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

TL;DR

This paper develops a physico-chemical model for target molecule depletion during hybridisation on oligonucleotide microarrays, distinguishing local and global depletion regimes, and demonstrates the importance of accounting for depletion effects in microarray calibration.

Contribution

It introduces a model incorporating target depletion effects into hybridisation analysis and applies it to real data, highlighting the impact on target concentration estimates.

Findings

Global depletion explains the Affymetrix HGU133a data well.

Ignoring depletion leads to underestimation of target concentrations.

The hook curve method can distinguish depletion regimes.

Abstract

The effect of target molecule depletion from the supernatant solution is incorporated into a physico-chemical model of hybridisation 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 dataset, 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.