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A strategy for oligonucleotide microarray probe reduction

Alena A Antipova12, Pablo Tamayo1 and Todd R Golub13*

Author Affiliations

1 Center for Genome Research, Whitehead Institute/Massachusetts Institute of Technology, Cambridge, MA 02139, USA

2 Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA

3 Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA 02115, USA

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Genome Biology 2002, 3:research0073-research0073.4  doi:10.1186/gb-2002-3-12-research0073

Published: 25 November 2002



One of the factors limiting the number of genes that can be analyzed on high-density oligonucleotide arrays is that each transcript is probed by multiple oligonucleotide probes. To reduce the number of probes required for each gene, a systematic approach to choosing the most representative probes is needed. A method is presented for reducing the number of probes per gene while maximizing the fidelity to the original array design.


The methodology has been tested on a dataset comprising 317 Affymetrix HuGeneFL GeneChips. The performance of the original and reduced probe sets was compared in four cancer-classification problems. The results of these comparisons show that reduction of the probe set by 95% does not dramatically affect performance, and thus illustrate the feasibility of substantially reducing probe numbers without significantly compromising sensitivity and specificity of detection.


The strategy described here is potentially useful for designing small, limited-probe genome-wide arrays for screening applications.