Summary
I describe the approaches for choosing primer parameters and calculating primer properties to build a statistical model for PCR primer design. Statistical modeling allows you to fine-tune the PCR primer design for your standard PCR conditions. It is most appropriate for the large organizations routinely performing PCR on the large scale or for the instruments that utilize PCR. This chapter shows how to use the statistical model to optimize the PCR primer design and to cluster primers for multiplex PCR. These methods have been developed to optimize single-nucleotide polymorphism–identification technology (SNP-IT) reaction for SNP genotyping and implemented in the Autoprimer program (http://www.autoprimer.com). The approaches for combining the individual primer scores into statistical model are described in the next chapter.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Yuryev A, Huang J, Pohl M, Patch R, Watson F, Bell P, Donaldson M, Phillips MS, and Boyce-Jacino MT (2002) Predicting the success of primer extension genotyping assays using statistical modeling. Nucleic Acids Res 30(23), e131.
Egan JP (1975) Signal Detection Theory and ROC Analysis, Academic Press, New York.
Onodera K and Melcher U (2004) Selection for 3′ end triplets for polymerase chain reaction primers. Mol Cell Probes 18(6), 369–372.
SantaLucia J Jr (1996) A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics. Proc Natl Acad Sci USA 95, 1460–1465.
Mathews DH, Sabina J, Zuker M, and Turner DH (1999) Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol 288, 911–940.
Yuryev A, Huang J, Scott KE, Kuebler J, Donaldson M, Phillips MS, Pohl M, and Boyce-Jacino MT (2004) Primer design and marker clustering for multiplex SNP-IT primer extension genotyping assay using statistical modeling. Bioinformatics 20(18), 3526–3532.
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2007 Humana Press
About this protocol
Cite this protocol
Yuryev, A. (2007). PCR Primer Design Using Statistical Modeling. In: Yuryev, A. (eds) PCR Primer Design. Methods in Molecular Biology™, vol 402. Humana Press. https://doi.org/10.1007/978-1-59745-528-2_5
Download citation
DOI: https://doi.org/10.1007/978-1-59745-528-2_5
Publisher Name: Humana Press
Print ISBN: 978-1-58829-725-9
Online ISBN: 978-1-59745-528-2
eBook Packages: Springer Protocols