Santa Clara, Calif.-based Affymetrix Inc. also recently launched a human genome microarray product, the GeneChip® Human Genome U133 set.1 However, the two products differ in three key areas. One difference involves the strategy each company adopts to maximize sensitivity and specificity. MWG, an oligo-synthesis company, places a single 50-nucleotide-long probe species per gene. In contrast, according to an Affymetrix Technical Note,2 Affymetrix places several pairs of 25-nucleotide-long probes per gene—11 pairs, in the case of the Human Genome U133 set—each consisting of a perfectly matched oligo and an oligo containing a mismatch at nucleotide 13.
Also, while Affymetrix synthesizes its probes directly on the chips using a photolithographic process, MWG's oligos are synthesized separately. Then, prior to arraying, the company purifies these oligos, rather than spotting crude mixtures, and tests them for quality control using matrix-assisted laser desorption ionization (MALDI) mass spectrometry.
Finally, MWG's chips can be read using any ...
