An automated approach of designing multiplex PCR primers for the amplification of exons

Abstract

This paper presents a new program to design specific and reliable primers for amplification of exons in a multiplex PCR. The program is composed of two components: a data acquisition component and a data processing component. The data acquisition component automates time-consuming steps of preparing data for the primers design algorithms. It provides up-to-date information about selected genes including coding sequences and locations of SNPs. The data processing component automates the process of grouping candidate primers into an optimal set for the multiplex PCR by checking their specificity. It is an original and unconventional method that combines the hierarchical clustering and the separate-and-conquer strategy. The results obtained for various genes and presented in this paper prove that the proposed method is an effective way to design an optimal set of primers for the multiplex PCR. © 2013 Springer-Verlag.