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Genome Biol. 2002;3(12):RESEARCH0073. Epub 2002 Nov 25.

A strategy for oligonucleotide microarray probe reduction.

Author information

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

Abstract

BACKGROUND:

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.

RESULTS:

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.

CONCLUSIONS:

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

PMID:
12537562
[PubMed - indexed for MEDLINE]
PMCID:
PMC151175
Free PMC Article

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