Microarray oligonucleotide probe designer (MOPeD): A web service

• Type of Material: Article
• Authors: Viren C. Patel, Emory University; Kajari Mondal, Emory University; Amol Carl Shetty, Emory University; Vanessa L. Horner, Emory University; Jirair K. Bedoyan, University of Michigan, Ann Arbor; Donna Martin, University of Michigan, Ann Arbor; Tamara Caspary, Emory University; David J Cutler, Emory University; Michael Zwick, Emory University
• Language: English
• Date: 2010-11-01
• Publisher: Dove Medical Press
• Publication Version: Final Published Version
• Copyright Statement: © 2010 Patel et al, publisher and licensee Dove Medical Press Ltd. This is an Open Access article which permits unrestricted noncommercial use, provided the original work is properly cited.
• License: Creative Commons Attribution-Noncommercial 3.0 Unported
• Final Published Version (URL): http://www.dovepress.com/microarray-oligonucleotide-probe-designer-a-web-service-peer-reviewed-article-OAB
• Title of Journal or Parent Work: Open Access Bioinformatics
• ISSN: 1179-2701
• Volume: 2
• Issue: 2010
• Start Page: 145
• End Page: 155
• Grant/Funding Information: This work was supported in part by the National Institutes of Health/National Institute of Mental Health and Gift Fund (grant number MH076439) to MEZ, the Simons Foundation Autism Research Initiative (MEZ), and the PHD Grant (UL1 RR025008, KL2 RR025009 or TL1 RR025010) from the Clinical and Translational Science Award program, National Institutes of Health, National Center for Research Resources.
• Keywords: genomic selection; software; oligonucleotide; microarray; next-generation sequencing
• Research Categories: Biology, Genetics

Abstract

Methods of genomic selection that combine high-density oligonucleotide microarrays with next-generation DNA sequencing allow investigators to characterize genomic variation in selected portions of complex eukaryotic genomes. Yet choosing which specific oligonucleotides to be use can pose a major technical challenge. To address this issue, we have developed a software package called MOPeD (Microarray Oligonucleotide Probe Designer), which automates the process of designing genomic selection microarrays. This web-based software allows individual investigators to design custom genomic selection microarrays optimized for synthesis with Roche NimbleGen’s maskless photolithography. Design parameters include uniqueness of the probe sequences, melting temperature, hairpin formation, and the presence of single nucleotide polymorphisms. We generated probe databases for the human, mouse, and rhesus macaque genomes and conducted experimental validation of MOPeD-designed microarrays in human samples by sequencing the human X chromosome exome, where relevant sequence metrics indicated superior performance relative to a microarray designed by the Roche NimbleGen proprietary algorithm. We also performed validation in the mouse to identify known mutations contained within a 487-kb region from mouse chromosome 16, the mouse chromosome 16 exome (1.7 Mb), and the mouse chromosome 12 exome (3.3 Mb). Our results suggest that the open source MOPeD software package and website (http://moped.genetics.emory.edu/) will make a valuable resource for investigators in their sequence-based studies of complex eukaryotic genomes.