title: Systematic spatial bias in DNA microarray hybridization is caused by probe spot position-dependent variability in lateral diffusion.
abstract: 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.
  
  
  RESULTS
  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.
authors.affiliation: Department of Microbial Ecology, Vienna Ecology Center, Faculty of Life Sciences, University of Vienna, Wien, Austria.
authors.forename: Doris
authors.initials: D
authors.lastname: Steger
authors.forename: David
authors.initials: D
authors.lastname: Berry
authors.forename: Susanne
authors.initials: S
authors.lastname: Haider
authors.forename: Matthias
authors.initials: M
authors.lastname: Horn
authors.forename: Michael
authors.initials: M
authors.lastname: Wagner
authors.forename: Roman
authors.initials: R
authors.lastname: Stocker
authors.forename: Alexander
authors.initials: A
authors.lastname: Loy
mesh_terms: D000465:Algorithms; D004058:Diffusion; D008956:Models, Chemical; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization / Q000379:methods*; D015341:Nucleic Acid Probes / Q000737:chemistry / Q000235:genetics*; D009696:Nucleic Acids / Q000737:chemistry / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015203:Reproducibility of Results; D013499:Surface Properties
chemical_list: D015341:Nucleic Acid Probes; D009696:Nucleic Acids