A strategy for oligonucleotide microarray probe reduction
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 representati...
| Main Authors: | , , |
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| Other Authors: | |
| Format: | Article |
| Language: | English |
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BioMed Central Ltd
2010
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| Online Access: | http://hdl.handle.net/1721.1/59013 |
| _version_ | 1826202118169559040 |
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| author | Antipova, Alena A. Tamayo, Pablo Golub, Todd R. |
| author2 | Massachusetts Institute of Technology. Department of Chemistry |
| author_facet | Massachusetts Institute of Technology. Department of Chemistry Antipova, Alena A. Tamayo, Pablo Golub, Todd R. |
| author_sort | Antipova, Alena A. |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T12:02:09Z |
| format | Article |
| id | mit-1721.1/59013 |
| institution | Massachusetts Institute of Technology |
| language | English |
| last_indexed | 2024-09-23T12:02:09Z |
| publishDate | 2010 |
| publisher | BioMed Central Ltd |
| record_format | dspace |
| spelling | mit-1721.1/590132022-09-27T23:40:45Z A strategy for oligonucleotide microarray probe reduction Antipova, Alena A. Tamayo, Pablo Golub, Todd R. Massachusetts Institute of Technology. Department of Chemistry Whitehead Institute for Biomedical Research Antipova, Alena A. Tamayo, Pablo Golub, Todd R. 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. 2010-10-12T14:09:51Z 2010-10-12T14:09:51Z 2002-11 2002-09 2010-09-03T16:07:02Z Article http://purl.org/eprint/type/JournalArticle 1465-6906 http://hdl.handle.net/1721.1/59013 Genome Biology. 2002 Nov 25;3(12):research0073-research0073.4 12537562 en http://dx.doi.org/10.1186/gb-2002-3-12-research0073 Genome Biology Creative Commons Attribution Antipova et al.; licensee BioMed Central Ltd. application/pdf BioMed Central Ltd BioMed Central Ltd |
| spellingShingle | Antipova, Alena A. Tamayo, Pablo Golub, Todd R. A strategy for oligonucleotide microarray probe reduction |
| title | A strategy for oligonucleotide microarray probe reduction |
| title_full | A strategy for oligonucleotide microarray probe reduction |
| title_fullStr | A strategy for oligonucleotide microarray probe reduction |
| title_full_unstemmed | A strategy for oligonucleotide microarray probe reduction |
| title_short | A strategy for oligonucleotide microarray probe reduction |
| title_sort | strategy for oligonucleotide microarray probe reduction |
| url | http://hdl.handle.net/1721.1/59013 |
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