Confronting Two-pair Primer Design for Enzyme-free SNP Genotyping Based on a Genetic Algorithm

Overview

Journal BMC Bioinformatics

Publisher Biomed Central

Specialty Biology

Date 2010 Oct 15

PMID 20942913

Citations 4

Authors

Cheng-Hong Yang

Yu-Huei Cheng

Li-Yeh Chuang

Hsueh-Wei Chang

Affiliations

Soon will be listed here.

Abstract

Background: Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) method produces allele-specific DNA bands of different lengths by adding four designed primers and it achieves the single nucleotide polymorphism (SNP) genotyping by electrophoresis without further steps. It is a time- and cost-effective SNP genotyping method that has the advantage of simplicity. However, computation of feasible CTPP primers is still challenging.

Results: In this study, we propose a GA (genetic algorithm)-based method to design a feasible CTPP primer set to perform a reliable PCR experiment. The SLC6A4 gene was tested with 288 SNPs for dry dock experiments which indicated that the proposed algorithm provides CTPP primers satisfied most primer constraints. One SNP rs12449783 in the SLC6A4 gene was taken as an example for the genotyping experiments using electrophoresis which validated the GA-based design method as providing reliable CTPP primer sets for SNP genotyping.

Conclusions: The GA-based CTPP primer design method provides all forms of estimation for the common primer constraints of PCR-CTPP. The GA-CTPP program is implemented in JAVA and a user-friendly input interface is freely available at http://bio.kuas.edu.tw/ga-ctpp/.

Citing Articles

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