Multiplex PCR finds application in such areas as pathogen detection, forensics, gene expression analysis, and SNP genotyping. While the technique is both sensitive and economical and enhances throughput, it is not without its challenges. This article addresses some of the difficulties for those who choose multiplexing, and offers useful tools to help overcome some of the complex design challenges. Tips include paying close attention to primer design, testing each primer individually, and tweaking the reaction conditions.
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