Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags.
Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags.
复制标题
鉴定具有低覆盖度、配偶配对限制标签的中等大小基因组缺失
DOI：
10.1186/1471-2164-14-51
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发表时间：
2013-01-24
期刊：
影响因子：
4.4
通讯作者：
Wu CI
中科院分区：
文献类型：
--
作者：
Gong Q;Tao Y;Yang JR;Cai J;Yuan Y;Ruan J;Yang J;Liu H;Li W;Lu X;Zhuang SM;Wang SM;Wu CI
背景基因组缺失广泛存在于许多物种中。已经开发了基于变异测序的方法来识别缺失，但它们的权力来检测那些影响中等大小的区域的缺失是有限的，当测序coverage is low.ResultsWe提出了一个具有成本效益的方法，用于识别中等大小的缺失在基因组区域低基因组覆盖率。从人癌组织分别构建两个配对文库，以从用4-碱基限制酶消化的限制片段产生配对短读段（双标签）。收集总共3Gb的配对读段（1.0×基因组大小），并且通过鉴定与参考基因组序列具有无序比对的双标签来推断175个缺失。桑格测序结果证实总体检测准确率为95%。良好的再现性被验证的缺失，由两个library.ConclusionsWe检测提供了一种方法来准确地识别中等大小的缺失，在大基因组低序列覆盖率。它可应用于比较基因组学研究以及种系和体细胞变异的鉴定。
BackgroundGenomic deletions are known to be widespread in many species. Variant sequencing-based approaches for identifying deletions have been developed, but their powers to detect those deletions that affect medium-sized regions are limited when the sequencing coverage is low.ResultsWe present a cost-effective method for identifying medium-sized deletions in genomic regions with low genomic coverage. Two mate-paired libraries were separately constructed from human cancerous tissue to generate paired short reads (ditags) from restriction fragments digested with a 4-base restriction enzyme. A total of 3 Gb of paired reads (1.0× genome size) was collected, and 175 deletions were inferred by identifying the ditags with disorder alignments to the reference genome sequence. Sanger sequencing results confirmed an overall detection accuracy of 95%. Good reproducibility was verified by the deletions that were detected by both libraries.ConclusionsWe provide an approach to accurately identify medium-sized deletions in large genomes with low sequence coverage. It can be applied in studies of comparative genomics and in the identification of germline and somatic variants.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
17.1
作者：
Leary RJ;Kinde I;Diehl F;Schmidt K;Clouser C;Duncan C;Antipova A;Lee C;McKernan K;De La Vega FM;Kinzler KW;Vogelstein B;Diaz LA Jr;Velculescu VE
通讯作者：
Velculescu VE
影响因子：
30.8
作者：
Iafrate, AJ;Feuk, L;Lee, C
通讯作者：
Lee, C
影响因子：
56.9
作者：
Sebat, J;Lakshmi, B;Wigler, M
通讯作者：
Wigler, M
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