An automatic high-throughput single nucleotide polymorphism genotyping approach based on universal tagged arrays and magnetic nanoparticles.

Recent developments in highly parallel genome-wide studies are transforming the association of human health and diseases. In these studies, multiple SNP loci from large amount of samples need to be investigated to obtain a result with a high degree of confidence. Herein, we describe a novel, cost-effective and automated method for high-throughput single nucleotide polymorphisms (SNPs) genotyping based on universal tagged array and magnetic separation. By using two kinds of functionalized magnetic nanoparticles, the whole operation procedure including genome DNA extraction and SNP genotyping can be automatically performed by JANUS automated workstation (Perkin Elmer Inc.). Four different SNPs loci from 80 samples were scored using only one pair of universal dual-color probes, the phase of numerous SNPs can be automated assessed simultaneously. The results demonstrated that the expected scores and good discrimination were obtained between the two alleles from these four SNP loci. Due to adequately taking the advantages of high parallel read-out and intrinsically scalable properties of microarray, and the automated magnetic separation handling technology is highly adaptable fro multiplexing sample preparation and automated SNP analysis, also avoid the complex procedure including purification and concentration, the new strategy is high-throughput, simple, flexible, cost-effective, and will be very suitable for large-scale genotyping.