Empirical Evaluation of Oligonucleotide Probe Selection for DNA Microarrays

• Type of Material: Article
• Authors: Jennifer Mulle, Emory University; Viren C. Patel, Emory University; Stephen Warren, Emory University; Madhuri Hegde, Emory University; David J Cutler, Emory University; Michael Zwick, Emory University
• Language: English
• Date: 2010-03-29
• Publisher: Public Library of Science
• Publication Version: Final Published Version
• Copyright Statement: © 2010 Mulle et al.
• License: Creative Commons Attribution 3.0 Unported
• Final Published Version (URL): http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0009921
• Title of Journal or Parent Work: PLoS ONE
• ISSN: 1932-6203
• Volume: 5
• Issue: 3
• Start Page: 1
• End Page: 7
• Grant/Funding Information: J.G.M. was supported by a Kirschstein National Research Service Award (NRSA) fellowship and a NARSAD Young Investigator award (http://www.narsad.org/).
• Research Categories: Biology, Genetics

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.