Improvement of Low-Density Microelectronic Array Technology to Characterize 14 Mutations/Single-Nucleotide Polymorphisms from Several Human Genes on a Large Scale (Technical Briefs‪)‬

Large-scale human genetic studies require new technologies to genotype several samples with relative ease, high accuracy, and reasonable costs. Among the available approaches, a microelectronic array technology has been developed for DNA hybridization analysis of mutations/ single-nucleotide polymorphisms (SNPs) (1-4). The microelectronic array system (NanoChip[R] Molecular Biology Workstation; Nanogen) produces a defined electric field that allows charged molecules, such as nucleic acids, to be transported to any test site, or pad, on the electronic chip (NanoChip cartridge). Electronic-based molecule addressing can rapidly achieve a high concentration of amplicons on each pad of the cartridge. Control of temperature allows use of an optimal thermal stringency to characterize a SNP/mutation in all 100 pads of a cartridge simultaneously (5, 6). A thin hydrogel permeation layer overlies the pads; the presence of avidin or streptavidin in this layer allows the binding of biotinylated PCR products. Although the technology is attractive, only a few protocols for its use have been published (7-11). We describe the development, optimization, and validation of a high-throughput method for SNPs and mutations analysis that allows performance of 1372 characterizations on each chip.