Affymetrix's ability to put a lot of information on a single array stems from its photolithographic array production process. All of Affymetrix's GeneChip arrays are synthesized using photolithographic masks to direct light onto the surface of a wafer, and then synthesize oligonucleotide probes on the surface one base at a time.1 Thus, Affymetrix can synthesize a larger number of probes in a small space without increasing the cost of the array. "The great thing about this process is it's exceptionally parallel, so it doesn't take any more work to put 500,000 features on the array than it does to put, say, 100 features on an array," says Kerr. Additionally, Affymetrix improved its probe selection process; the company's previous human array product used 16 pairs of probes per transcript, whereas the U133 set uses 11 probes per transcript. This translates into more information per array: "If we can use fewer data ...
Arraying the Genome
Santa Clara, Calif.-based Affymetrix's new GeneChip® Human Genome U133 set is the first commercially available microarray set designed using the April 2001 draft of the human genome. Affymetrix incorporated 2.7 million source sequences in the array's design; the final product includes 45,000 probes in a two-array set representing 39,000 transcripts from 33,000 well-substantiated genes. "Each of the arrays in the set has over 500,000 individual oligonucleotide features," says marketing direct
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Aileen Constans
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