Earl Hubbell, Pavel A. Pevzne
Abstract
One current approach to quality
control in DNA array manufacturing is to synthesize a small set
of test probes that detect variation in the manufacturing process.
These fidelity probes consist of identical copies of the same
probe, but they are deliberately manufactured using different
steps of the manufacturing process. A known target is hybridized
to these probes, and those hybridization results are indicative
of the quality of the manufacturing process. It is not only desirable
to detect variations, but also to analyze the variations that
occur, indicating in what process step the manufacture changed.
We describe a combinatorial approach which constructs a small
set of fidelity probes that not only detect variations, but also
point out the manufacturing step in which a variation has occurred.
This algorithm is currently being used in mass-production of DNA
arrays at Affymetrix.