SNP-specific extraction of haplotype-resolved targeted genomic regions.
SNP-specific extraction of haplotype-resolved targeted genomic regions.
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DOI：
10.1093/nar/gkn345
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发表时间：
2008-09
影响因子：
14.9
通讯作者：
Monos D
中科院分区：
文献类型：
--
作者：
Dapprich J;Ferriola D;Magira EE;Kunkel M;Monos D
随着对复杂性状进行全面遗传分析的基因分型平台的出现，已有大量研究报道了特定的单核苷酸多态(SNPs)与常见疾病或药物反应的关系。然而，对这些相关区域的详细遗传分析，将特定的多态与表型相关联，一直滞后。这主要是由于缺乏提供有关特定SNPs周围基因组区域的额外序列信息的技术，最好是单倍体形式。重新测序的浓缩方法应具有特异性，以提供与感兴趣的单核苷酸多态相关的DNA，具有足够的质量，以便以具有成本效益和高通量的方式使用。我们描述了一种简单、自动化的方法，目标是特定的基因组DNA序列，可以直接用于下游应用。该方法通过将寡核苷酸与生物素化的核苷酸杂交并酶促延长目标SNPs两侧的单倍体染色体区域，基于它们与区分一个等位基因与任何其他不同序列的独特序列元素的选择性结合。目标基因组区域由包被链霉亲和素的磁性颗粒捕获，并通过标准的基因分型、测序或微阵列分析进行分析。我们应用这项技术来确定主要组织相容性复合体的∼150kb基因组区域上的连续分子单倍型。
The availability of genotyping platforms for comprehensive genetic analysis of complex traits has resulted in a plethora of studies reporting the association of specific single-nucleotide polymorphisms (SNPs) with common diseases or drug responses. However, detailed genetic analysis of these associated regions that would correlate particular polymorphisms to phenotypes has lagged. This is primarily due to the lack of technologies that provide additional sequence information about genomic regions surrounding specific SNPs, preferably in haploid form. Enrichment methods for resequencing should have the specificity to provide DNA linked to SNPs of interest with sufficient quality to be used in a cost-effective and high-throughput manner. We describe a simple, automated method of targeting specific sequences of genomic DNA that can directly be used in downstream applications. The method isolates haploid chromosomal regions flanking targeted SNPs by hybridizing and enzymatically elongating oligonucleotides with biotinylated nucleotides based on their selective binding to unique sequence elements that differentiate one allele from any other differing sequence. The targeted genomic region is captured by streptavidin-coated magnetic particles and analyzed by standard genotyping, sequencing or microarray analysis. We applied this technology to determine contiguous molecular haplotypes across a ∼150 kb genomic region of the major histocompatibility complex.
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影响因子：
56.9
作者：
Duerr, Richard H.;Taylor, Kent D.;Cho, Judy H.
通讯作者：
Cho, Judy H.
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通讯作者：
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