What is Genome Sequence Scanning?

Genome Sequence Scanning (GSS) is a bacterial identification technology that detects sequence-specific fluorescent tags on long DNA molecules that have been extracted and purified directly from biological samples. Key to the efficacy and sensitivity of the GSS technology is the microfluidic funnel used for high-throughput stretching and scanning of long strands of single DNA molecules. In the proprietary GSS detection funnels, purified and tagged DNA molecules flow in a linear conformation at high speed past a series of lasers and optical sensors, which record the length and pattern of the labels on each DNA fragment. The labels create a barcode of the DNA in the sample, which is compared to an onboard database of barcodes to identify the serotype/strain type for the organism.

The continuous-flow microfluidic funnel is critical to the rapid throughput and strain typing of sample bacteria by GSS, and PathoGenetix physics research has worked to improve the rate and reliability of DNA stretching in order to optimize the technology’s throughput and accuracy.  PathoGenetix’s APS presentation, scheduled for Wednesday afternoon, March 5, 2014, details multiple complementary mechanisms used to maximize throughput in the GSS detection funnels, including:

Optimized funnel geometry to maximize fluid velocity while maintaining uniform stretching over the desired range of DNA lengths

Improved retention of well-stretched DNA by minimizing relaxation and hydrodynamic tumbling using constant strain rate detection channels

Normalizing DNA elasticity using sheathing-flow single molecule intercalation.