Figure 1.

Schematic representation of chip array system. Probes on the array are arranged in sets of five. Each probe in the set is complementary to the reference sequence except for a mismatch position, called the “substitution” position. At the substitution position, each of the four possible nucleotides (A, C, G, T) and a single base pair deletion are represented in the probe set. Assay conditions optimize hybridization of the fluorescently labeled DNA target to the probe that best matches its sequence. This hybrid yields a higher fluorescence intensity relative to the other four target–probe hybrids in the set. There are probe sets complementary to every base in the p53 gene (figure courtesy of Affymetrix).