An approach was presented to type multiplex single nucleotide polymorphism (SNP) by means of magnetic particles and amplification of whole genome products using universal linker-PCR. The linker-PCR products were captured by magnetic particles modified with streptavidin to fabricate SNP library. Each SNP locus in the library was interrogated by hybridization with a pair of dual-color fluorescence (Cy3, Cy5) probe, and the genotypes could be simultaneously identified by scanning the microarray printed with the denatured fluorescent probes on an unmodified glass slide. This method was applied to analysis the methylenetetrahydrofolate reductase (MTHFR) gene C677T and A1298C polymorphisms for ten different samples. The fluorescent ratios (match/mismatch signal) of homozygous samples were over 3. This simple and reliable genotyping method is suitable for high-throughput genotyping for multiplex loci, and will find a wide potential application to research and medical diagnosis.

Key words: linker-PCR, magnetic particle, dual-color hybridization, SNP type