Single Nucleotide Polymorphism Genotyping and Point Mutation Detection by Ligation on Microarrays

Abstract

Based on the principle of sequencing by ligation, a novel method referred to as "Minisequencing by ligation" for detecting known single nucleotide variant in high-throughput assay formats is reported in this article. By designing a sequencing primer and fluorescently labeled probes each with a "discriminating" base according to the single base variation, this method can be used to analyze single nucleotide polymorphism (SNP) or point mutation in a number of samples in parallel. In our current study, three known nucleotides at a given position of three DNA templates with different CG contents are firstly genotyped on aldehyde-modified slide to testify the feasibility and optimize the reaction conditions. Then, by performing ligation reaction between phosphorylated 5' end of the sequencing primer and hydroxylated 3' end of the labeled probe or phosphorylated 5' end of the labeled probe and hydroxylated 3' end of the sequencing primer, a SNP locus (rs1800497 (C/T)) and a point mutation (Mt1555 (A/G)) have been accurately detected on aldehyde-modified microarray and Sepharose beads in acrylamide gel, respectively. It has demonstrated that "minisequencing by ligation," as a promising methodology, can perform point mutation and SNP analysis in a simple, cost-effective, robust and high-throughput way.