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Microarray oligonucleotide probe designer: a Web service

Authors Patel VC, Mondal K, Shetty AC, Horner VL, Bedoyan JK, Martin D, Caspary T, Cutler DJ, Zwick M

Published 2 November 2010 Volume 2010:2 Pages 145—155


Review by Single-blind

Peer reviewer comments 2

Viren C Patel1*, Kajari Mondal1*, Amol Carl Shetty1*, Vanessa L Horner1, Jirair K Bedoyan2, Donna Martin2,3, Tamara Caspary1, David J Cutler1, Michael E Zwick1

1Department of Human Genetics, Emory University School of Medicine, Atlanta, GA, USA; 2Department of Pediatrics, 3Department of Human Genetics, University of Michigan, Ann Arbor, MI, USA; *These authors contributed equally to this work.

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. However, choosing the specific oligonucleotides to be used 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 MOPeDdesigned 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 Web site ( will make a valuable resource for investigators in their sequence-based studies of complex eukaryotic genomes.

Keywords: genomic selection, oligonucleotide, microarray, next-generation sequencing, software

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