ArticlePloS one2011
Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Expression of the ZIP/SLC39A transporters in β-cells: a systematic review and integration of multiple datasets.BMC genomics · 2017Pooled it
- Probe-target hybridization depends on spatial uniformity of initial concentration condition across large-format chips.Scientific reports · 2020Article
- Adenoviral detection by recombinase polymerase amplification and vertical flow paper microarray.Analytical and bioanalytical chemistry · 2019Article
- "RADIOTRANSCRIPTOMICS": A synergy of imaging and transcriptomics in clinical assessment.Quantitative biology (Beijing, China) · 2016Article
- A revised design for microarray experiments to account for experimental noise and uncertainty of probe response.PloS one · 2014Article
- Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome.Genome biology · 2013Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
backgroundThe 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. METHODOLOGY/PRINCIPAL
findingsThis 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.
conclusionsReciprocal 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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