title: Empirical evaluation of oligonucleotide probe selection for DNA microarrays.
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.
authors.affiliation: Department of Human Genetics, Emory University School of Medicine, Atlanta, Georgia, United States of America. jmulle@emory.edu
authors.forename: Jennifer G
authors.initials: JG
authors.lastname: Mulle
authors.forename: Viren C
authors.initials: VC
authors.lastname: Patel
authors.forename: Stephen T
authors.initials: ST
authors.lastname: Warren
authors.forename: Madhuri R
authors.initials: MR
authors.lastname: Hegde
authors.forename: David J
authors.initials: DJ
authors.lastname: Cutler
authors.forename: Michael E
authors.initials: ME
authors.lastname: Zwick
mesh_terms: D041321:Chromosomes, Human, X / Q000235:genetics; D055028:Comparative Genomic Hybridization / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods; D005821:Genetic Techniques; D006801:Humans; D008957:Models, Genetic; D015999:Multivariate Analysis; D020388:Muscular Dystrophy, Duchenne / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015345:Oligonucleotide Probes / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods; D013696:Temperature
chemical_list: D015345:Oligonucleotide Probes