Multiplex single nucleotide polymorphism genotyping by adapter ligation-mediated allele-specific amplification

Abstract

An improved approach for increasing the multiplex level of single nucleotide polymorphism (SNP) typing by adapter ligation-mediated allele-specific amplification (ALM–ASA) has been developed. Based on an adapter ligation, each reaction requires n allele-specific primers plus an adapter-specific primer that is common for all SNPs. Thus, only n + 1 primers are used for an n-plex PCR amplification. The specificity of ALM–ASA was increased by a special design of the adapter structure and PCR suppression. Given that the genetic polymorphisms in the liver enzyme cytochrome P450 CYP2D6 (debrisoquine 4-hydroxylase) have profound effects on responses of individuals to a particular drug, we selected 17 SNPs in the CYP2D6 gene as an example for the multiplex SNP typing. Without extensive optimization, we successfully typed 17-plex SNPs in the CYP2D6 gene by ALM–ASA. The results for genotyping 70 different genome samples by the 17-plex ALM–ASA were completely consistent with those obtained by both Sanger’s sequencing and PCR restriction fragment length polymorphism (PCR–RFLP) analysis. ALM–ASA is a potential method for SNP typing at an ultra-low cost because of a high multiplex level and a simple optimization step for PCR. High-throughput SNP typing could be readily realized by coupling ALM–ASA with a well-developed automation device for sample processing.