Characterization of missing human genome sequences and copy-number polymorphic insertions.
Characterization of missing human genome sequences and copy-number polymorphic insertions.
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DOI：
10.1038/nmeth.1451
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发表时间：
2010-05
期刊：
影响因子：
48
通讯作者：
Eichler, Evan E.
中科院分区：
文献类型：
--
作者：
Kidd, Jeffrey M.;Sampas, Nick;Antonacci, Francesca;Graves, Tina;Fulton, Robert;Hayden, Hillary S.;Alkan, Can;Malig, Maika;Ventura, Mario;Giannuzzi, Giuliana;Kallicki, Joelle;Anderson, Paige;Tsalenko, Anya;Yamada, N. Alice;Tsang, Peter;Kaul, Rajinder;Wilson, Richard K.;Bruhn, Laurakay;Eichler, Evan E.
人类基因组结构变异的程度表明，基因组中必然存在一些部分尚未在序列层面被发现、注释和描述特征。我们提供了一种资源，并对对应720个基因组位点的2363个新的插入序列进行了分析。我们表明，与近期来自短读长下一代测序数据的从头测序组装结果相比，这些序列中有相当大一部分要么缺失，要么片段化，要么错误分配。我们确定这些新插入序列中有18 - 37%是拷贝数多态的，包括在欧洲人、亚洲人和非洲人之间显示出广泛群体分层的位点。对其中156个插入序列的完整测序确定了参考基因组中尚未呈现的新外显子和保守的非编码序列。我们开发了一种方法，通过将下一代测序数据集映射到断点来准确地对这些新插入序列进行基因分型，从而为描述先前单核苷酸多态性微阵列无法检测的区域的拷贝数状态提供了一种手段。
The extent of human genomic structural variation suggests that there must be portions of the genome yet to be discovered, annotated and characterized at the sequence level. We present a resource and analysis of 2,363 novel insertion sequences corresponding to 720 genomic loci. We show that a substantial fraction of these sequences are either missing, fragmented or mis-assigned when compared to recent de novo sequence assemblies from short-read next-generation sequence data. We determine that 18–37% of these novel insertions are copy-number polymorphic, including loci that show extensive population stratification among Europeans, Asians and Africans. Complete sequencing of 156 of these insertions identifies novel exons and conserved non-coding sequences not yet represented in the reference genome. We develop a method to accurately genotype these novel insertions by mapping next-generation sequencing datasets to the breakpoint thereby providing a means to characterize copy-number status for regions previously inaccessible to SNP microarrays.
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影响因子：
30.8
作者：
Alkan, Can;Kidd, Jeffrey M.;Marques-Bonet, Tomas;Aksay, Gozde;Antonacci, Francesca;Hormozdiari, Fereydoun;Kitzman, Jacob O.;Baker, Carl;Malig, Maika;Mutlu, Onur;Sahinalp, S. Cenk;Gibbs, Richard A.;Eichler, Evan E.
通讯作者：
Eichler, Evan E.
影响因子：
64.8
作者：
Eichler, Evan E.;Nickerson, Deborah A.;Altshuler, David;Bowcock, Anne M.;Brooks, Lisa D.;Carter, Nigel P.;Church, Deanna M.;Felsenfeld, Adam;Guyer, Mark;Lee, Charles;Lupski, James R.;Mullikin, James C.;Pritchard, Jonathan K.;Sebat, Jonathan;Sherry, Stephen T.;Smith, Douglas;Valle, David;Waterston, Robert H.
通讯作者：
Waterston, Robert H.
影响因子：
30.8
作者：
Enattah, NS;Sahi, T;Järvelä, I
通讯作者：
Järvelä, I
影响因子：
64.8
作者：
通讯作者：
--
影响因子：
14.9
作者：
Pruitt KD;Tatusova T;Klimke W;Maglott DR
通讯作者：
Maglott DR