SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data.
SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data.
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SNP HitLink：使用密集SNP数据的高通量链接分析系统。
DOI：
10.1186/1471-2105-10-121
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发表时间：
2009-04-24
影响因子：
3
通讯作者：
Tsuji S
中科院分区：
文献类型：
--
作者：
Fukuda Y;Nakahara Y;Date H;Takahashi Y;Goto J;Miyashita A;Kuwano R;Adachi H;Nakamura E;Tsuji S
在最近的十年中，基于微阵列的单核苷酸多态性（SNP）数据越来越广泛地用作疾病相关基因位点鉴定中的连锁分析的标记。虽然基于微阵列的SNP分析与基于微卫星的分析相比显著减少了基因分型时间和成本，但将这些巨大的数据应用于连锁分析程序是耗时的步骤，因此需要高通量平台。我们开发了SNP HiTLink（SNP High Tupt Linkage Analysis System）。在该系统中，可以直接导入AffytomeMapping 100 k/500 k阵列集和全基因组人类SNP阵列5.0/6.0的SNP芯片数据，并将其传递到参数或无模型连锁分析程序; MLINK、Superlink、Merlin和Allegro。实现了各种标记选择功能，以避免输入错误数据、连锁平衡标记或选择信息数据的影响。使用100 k SNP数据集的结果与从使用微卫星标记的分析获得的结果在获得的LOD分数方面相当或甚至上级。一般的个人计算机足以执行该过程，因为全基因组分析的运行时间不到几个小时。该系统可广泛应用于利用基于微阵列的SNP数据的连锁分析，并且可以期望高通量和可靠的连锁分析。
During this recent decade, microarray-based single nucleotide polymorphism (SNP) data are becoming more widely used as markers for linkage analysis in the identification of loci for disease-associated genes. Although microarray-based SNP analyses have markedly reduced genotyping time and cost compared with microsatellite-based analyses, applying these enormous data to linkage analysis programs is a time-consuming step, thus, necessitating a high-throughput platform. We have developed SNP HiTLink (SNP High Throughput Linkage analysis system). In this system, SNP chip data of the Affymetrix Mapping 100 k/500 k array set and Genome-Wide Human SNP array 5.0/6.0 can be directly imported and passed to parametric or model-free linkage analysis programs; MLINK, Superlink, Merlin and Allegro. Various marker-selecting functions are implemented to avoid the effect of typing-error data, markers in linkage equilibrium or to select informative data. The results using the 100 k SNP dataset were comparable or even superior to those obtained from analyses using microsatellite markers in terms of LOD scores obtained. General personal computers are sufficient to execute the process, as runtime for whole-genome analysis was less than a few hours. This system can be widely applied to linkage analysis using microarray-based SNP data and with which one can expect high-throughput and reliable linkage analysis.
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影响因子：
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作者：
Gaunt, Tom R.;Rodriguez, Santiago;Day, Ian N. M.
通讯作者：
Day, Ian N. M.
影响因子：
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