title: Associate PCR-RFLP assay design with SNPs based on genetic algorithm in appropriate parameters estimation.
abstract: Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) is a commonly used laboratory technique and useful in small-scale basic research studies of complex genetic diseases that are associated with single nucleotide polymorphisms (SNPs). Before PCR-RFLP assay for SNP genotyping can be performed, a feasible primer pair observes numerous constraints and an available restriction enzyme for discriminating a target SNP, are required. The computation of feasible PCR-RFLP primers and find available restriction enzymes simultaneously aim at a target SNP is a challenging problem. Here, we propose an available method which combines the updated core of SNP-RFLPing with a genetic algorithm to reliably mine available restriction enzymes and search for feasible PCR-RFLP primers. We have in silico simulated the method in the SLC6A4 gene under different parameter settings and provided an appropriate parameter setting. The wet laboratory validation showed that it indeed usable in providing the available restriction enzymes and designing feasible primers that fit the common primer constraints. We have provided an easy and kindly interface to assist the researchers designing their PCR-RFLP assay for SNP genotyping. The program is implemented in JAVA and is freely available at http://bio.kuas.edu.tw/ganpd/.
authors.affiliation: Department of Chemical Engineering & Institute of Biotechnology and Chemical Engineering, I-Shou University, Kaohsiung 84008, Taiwan. chuang@isu.edu.tw
authors.forename: Li-Yeh
authors.initials: LY
authors.lastname: Chuang
authors.forename: Yu-Huei
authors.initials: YH
authors.lastname: Cheng
authors.forename: Cheng-Huei
authors.initials: CH
authors.lastname: Yang
authors.forename: Cheng-Hong
authors.initials: CH
authors.lastname: Yang
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D005838:Genotype; D008957:Models, Genetic; D016133:Polymerase Chain Reaction; D012150:Polymorphism, Restriction Fragment Length; D020641:Polymorphism, Single Nucleotide; D050486:Serotonin Plasma Membrane Transport Proteins / Q000235:genetics*
chemical_list: C493230:SLC6A4 protein, human; D050486:Serotonin Plasma Membrane Transport Proteins