G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration

Background: The brightness of the probe spots on expression microarrays intends to measure the abundance of specific mRNA targets. Probes with runs of at least three guanines (G) in their sequence show abnormal high intensities which reflect rather probe effects than target concentrations. This G-bias requires correction prior to downstream expression analysis. Results: Longer runs of three or more consecutive G along the probe sequence and in particular triple degenerated G at its solution end ((GGG)1-effect) are associated with exceptionally large probe intensities on GeneChip expression arrays. This intensity bias is related to non-specific hybridization and affects both perfect match and mismatch probes. The (GGG)1-effect tends to increase gradually for microarrays of later GeneChip generations. It was found for DNA/RNA as well as for DNA/DNA probe/target-hybridization chemistries. Amplification of sample RNA using T7-primers is associated with strong positive amplitudes of the G-...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Mario Fasold, Peter F. Stadler, Hans Binder
• Keywords: BMCBI 2010, Business, Dependent Sensitivity Models, Probe Intensities, Probe Sequence