Detection of multiple SNPs in numerous samples with polyacrylamide gel-based microarray.

Previously we have developed polyacrylamide gel-based DNA microarray to genotype single nucleotide polymorphism (SNP) in a large number of samples, which has been proved as a simple and robust platform for high-throughput SNP screening. Here we improved this method to detect multiple SNPs by introducing multiplex polymerase chain reaction (multiplex-PCR) and immobilizing the products of multiplex-PCR to fabricate gel-based microarray and applying universal dual-color detectors in hybridization. In this report, five SNPs (rs191296, rs2280073, rs17599165, rs17599416 and rs7660336) of GABRA4 gene were chosen and successfully analyzed with the improved platform. Our experiment demonstrated that 3-dimentional polyacrylamide gel-based microarray of multiplex-PCR products make the platform for multiple SNPs genotyping becoming more labor-saving and time-saving. Appling the universal dual-color fluorescent detectors can reduce the cost over two-thirds for multiple SNPs analysis. It is concluded that the multiplex-PCR combined with the gel-based microarray hybridized with universal dual-color fluorescent detectors is efficient, rapid and simple for the detection of a single nucleotide mismatch, and may be very competitive in the efficiency, fidelity and cost for constructing DNA microarrays.