Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays.
Comprehensive quality control utilizing the prehybridization third-dye image leads to accurate gene expression measurements by cDNA microarrays.
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DOI：
10.1186/1471-2105-7-378
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发表时间：
2006-08-14
影响因子：
3
通讯作者：
Hessner MJ
中科院分区：
文献类型：
--
作者：
Wang X;Jia S;Meyer L;Xiang B;Chen LY;Jiang N;Moreno C;Jacob HJ;Ghosh S;Hessner MJ
使用微阵列进行基因表达谱分析已成为重要的遗传工具。学术实验室制备的点阵具有成本低、设计和内容灵活性高等优点，但往往受到质量控制 (QC) 问题敏感性的限制。此前，我们报道了一种新型三色微阵列技术，可实现阵列制造质量控制。在本报告中，我们进一步研究了其在现场数据质量控制方面的优势。我们发现可用于杂交的结合探针数量不足会导致比率测量中显着的基因特异性压缩、数据变异性增加以及打印引脚依赖性异质性。此类问题的影响可以通过质量分数的定义来捕获，并通过质量相关的过滤和标准化来有效控制。我们将使用我们的数据处理流程得出的基因表达测量结果与对照克隆中已知的加标输入比率以及定量实时 RT-PCR 的测量结果进行了比较。在每种情况下，都观察到高度线性关系（R2>0.94），微阵列测量中具有适度的压缩（校正因子<1.17）。我们的微阵列分析和技术进步能够更好地剖析数据变异性的来源，从而实现更有效的质量控制。利用 cDNA 微阵列技术可以实现高度准确的基因表达测量。
Gene expression profiling using microarrays has become an important genetic tool. Spotted arrays prepared in academic labs have the advantage of low cost and high design and content flexibility, but are often limited by their susceptibility to quality control (QC) issues. Previously, we have reported a novel 3-color microarray technology that enabled array fabrication QC. In this report we further investigated its advantage in spot-level data QC. We found that inadequate amount of bound probes available for hybridization led to significant, gene-specific compression in ratio measurements, increased data variability, and printing pin dependent heterogeneities. The impact of such problems can be captured through the definition of quality scores, and efficiently controlled through quality-dependent filtering and normalization. We compared gene expression measurements derived using our data processing pipeline with the known input ratios of spiked in control clones, and with the measurements by quantitative real time RT-PCR. In each case, highly linear relationships (R2>0.94) were observed, with modest compression in the microarray measurements (correction factor<1.17). Our microarray analytical and technical advancements enabled a better dissection of the sources of data variability and hence a more efficient QC. With that highly accurate gene expression measurements can be achieved using the cDNA microarray technology.
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影响因子：
4.4
作者：
Hessner MJ;Singh VK;Wang X;Khan S;Tschannen MR;Zahrt TC
通讯作者：
Zahrt TC
影响因子：
2.7
作者：
Wang, YM;Wang, XJ;Ghosh, S
通讯作者：
Ghosh, S
影响因子：
3.4
作者：
Wang, XJ;Becker, FF;Gascoyne, PRC
通讯作者：
Gascoyne, PRC
影响因子：
4.1
作者：
Rajeevan, MS;Vernon, SD;Unger, ER
通讯作者：
Unger, ER
影响因子：
48
作者：
Bammler, T;Beyer, RP;Zarbl, H
通讯作者：
Zarbl, H