Physico-chemical modelling of target depletion during hybridization on oligonulceotide microarrays

The effect of target molecule depletion from the supernatant solution is incorporated into a physico-chemical model of hybridization on oligonucleotide microarrays. Two possible regimes are identified: local depletion, in which depletion by a given probe feature only affects that particular probe, and global depletion, in which all features responding to a given target species are affected. Examples are given of two existing spike-in data sets experiencing measurable effects of target depletion. The first of these, from an experiment by Suzuki et al using custom built arrays with a broad range of probe lengths and mismatch positions, is verified to exhibit local and not global depletion. The second data set, the well-known Affymetrix HGU133a latin square experiment, is shown to be very well explained by a global depletion model. It is shown that microarray calibrations relying on Langmuir isotherm models which ignore depletion effects will significantly underestimate specific target concentrations. It is also shown that a combined analysis of perfect match and mismatch probe signals in terms of a simple graphical summary, namely the hook curve method, can discriminate between cases of local and global depletion.