Technical Note, Design and Performance of the GeneChip® Human Genome U133 Plus 2.0 and Human Genome U133A 2.0 Array

The GeneChip® Human Genome U133 Plus 2.0 (HG-U133 Plus 2.0) and GeneChip Human Genome U133A 2.0 (HG-U133A 2.0) Arrays represent the latest evolution in the Affymetrix® GeneChip Expression Analysis Platform, offering the most comprehensive tool for the analysis of genome-wide expression on a single array. The HG-U133 Plus 2.0 Array includes all of the probe sets from the previous generation HG-U133A and HG-U133B Arrays, as well as nearly 10,000 additional probe sets. The increased feature density of the HG-U133 Plus 2.0 Array offers researchers the ability to measure transcription over the entire human genome in a single hybridization. Greater than 54,000 probe sets are used to analyze the expression level of more than 47,000 transcripts and variants, including approximately 38,500 well-characterized human genes. The HG-U133A 2.0 Array also leverages this high-density design to include the content of the previous HG-U133A Array on a smaller format for more efficient analysis. More than 22,000 probe sets are employed to analyze the expression level of over 18,400 transcripts and variants, including more than 14,500 well-characterized human genes. Extensive testing on both arrays revealed that data from the HG-U133A Array are similar to data generated on the higher density HG-U133 Plus 2.0 and HG-U133A 2.0 Arrays. In terms of assay sensitivity, control spikes were routinely detected in a complex background at a transcript concentration of one copy per 200,000. Technical Note GeneChip Human Genome U133 Plus 2.0