Megapixel DNA Replication Technology Promises More Sensitive Faster Diagnostics

A DNA measurement platform that is more sensitive and accurate for sample screening could improve a range of genetic diagnostics and screenings where precise measurement is crucial. This includes the early detection of cancer, prenatal diagnostics, the analysis of single cell gene expression, and the detection of pathogens in food products.

The new digital polymerase chain reaction (PCR) device uses liquid surface tension to partition DNA samples into arrays of 1,000,000 chambers or more. This enables direct counting of single molecules isolated in individual chambers.

Digital PCR refers to a new generation of DNA replication techniques that offer increased sensitivity and density over the original technique. The greatest number of chambers available in commercially available implementations of digital PCR, using integrated microvalves, is 36,960. However, further scalability is limited by the maximum density at which valves may be reliably fabricated.

The density of reaction chambers achieved by the new platform exceeds more traditional valve-based digital PCR techniques by a factor of 100, translating directly into improved performance.

"This solves some major technical issues that have limited the scale and accuracy of traditional digital PCR techniques," says Assistant Professor Carl Hansen with the University of British Columbia (UBC; Vancouver, Canada) department of physics and astronomy and center for high-throughput biology. "It creates defect-free arrays of millions of uniform volume subreactions, and controls dehydration of these reactions during thermocycling."

Prof. Hansen believes that the digital PCR can be scaled up to hold up to approximately 10,000,000 chambers on a standard 2.54-cm (one-inch) format. The UBC scientists also found the new megapixel technique set new benchmarks in detecting rare mutations--defined as the lowest measurable ratio of two target sequences differing by a single nucleotide variation as well as new limits in the detection of subtle differences in sequence abundance. Partitioning of a one-million-chamber array takes approximately one minute.

"Our solution, or something using the same techniques, could enable a new degree of precision in measurements in biomedical research and diagnostics. The dramatic increase in assay density has important implications for the adoption of digital PCR as an economical, fast, and routine analytical tool," added Prof. Hansen.

A description of the megapixel platform was published July 3, 2011, in Nature Methods.

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