An integrated microelectronic hybridization system for genomic research and diagnostic applications

Nanogen is developing an integrated microelectronic system for rapid multiplex hybridization analysis. This integrated system includes an electronically active DNA array microchip mounted on an integrated microfluidic/electronic circuit card (cartridge), and a fully automated analysis instrument. The test sample is placed into the DNA chip cartridge, which is then inserted into the instrument, like a CD or floppy disk into a desk top computer. The ultimate goal is to provide multiplex hybridization, site independent electronic stringency, detection, data analysis, and presentation within time periods as short as 10 to 15 minutes. A research system will provide the capability to "make your own chip". Active DNA microchip arrays with 25 and 100 test sites (80 micron diameter) are being developed for both research and infectious disease diagnostic applications. DNA chip arrays with 400 test sites and on board semiconductor switching control are being developed for genomic research applications, and evolving genetic disease and cancer diagnostics. A high density DNA chip with 10,000 test sites is now being designed for drug discovery and gene expression applications. To date, we have demonstrated rapid and sensitive hybridization analysis for p53 (exons 5, 7, 8), H-ras (codons 12), HLA, B-globin, a number of human STR loci, a number of human SNP loci, and a large number of bacterial, viral, and antibiotic resistance targets. Point mutation analysis by electronic stringency has been carried out for a number of different single-stranded target sequences on a 100 test site active electronic DNA microchip. The test sequences included P53 Exon 8, P53 Exon 7, Ras 12, and single nucleotide polymorphic marker (DTD) single-stranded DNA sequences. Good point mutation discriminations were achieved within 30 seconds. In general, active Nanogen arrays require relatively lower probe densities for scanning mutations in DNA fragments. In addition to speed, sensitivity and selectivity, other advantages of the technology include the ability to directly analyze substantially double-stranded PCR and other amplicons. Electronic sample preparation and complexity reduction components are also being developed for integration into the final system.