A verification protocol for the probe sequences of Affymetrix genome arrays reveals high probe accuracy for studies in mouse, hu

Background: The Affymetrix GeneChip technology uses multiple probes per gene to measure its expression level. Individual probe signals can vary widely, which hampers proper interpretation. This variation can be caused by probes that do not properly match their target gene or that match multiple genes. To determine the accuracy of Affymetrix arrays, we developed an extensive verification protocol, for mouse arrays incorporating the NCBI RefSeq, NCBI UniGene Unique, NIA Mouse Gene Index, and UCSC mouse genome databases. Results: Applying this protocol to Affymetrix Mouse Genome arrays (the earlier U74Av2 and the newer 430 2.0 array), the number of sequence-verified probes with perfect matches was no less than 85% and 95%, respectively; and for 74% and 85% of the probe sets all probes were sequence verified. The latter percentages increased to 80% and 94% after discarding one or two unverifiable probes per probe set, and even further to 84% and 97% when, in addition, allowing for one or ...

• Type: Journal
• Year: 2007
• Where: BMCBI
• Authors: Rudi Alberts, Peter Terpstra, Menno Hardonk, Leonid V. Bystrykh, Gerald de Haan, Rainer Breitling, Jan Peter Nap, Ritsert C. Jansen
• Keywords: Affymetrix, Affymetrix GeneChip Technology, BMCBI 2007, Mouse Arrays