U.S. Genomics' genomic mapping technologies enable rapid, large-scale mapping of whole genomes by directly analyzing single linearized genomic DNA molecule fragments up to 500 kb in length from a simple restriction digest.

Short universal probes are hybridized to these fragments and proprietary microfluidics stretch the DNA to full contour length and deliver the individual molecules to be read by the laser excitation and detection region in a linear fashion. The specific probe locations generate a spatially resolved map unique to each organism. This represents a genetic map of the DNA species.

Leveraging these unique characteristics of individual DNA molecules, DNA maps can be compared against a database of reference maps associated with known human and microbial species in search of a match. This provides a potential method to rapidly and accurately determine the presence of a given DNA species in a complex sample in diverse applications ranging from bio-security to microbial diagnostics and other diagnostic applications. For example, E. coli can be identified and individual strains typed from a complex background by searching for the unique identifier maps associated with the E. coli genome in several diagnostic applications.  The exceptional sensitivity and specificity of this approach has been demonstrated in a U.S. Government funded biodefense application developed by U.S. Genomics in which CDC category A&B organisms are identified in a complex environmental sample.  Key advantages associated with genomic mapping technology include:

• DNA maps are generated directly from genomic DNA, without the need for an amplication step, such as PCR, and thereby avoiding any amplification-bias.  This decreases cost and increases robustness and accuracy.
• DNA maps can be generated from complex samples and may be used to simultaneously determine the presence and identity of numerous (theoretically unlimited) different species in a sample, with a single test.
• DNA maps can be created directly from a sample, without the need for prior culturing of microorganisms, since very few molecules are required. In addition to faster results, maps from species which cannot be cultured can also be generated and identified.
• DNA maps can be generated for any species, whether or not complete primary sequence information is known.
• Unlike target specific approaches, assays for new species or targets can be generated from a common reagent set without the need for new target-specific reagents; simple updates of new threats to the database of map patterns enable immediate detection.

Genomic mapping technology may also be used to detect RNA and proteins directly in a highly multiplexable assay format. For this application, synthetic DNA fragments are fabricated with pre-existing identifier maps and integrated capture probes specific to a particular target RNA or protein. Multiple such constructs, each specific for a particular target, may be incorporated in a single assay. Secondary labels detected concurrently with identification maps provide quantitation of individual targets.