高达50%位于外显子上。这种均匀性使得外显子“捕获”中~60%的目标碱基和区域捕获中~80%的目标碱基至少具有平均覆盖率的一半。一列Illumina序列足以对89%的目标外显子空间称为高置信度基因型。
Targeting genomic loci by massively parallel sequencing requires new methods to enrich templates to be sequenced. We developed a capture method that uses biotinylated RNA “baits” to “fish” targets out of a “pond” of DNA fragments. The RNA is transcribed from PCR-amplified oligodeoxynucleotides originally synthesized on a microarray, generating sufficient bait for multiple captures at concentrations high enough to drive the hybridization. We tested this method with 170-mer baits that target >15,000 coding exons (2.5 Mb) and four regions (1.7 Mb total) using Illumina sequencing as read-out. About 90% of uniquely aligning bases fell on or near bait sequence; up to 50% lay on exons proper. The uniformity was such that ~60% of target bases in the exonic “catch”, and ~80% in the regional catch, had at least half the mean coverage. One lane of Illumina sequence was sufficient to call high-confidence genotypes for 89% of the targeted exon space.
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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：
14.9
作者：
Fredriksson S;Banér J;Dahl F;Chu A;Ji H;Welch K;Davis RW
通讯作者：
Davis RW
DOI：
10.1073/pnas.0702165104
发表时间：
2007-05-29
影响因子：
11.1
作者：
Dahl, Fredrik;Stenberg, Johan;Ji, Hanlee
通讯作者：
Ji, Hanlee
影响因子：
56.9
作者：
Shendure, J;Porreca, GJ;Church, GM
通讯作者：
Church, GM
亚洲个体的二倍体基因组序列
影响因子：
64.8
作者：
Wang, Jun;Wang, Wei;Li, Ruiqiang;Li, Yingrui;Tian, Geng;Goodman, Laurie;Fan, Wei;Zhang, Junqing;Li, Jun;Zhang, Juanbin;Guo, Yiran;Feng, Binxiao;Li, Heng;Lu, Yao;Fang, Xiaodong;Liang, Huiqing;Du, Zhenglin;Li, Dong;Zhao, Yiqing;Hu, Yujie;Yang, Zhenzhen;Zheng, Hancheng;Hellmann, Ines;Inouye, Michael;Pool, John;Yi, Xin;Zhao, Jing;Duan, Jinjie;Zhou, Yan;Qin, Junjie;Ma, Lijia;Li, Guoqing;Yang, Zhentao;Zhang, Guojie;Yang, Bin;Yu, Chang;Liang, Fang;Li, Wenjie;Li, Shaochuan;Li, Dawei;Ni, Peixiang;Ruan, Jue;Li, Qibin;Zhu, Hongmei;Liu, Dongyuan;Lu, Zhike;Li, Ning;Guo, Guangwu;Zhang, Jianguo;Ye, Jia;Fang, Lin;Hao, Qin;Chen, Quan;Liang, Yu;Su, Yeyang;San, A.;Ping, Cuo;Yang, Shuang;Chen, Fang;Li, Li;Zhou, Ke;Zheng, Hongkun;Ren, Yuanyuan;Yang, Ling;Gao, Yang;Yang, Guohua;Li, Zhuo;Feng, Xiaoli;Kristiansen, Karsten;Wong, Gane Ka-Shu;Nielsen, Rasmus;Durbin, Richard;Bolund, Lars;Zhang, Xiuqing;Li, Songgang;Yang, Huanming;Wang, Jian
通讯作者：
Wang, Jian