A strategy for oligonucleotide microarray probe reduction.
A strategy for oligonucleotide microarray probe reduction.
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DOI：
10.1186/gb-2002-3-12-research0073
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发表时间：
2002
期刊：
影响因子：
12.3
通讯作者：
中科院分区：
文献类型：
--
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限制高密度寡核苷酸阵列上可以分析的基因数量的因素之一是每个转录本都需要多个寡核苷酸探针来探测。为了减少每个基因所需的探针数量，需要一种系统的方法来选择最具代表性的探针。提出了一种可推广的经验方法，以减少每个基因的探针数量，同时最大限度地保持原始阵列设计的保真度。限制高密度寡核苷酸阵列上可以分析的基因数量的因素之一是每个转录本都需要多个寡核苷酸探针来探测。为了减少每个基因所需的探针数量，需要一种系统的方法来选择最具代表性的探针。提出了一种减少每个基因探针数量的方法，同时最大限度地保持原始阵列设计的保真度。该方法已在包含317 Affymetrix HuGeneFL基因芯片的数据集上进行了测试。在四个癌症分类问题中，比较了原始探针集和简化探针集的性能。这些比较的结果表明，减少95%的探针设置不会显着影响性能，从而说明了在不显着损害检测灵敏度和特异性的情况下大幅减少探针数量的可行性。这里描述的策略对于设计用于筛选应用的小的、有限探针的全基因组阵列是潜在的有用的。
One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number of probes required for each gene, a systematic approach to choosing the most representative probes is needed. A generalizable empiric method is presented for reducing the number of probes per gene while maximizing the fidelity to the original array design. One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number of probes required for each gene, a systematic approach to choosing the most representative probes is needed. A method is presented for reducing the number of probes per gene while maximizing the fidelity to the original array design. The methodology has been tested on a dataset comprising 317 Affymetrix HuGeneFL GeneChips. The performance of the original and reduced probe sets was compared in four cancer-classification problems. The results of these comparisons show that reduction of the probe set by 95% does not dramatically affect performance, and thus illustrate the feasibility of substantially reducing probe numbers without significantly compromising sensitivity and specificity of detection. The strategy described here is potentially useful for designing small, limited-probe genome-wide arrays for screening applications.