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| home > ebr > summer 2004 > performance comparison of 60-mer and 25-mer in situ synthesised oligonucleotide microarrays |
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European BioPharmaceutical Review
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Studies have suggested that 60-mer probes are more sensitive than 25-mer probes in microarray experiments, due to the longer length available for hybridisation (1). 60-mers are also more tolerant of sequence mismatches, which results in simplified analysis of highly polymorphic regions through the use of longer probes. We followed two different experimental approaches to compare the performance of 25-mers and 60-mers.
In the initial experiments, we evaluated two different microarrays manufactured with in situ synthesis inkjet printing, one employing 25-mer probes and the other 60-mer probes for each yeast open reading frame. In the second series of experiments, we evaluated 25-mer and 60-mer probes representing 500 human genes on a custom array containing 22,525 features. The genes were selected for this microarray either because they were known to be cancer related or because they were observed as up or down regulated in colon cancer samples experiments performed with Agilent Human 1A microarrays in earlier studies.
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