Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.
Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.
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DOI：
10.1371/journal.pone.0023727
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Loy A
中科院分区：
文献类型：
--
作者：
Steger D;Berry D;Haider S;Horn M;Wagner M;Stocker R;Loy A
核酸靶点与表面固定化探针的杂交是医学和生物学研究中广泛应用的多靶点平行检测方法。尽管应用广泛，但DNA微阵列技术仍然存在一些偏差和缺乏可重复性，部分原因是对表面杂交过程的不完全理解。特别是，个体微阵列杂交中的非随机空间变化经常被观察到，但支撑这种位置偏差的机制仍然没有完全解释。本研究确定并合理化了表面杂交强度的系统空间偏差，其特征是位于微阵列载玻片斑点区域边界的斑点信号强度显着增加。结合简化单探针块阵列格式的观察结果和数学模型的预测，发现造成这种偏差的机制是靶分子横向扩散的位置依赖性变化。数值模拟表明，微阵列孔的几何形状对空间偏置有很大的影响。微阵列杂交室的大小与表面结合探针的面积相互调节是一种简单有效的措施，可以减少或消除基于扩散的偏差，从而提高定量DNA微阵列杂交的均匀性和准确性。
The hybridization of nucleic acid targets with surface-immobilized probes is a widely used assay for the parallel detection of multiple targets in medical and biological research. Despite its widespread application, DNA microarray technology still suffers from several biases and lack of reproducibility, stemming in part from an incomplete understanding of the processes governing surface hybridization. In particular, non-random spatial variations within individual microarray hybridizations are often observed, but the mechanisms underpinning this positional bias remain incompletely explained. This study identifies and rationalizes a systematic spatial bias in the intensity of surface hybridization, characterized by markedly increased signal intensity of spots located at the boundaries of the spotted areas of the microarray slide. Combining observations from a simplified single-probe block array format with predictions from a mathematical model, the mechanism responsible for this bias is found to be a position-dependent variation in lateral diffusion of target molecules. Numerical simulations reveal a strong influence of microarray well geometry on the spatial bias. Reciprocal adjustment of the size of the microarray hybridization chamber to the area of surface-bound probes is a simple and effective measure to minimize or eliminate the diffusion-based bias, resulting in increased uniformity and accuracy of quantitative DNA microarray hybridization.
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影响因子：
3.4
作者：
Livshits, MA;Mirzabekov, AD
通讯作者：
Mirzabekov, AD
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影响因子：
14.9
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Demeter, Janos;Beauheim, Catherine;Gollub, Jeremy;Hernandez-Boussard, Tina;Jin, Heng;Maier, Donald;Matese, John C.;Nitzberg, Michael;Wymore, Farrell;Zachariah, Zachariah K.;Brown, Patrick O.;Sherlock, Gavin;Ball, Catherine A.
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影响因子：
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