PCR Primer Design Using Statistical Modeling

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.