Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.

<h4>Background</h4>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...

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Autores principales:	Doris Steger, David Berry, Susanne Haider, Matthias Horn, Michael Wagner, Roman Stocker, Alexander Loy
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/da232144e1bb4653adb09ff89d0cfb97
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spelling	oai:doaj.org-article:da232144e1bb4653adb09ff89d0cfb972021-11-18T06:47:44ZSystematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.1932-620310.1371/journal.pone.0023727https://doaj.org/article/da232144e1bb4653adb09ff89d0cfb972011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21858215/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions</h4>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.Doris StegerDavid BerrySusanne HaiderMatthias HornMichael WagnerRoman StockerAlexander LoyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 8, p e23727 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Doris Steger David Berry Susanne Haider Matthias Horn Michael Wagner Roman Stocker Alexander Loy Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.
description	<h4>Background</h4>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.<h4>Methodology/principal findings</h4>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.<h4>Conclusions</h4>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.
format	article
author	Doris Steger David Berry Susanne Haider Matthias Horn Michael Wagner Roman Stocker Alexander Loy
author_facet	Doris Steger David Berry Susanne Haider Matthias Horn Michael Wagner Roman Stocker Alexander Loy
author_sort	Doris Steger
title	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_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_sort	systematic spatial bias in dna microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/da232144e1bb4653adb09ff89d0cfb97
work_keys_str_mv	AT dorissteger systematicspatialbiasindnamicroarrayhybridizationiscausedbyprobespotpositiondependentvariabilityinlateraldiffusion AT davidberry systematicspatialbiasindnamicroarrayhybridizationiscausedbyprobespotpositiondependentvariabilityinlateraldiffusion AT susannehaider systematicspatialbiasindnamicroarrayhybridizationiscausedbyprobespotpositiondependentvariabilityinlateraldiffusion AT matthiashorn systematicspatialbiasindnamicroarrayhybridizationiscausedbyprobespotpositiondependentvariabilityinlateraldiffusion AT michaelwagner systematicspatialbiasindnamicroarrayhybridizationiscausedbyprobespotpositiondependentvariabilityinlateraldiffusion AT romanstocker systematicspatialbiasindnamicroarrayhybridizationiscausedbyprobespotpositiondependentvariabilityinlateraldiffusion AT alexanderloy systematicspatialbiasindnamicroarrayhybridizationiscausedbyprobespotpositiondependentvariabilityinlateraldiffusion
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Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.

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