Selecting degenerate multiplex PCR primers

Single Nucleotide Polymorphism (SNP) Genotyping is an important molecular genetics technique in the early stages of producing results that will be useful in the medical field. One of the proposed methods for performing SNP Genotyping requires amplifying regions of DNA surrounding a large number of SNP loci. In order to automate a portion of this method and make the use of SNP Genotyping more widespread, it is important to select a set of primers for the experiment. Selecting these primers can be formulated as the Multiple Degenerate Primer Design (MDPD) problem. An iterative beam-search algorithm, Multiple, Iterative Primer Selector (MIPS), is presented for MDPD. Theoretical and experimental analyses show that this algorithm performs well compared to the limits of degenerate primer design and the number of spurious amplifications should be small. Furthermore, MIPS outperforms an existing algorithm which was designed for a related degenerate primer selection problem. An implementation of the MIPS algorithm is available for research purposes from the website http://www.cse.wustl.edu/∼zhang/software/mips.