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Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays
DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behave consistently across experiments is essential to the design, production and performance of DNA microarrays. Here our aim was to improve on probe design parameters by empirically...
Autores principales: | , , , , , |
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Formato: | Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847945/ https://www.ncbi.nlm.nih.gov/pubmed/20360966 http://dx.doi.org/10.1371/journal.pone.0009921 |
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author | Mulle, Jennifer G. Patel, Viren C. Warren, Stephen T. Hegde, Madhuri R. Cutler, David J. Zwick, Michael E. |
author_facet | Mulle, Jennifer G. Patel, Viren C. Warren, Stephen T. Hegde, Madhuri R. Cutler, David J. Zwick, Michael E. |
author_sort | Mulle, Jennifer G. |
collection | PubMed |
description | DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behave consistently across experiments is essential to the design, production and performance of DNA microarrays. Here our aim was to improve on probe design parameters by empirically and systematically evaluating probe performance in a multivariate context. We used experimental data from 19 array CGH hybridizations to assess the probe performance of 385,474 probes tiled in the Duchenne muscular dystrophy (DMD) region of the X chromosome. Our results demonstrate that probe melting temperature, single nucleotide polymorphisms (SNPs), and homocytosine motifs all have a strong effect on probe behavior. These findings, when incorporated into future microarray probe selection algorithms, may improve microarray performance for a wide variety of applications. |
format | Text |
id | pubmed-2847945 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-28479452010-04-01 Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays Mulle, Jennifer G. Patel, Viren C. Warren, Stephen T. Hegde, Madhuri R. Cutler, David J. Zwick, Michael E. PLoS One Research Article DNA-based microarrays are increasingly central to biomedical research. Selecting oligonucleotide sequences that will behave consistently across experiments is essential to the design, production and performance of DNA microarrays. Here our aim was to improve on probe design parameters by empirically and systematically evaluating probe performance in a multivariate context. We used experimental data from 19 array CGH hybridizations to assess the probe performance of 385,474 probes tiled in the Duchenne muscular dystrophy (DMD) region of the X chromosome. Our results demonstrate that probe melting temperature, single nucleotide polymorphisms (SNPs), and homocytosine motifs all have a strong effect on probe behavior. These findings, when incorporated into future microarray probe selection algorithms, may improve microarray performance for a wide variety of applications. Public Library of Science 2010-03-29 /pmc/articles/PMC2847945/ /pubmed/20360966 http://dx.doi.org/10.1371/journal.pone.0009921 Text en Mulle et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Mulle, Jennifer G. Patel, Viren C. Warren, Stephen T. Hegde, Madhuri R. Cutler, David J. Zwick, Michael E. Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays |
title | Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays |
title_full | Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays |
title_fullStr | Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays |
title_full_unstemmed | Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays |
title_short | Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays |
title_sort | empirical evaluation of oligonucleotide probe selection for dna microarrays |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847945/ https://www.ncbi.nlm.nih.gov/pubmed/20360966 http://dx.doi.org/10.1371/journal.pone.0009921 |
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