A strategy for oligonucleotide microarray probe reduction
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gb-2002-3-12-research0073.pdf
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80.44 KB
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964df25447d33bff6250aa0578a00bb5
Author(s)
Antipova, Alena A.
Tamayo, Pablo
Golub, Todd R.
Date Issued
November 2002
Journal
Genome Biology
Publisher
BioMed Central Ltd
Citation
Genome Biology. 2002 Nov 25;3(12):research0073-research0073.4
Version
Final published version
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.
MIT Department
Massachusetts Institute of Technology. Department of Chemistry
Whitehead Institute for Biomedical Research
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Creative Commons Attribution
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DOI of Published Version
https://doi.org/10.1186/gb-2002-3-12-research0073
