Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays |
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Authors: | Jennifer G Mulle Viren C Patel Stephen T Warren Madhuri R Hegde David J Cutler Michael E Zwick |
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Institution: | Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America.;Ohio State University Medical Center, United States of America |
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Abstract: | 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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