Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion
Background 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 o...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | en_US |
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Public Library of Science
2011
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| Online Access: | http://hdl.handle.net/1721.1/66151 https://orcid.org/0000-0002-3199-0508 |
| _version_ | 1811084087849385984 |
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| author | Steger, Doris Berry, David Haider, Susanne Horn, Matthias Wagner, Michael Stocker, Roman Loy, Alexander |
| author2 | Massachusetts Institute of Technology. Department of Civil and Environmental Engineering |
| author_facet | Massachusetts Institute of Technology. Department of Civil and Environmental Engineering Steger, Doris Berry, David Haider, Susanne Horn, Matthias Wagner, Michael Stocker, Roman Loy, Alexander |
| author_sort | Steger, Doris |
| collection | MIT |
| description | Background
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.
Methodology/Principal Findings
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.
Conclusions
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. |
| first_indexed | 2024-09-23T12:44:33Z |
| format | Article |
| id | mit-1721.1/66151 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T12:44:33Z |
| publishDate | 2011 |
| publisher | Public Library of Science |
| record_format | dspace |
| spelling | mit-1721.1/661512022-09-28T09:48:12Z Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion Steger, Doris Berry, David Haider, Susanne Horn, Matthias Wagner, Michael Stocker, Roman Loy, Alexander Massachusetts Institute of Technology. Department of Civil and Environmental Engineering Stocker, Roman Stocker, Roman Background 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. Methodology/Principal Findings 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. Conclusions 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. Austrian Science Fund (P18836-B17) Austrian Science Fund (P20185-B17 ) Austrian Science Fund (P16566-B14) Austria. Federal Ministry of Science and Research (GEN-AU III InflammoBiota) National Institutes of Health (U.S.) (1-R21-EB008844 to RS) National Science Foundation (U.S.) (OCE-0744641-CAREER) 2011-10-03T14:44:55Z 2011-10-03T14:44:55Z 2011-08 2011-02 Article http://purl.org/eprint/type/JournalArticle 1932-6203 http://hdl.handle.net/1721.1/66151 Steger, Doris et al. “Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion.” Ed. Cynthia Gibas. PLoS ONE 6 (2011): e23727. https://orcid.org/0000-0002-3199-0508 en_US http://dx.doi.org/10.1371/journal.pone.0023727 PLoS ONE Creative Commons Attribution http://creativecommons.org/licenses/by/2.5/ application/pdf Public Library of Science PLoS |
| spellingShingle | Steger, Doris Berry, David Haider, Susanne Horn, Matthias Wagner, Michael Stocker, Roman Loy, Alexander Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion |
| title | Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion |
| title_full | Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion |
| title_fullStr | Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion |
| title_full_unstemmed | Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion |
| title_short | Systematic Spatial Bias in DNA Microarray Hybridization Is Caused by Probe Spot Position-Dependent Variability in Lateral Diffusion |
| title_sort | systematic spatial bias in dna microarray hybridization is caused by probe spot position dependent variability in lateral diffusion |
| url | http://hdl.handle.net/1721.1/66151 https://orcid.org/0000-0002-3199-0508 |
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