Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.
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DOI：
10.1038/nbt.2303
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发表时间：
2012-08
影响因子：
46.9
通讯作者：
中科院分区：
文献类型：
--
作者：
我们描述了纳米通道阵列上的基因组作图。在这种方法中，单个DNA分子中的特定序列基序被荧光标记，并且DNA分子在纳米流体装置上的数千个硅通道中均匀拉伸。荧光成像允许构建序列基序出现之间的物理距离的图。我们展示了分析，单独和混合物，95个细菌人工染色体（BAC）克隆，覆盖4.7 Mb的人类主要组织相容性复合体区域。我们获得了准确的、单倍型分辨的序列基序图，长度为数百个碱基，导致BAC的中位数覆盖率为114×。最后的序列基序图谱组装包含三个重叠群。标记之间的平均距离为9 kb，我们检测到22个单倍型差异。我们还使用序列基序图为测序数据的从头组装提供支架。纳米通道基因组作图应有助于从二倍体生物体的复杂区域重新组装测序读数、单倍型和结构变异分析以及比较基因组学。
We describe genome mapping on nanochannel arrays. In this approach, specific sequence motifs in single DNA molecules are fluorescently labeled, and the DNA molecules are uniformly stretched in thousands of silicon channels on a nanofluidic device. Fluorescence imaging allows the construction of maps of the physical distances between occurrences of the sequence motifs. We demonstrate the analysis, individually and as mixtures, of 95 bacterial artificial chromosome (BAC) clones that cover the 4.7-Mb human major histocompatibility complex region. We obtain accurate, haplotype-resolved, sequence motif maps hundreds of kilobases in length, resulting in a median coverage of 114× for the BACs. The final sequence motif map assembly contains three contigs. With an average distance of 9 kb between labels, we detect 22 haplotype differences. We also use the sequence motif maps to provide scaffolds for de novo assembly of sequencing data. Nanochannel genome mapping should facilitate de novo assembly of sequencing reads from complex regions in diploid organisms, haplotype and structural variation analysis and comparative genomics.
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影响因子：
9.8
作者：
Church DM;Goodstadt L;Hillier LW;Zody MC;Goldstein S;She X;Bult CJ;Agarwala R;Cherry JL;DiCuccio M;Hlavina W;Kapustin Y;Meric P;Maglott D;Birtle Z;Marques AC;Graves T;Zhou S;Teague B;Potamousis K;Churas C;Place M;Herschleb J;Runnheim R;Forrest D;Amos-Landgraf J;Schwartz DC;Cheng Z;Lindblad-Toh K;Eichler EE;Ponting CP;Mouse Genome Sequencing Consortium
通讯作者：
Mouse Genome Sequencing Consortium
影响因子：
4
作者：
Cao, H;Tegenfeldt, JO;Chou, SY
通讯作者：
Chou, SY
影响因子：
30.8
作者：
Iafrate, AJ;Feuk, L;Lee, C
通讯作者：
Lee, C
DOI：
10.1073/pnas.95.14.8046
发表时间：
1998-07-07
影响因子：
11.1
作者：
Jing, JP;Reed, J;Schwartz, DC
通讯作者：
Schwartz, DC
影响因子：
7
作者：
Li, Ruiqiang;Zhu, Hongmei;Wang, Jun
通讯作者：
Wang, Jun