AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays.
AccuTyping: new algorithms for automated analysis of data from high-throughput genotyping with oligonucleotide microarrays.
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DOI：
10.1093/nar/gkl601
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发表时间：
2006
影响因子：
14.9
通讯作者：
Li H
中科院分区：
文献类型：
--
作者：
Hu G;Wang HY;Greenawalt DM;Azaro MA;Luo M;Tereshchenko IV;Cui X;Yang Q;Gao R;Shen L;Li H
基于微阵列的单核苷酸多态性 (SNP) 分析在大规模遗传研究中有许多应用。为了尽量减少实验变异的影响，在基因型确定之前，微阵列数据通常需要进行不同方面的处理，包括背景扣除、归一化和低信号过滤。尽管许多算法对于这些目的来说都很复杂，但偏差仍然存在。本文介绍了SNP微阵列数据分析的新算法以及基于这些算法开发的软件AccuTyping。该算法利用了每次检测中包含的大量 SNP，并且根据信号强度之间的比率进行排序后，顶部和底部 20% 的 SNP 可以安全地视为纯合子。然后将这些 SNP 用作颜色通道标准化和背景扣除的对照。基因型识别是基于使用两个截止值的信号强度比的对数进行的，该截止值是在使用约 160 000 个基因型的数据集训练程序后确定的，并通过非微阵列方法进行验证。 AccuTyping 用于确定 DNA 和精子样本的 >300 000 种基因型。结果显示准确度 >99%。 AccuTyping 可以从 下载。
Microarray-based analysis of single nucleotide polymorphisms (SNPs) has many applications in large-scale genetic studies. To minimize the influence of experimental variation, microarray data usually need to be processed in different aspects including background subtraction, normalization and low-signal filtering before genotype determination. Although many algorithms are sophisticated for these purposes, biases are still present. In the present paper, new algorithms for SNP microarray data analysis and the software, AccuTyping, developed based on these algorithms are described. The algorithms take advantage of a large number of SNPs included in each assay, and the fact that the top and bottom 20% of SNPs can be safely treated as homozygous after sorting based on their ratios between the signal intensities. These SNPs are then used as controls for color channel normalization and background subtraction. Genotype calls are made based on the logarithms of signal intensity ratios using two cutoff values, which were determined after training the program with a dataset of ∼160 000 genotypes and validated by non-microarray methods. AccuTyping was used to determine >300 000 genotypes of DNA and sperm samples. The accuracy was shown to be >99%. AccuTyping can be downloaded from .
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影响因子：
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通讯作者：
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