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The Flexible matriXarray Chip System: A New Perspective,,,for Probe Optimization in Gene-Expression Profiling

Probe Optimization Is Crucial

The importance of the flexible production of customized arrays becomes obvious when different probes that detect the same gene are analyzed. Probe design software solutions are not yet able to provide probes with identical thermodynamic behavior. Furthermore, the in silico check for probe specificity is largely related to the transcriptome analyzed, as well as to the amount of sequence information available. Even for the human genome, this information is far from being complete. Currently, microarray vendors are addressing this problem with two different approaches. In the first approach, one probe per gene is offered with in silico and sometimes experimental validation. In the other approach, different probes per gene are used together with platformspecific algorithms to calculate the result. In conclusion, the optimization of probes used in array experiments is of major importance, especially when questions concerning genome-wide screening of gene-expression profiles must be answered.

New Concept for Probe Optimization

Roche Applied Science has developed a new concept for probe optimization using the matriXarray Chip System. The systematic approach analyzes probe profiles and is based on the assumption that specific probes show similar signal-intensity patterns in different samples (e.g., tissues). Preliminary experiments in three different rat tissues demonstrate the feasibility of this approach: a total of 57 different genes are included in the analysis (15 specific for kidney, 1 specific for kidney and liver, 18 specific for liver, and 23 specific for brain) together with 11 housekeeping genes. The chips were hybridized in duplicate. The mean average signal intensity after local backgro
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