A bead-based single nucleotide polymorphism (SNP) detection using melting temperature on a microchip

Abstract

Single nucleotide polymorphism (SNP) is not only one of the most common genetic variances in a human genome, but it also serves a crucial biomarker greatly affecting the phenotypes of individuals. Moreover, SNP had shown its importance by making contributions in many aspects, including species classification for pests, pesticide resistance detection, and disease diagnostic for human beings. Most of today’s SNP detection techniques utilize enzymes or modification of DNA, leading to the requirement of high reagent cost or complex procedures. Therefore, a new SNP genotyping scheme has been developed to address these issues by conducting melting curve analysis on the DNA target sequences, which are conjugated onto polystyrene microbeads in a microfluidic device. The microbeads function as a solid vehicle for capturing the DNA duplexes, providing a larger surface-to-volume ratio for reaction and allowing it to be hydrodynamically confined for melting curve analysis. A prototype device serving as a basis for this proposed scheme was successfully tested, detecting the SNP of ataxia–telangiectasia-mutated gene from both synthetic DNA and genomic DNA of Landrace sows. This bead-based SNP detection only required a minimal reagent amount and simplified the sample preparation procedures, thereby preserving it as a flexible and accurate detection scheme. All these characteristics show great promise in this bead-based SNP detection.