Summary

A single-nucleotide polymorphism (SNP) is a variation in a single nucleotide that occurs at a specific position in the genome, where each variation is present to some appreciable degree within a population. SNPs are caused by conversion, transversion, insertion or deletion of nucleotide. Some SNPs affect gene function directly and lead to changes of biological character. SNPs are abundant in genome and widely used in study of population genetics and disease genes.

PCR-LDR SNP Typing

PCR-LDR combines PCR and Ligase Detection Reaction (LDR) to detect SNP in genome. LDR can detect SNPs by the mechanism of thermostable ligase. Ligase-based assays are ideal for multiplexing, since several primer sets can ligate along a gene without the interference encountered in polymerase-based assays. The optimal multiplex detection scheme involves a primary PCR amplification, followed by LDR (two primers, same strand) detection. The thermostable ligase and engineered mutants exhibit high fidelity in discriminating all possible matched and mismatched base pairs. The discrimination is improved by using primers containing the discriminating base on the 3' side of the ligation junction.

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