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European Biopharmaceutical Review

Performance Comparison of 60-mer and 25-mer In Situ Synthesised Oligonucleotide Microarrays

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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By Stephanie Fulmer-Smentek, Senior R&D Research Scientist at Agilent Technologies Inc and Luis Lombardia, Research Associate at Centro Nacional de Investigaciones Oncologicas (CNIO)*

Stephanie Fulmer-Smentek earned her PhD in Human Genetics from Johns Hopkins University in 1997. She then undertook postdoctoral research at Stanford University in the Department of Genetics. Stephanie joined Agilent Technologies Inc in 2000, and is now a Senior R&D Research Scientist in the Bioresearch Solutions Unit.


Luis Lombardia earned his PhD from Universidade Da Coruсa in 1998. He then spent two years as a postdoctoral fellow in CEA (Commisariat а l'Йnergie Atomique, Paris, France). Since 2001, Luis has been a Research Associate in the Genomics Unit of the Centro Nacional de Investigaciones Oncolуgicas.

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Stephanie Fulmer-Smentek
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Luis Lombardia
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