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Nucleic Acids Research 2005 33(Web Server Issue):W548-W552; doi:10.1093/nar/gki483
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

SOP3v2: web-based selection of oligonucleotide primer trios for genotyping of human and mouse polymorphisms

Steven Ringquist, Christopher Pecoraro, Crystal M. S. Gilchrist, Alexis Styche, William A. Rudert, Panagiotis V. Benos1 and Massimo Trucco*

Division of Immunogenetics, Department of Pediatrics, Rangos Research Center, Children's Hospital of Pittsburgh, University of Pittsburgh School of Medicine 3460 Fifth Avenue, Pittsburgh, PA 15213, USA 1Department of Computational Biology and Bioinformatics, University of Pittsburgh School of Medicine Pittsburgh, PA 15261, USA

*To whom correspondence should be addressed. Tel: +1 412 692 6570; Fax: +1 412 692 5809; Email: mnt{at}pitt.edu

Received February 14, 2005. Revised March 29, 2005. Accepted April 18, 2005.

SOP3v2 is a database-driven graphical web-based application for facilitating genotyping assay design. SOP3v2 accepts data input in numerous forms, including gene names, reference sequence numbers and physical location. For each entry, the application presents a set of recommended forward and reverse PCR primers, along with a sequencing primer, which is optimized for sequence-based genotyping assays. SOP3v2-generated oligonucleotide primer trios enable analysis of single nucleotide polymorphisms (SNPs) as well as insertion/deletion polymorphisms found in genomic DNA. The application's database was generated by warehousing information from the National Center for Biotechnology Information (NCBI) dbSNP database, genomic DNA sequences from human and mouse, and LocusLink gene attribute information. Query results can be sorted by their biological relevance, such as nonsynonymous coding changes or physical location. Human polymorphism queries may specify ethnicity, haplotype and validation status. Primers are developed using SOP3v2's core algorithm for evaluating primer candidates through stability tests and are suitable for use with sequence-based genotyping methods requiring locus-specific amplification. The method has undergone laboratory validation. Of the SOP3v2-designed primer trios that were tested, a majority (>80%) have successfully produced genotyping data. The application may be accessed via the web at http://imgen.ccbb.pitt.edu/sop3v2.


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