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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...

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Autores principales: Mulle, Jennifer G., Patel, Viren C., Warren, Stephen T., Hegde, Madhuri R., Cutler, David J., Zwick, Michael E.
Formato: Texto
Lenguaje:English
Publicado: Public Library of Science 2010
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.
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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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