title: Mutagenic primer design for mismatch PCR-RFLP SNP genotyping using a genetic algorithm.
abstract: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is useful in small-scale basic research studies of complex genetic diseases that are associated with single nucleotide polymorphism (SNP). Designing a feasible primer pair is an important work before performing PCR-RFLP for SNP genotyping. However, in many cases, restriction enzymes to discriminate the target SNP resulting in the primer design is not applicable. A mutagenic primer is introduced to solve this problem. GA-based Mismatch PCR-RFLP Primers Design (GAMPD) provides a method that uses a genetic algorithm to search for optimal mutagenic primers and available restriction enzymes from REBASE. In order to improve the efficiency of the proposed method, a mutagenic matrix is employed to judge whether a hypothetical mutagenic primer can discriminate the target SNP by digestion with available restriction enzymes. The available restriction enzymes for the target SNP are mined by the updated core of SNP-RFLPing. GAMPD has been used to simulate the SNPs in the human SLC6A4 gene under different parameter settings and compared with SNP Cutter for mismatch PCR-RFLP primer design. The in silico simulation of the proposed GAMPD program showed that it designs mismatch PCR-RFLP primers. The GAMPD program is implemented in JAVA and is freely available at http://bio.kuas.edu.tw/gampd/.
authors.affiliation: Department of Network Systems, Toko University, Chiayi, Taiwan. chyang@cc.kuas.edu.tw
authors.forename: Cheng-Hong
authors.initials: CH
authors.lastname: Yang
authors.forename: Yu-Huei
authors.initials: YH
authors.lastname: Cheng
authors.forename: Cheng-Huei
authors.initials: CH
authors.lastname: Yang
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
mesh_terms: D000465:Algorithms; D020137:Base Pair Mismatch; D017931:DNA Primers / Q000737:chemistry*; D005838:Genotype; D006801:Humans; D009154:Mutation; D016133:Polymerase Chain Reaction / Q000379:methods; D012150:Polymorphism, Restriction Fragment Length / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide
chemical_list: D017931:DNA Primers