Embedded Technologies Help Make High-Speed DNA Testing More Intuitive

DNA analysis has gone from mere theory to a heavily relied upon analytic and diagnostic tool in just a few short decades. But as invaluable as DNA can be, its longtime drawbacks have been the time required to replicate enough of it from very small samples to conduct thorough analyses, and the bottlenecks in labs where too few workers are trained in DNA replication techniques.

BJS Biotechnologies, a London-based firm specializing in technology for the medical field, recently set out to change all that. Its solution—called xxpress™, is a proprietary machine that speeds up DNA replication. It also employs embedded technology that fuels its user-friendly ­­interface that can step nearly any lab technician through the DNA replication process with no training.

A History of Innovation

BJS Biotechnologies made its first foray into DNA testing by making traditional thermal cycler blocks for a number of other biotechnology companies. “For such equipment, you need highly conductive thermal blocks to guarantee an even temperature,” Nick Burroughs, COO of BJS, says. BJS makes its thermal blocks from silver, which it “electroforms” into the complex shapes required by the thermal cycling process for DNA replication.

That knowledge turned into a prototype for a full-blown DNA replication machine, and ended in xxpress. Thanks to an innovative industrial design with a low thermal mass and a powerful graphical user interface to reduce setup time, the speed with which researchers can replicate DNA has dropped from hours and days to as little as 10 minutes with xxpress.

With typical DNA analysis taking as long as 90 to 120 minutes to go through 40 cycles, Burroughs often encounters disbelief when he explains that his company’s solution can complete that process in just 10 minutes. “DNA replication involves heating and cooling cycles, and with xxpress, BJS Biotechnologies can do the heat and cooling cycles faster than anyone else.”

The Nuts and Bolts

“Because of its design and componentry, the xxpress thermal cycler enables the world’s most thermally uniform PCR tests, in addition to its speeds,” Burroughs says. It is so fast that it can handle about the same workload as five standard thermal cyclers. “Our technology uses the consumable as the resistive element within an electrical circuit to provide heating that—along with forced air cooling—delivers rapid thermal cycling.”

The key to high-speed temperature change is to keep the thermal mass low, making the amount of heat that needs to be moved in and out small. For that process, BJS uses a thin strip of aluminum. What’s unique is how they manage to control the temperature by running electrical currents along different paths across the strip to provide heat where it is required.

Mastering the high-speed process for thermal cycling was a major coup, but the BJS team realized that even with faster thermal cycling, xxpress would not be living up to its promise if it weren’t also decidedly simple to use.

BJS Biotechnologies conducted market research and learned that often in test laboratories only one person was capable of setting up the DNA thermal cycling equipment. “We wanted a solution that any biotechnologist could use without formal training, and without having to open a technical manual,” says Burroughs.

“One of our key requirements was the seamless movement of graphical images that allowed for an interactive feel with the screen.” Burroughs said the company looked at a variety of options and chose an embedded accelerated processing unit (APU) because it combined the speed of a central processing unit with the graphics capability of a graphics processing unit (GPU). “We had looked at other processors, but the graphics were only decent with really powerful PCs. At the time, someone mentioned the APU with better integration of graphics right on the silicon—which was ideal. ”

Working closely with specialist graphical user interface design company, UI Centric, BJS

“We wanted a solution that was as simple to operate as a good TV—you should instinctively know how to operate it and it should support you in delivering good results.In normal operation we never want the user to open the manual; if they have to, then we have failed!”– Nick Burroughs, Chief Operations Officer, BJS

developed a tablet-like touch interface that guided the user through the process. “By keeping it simple and intuitive,” Burroughs says, “Anyone with a basic understanding of PCR can operate the machine and get results.”

Burroughs says the beauty of xxpress is that the APU allowed the GUI designers at UI Centric to create an intuitive touch screen user interface that mimics the way biotechnologists develop their experiments. The software guides the user through the process, selecting PCR types, chemistry choices, plate types, sample volumes and more. The system provides analysis of the results and the ability to export those results in various formats, including RDML and Microsoft Excel®.

Users work the machine like a slide show on a tablet, dragging a finger across to open the next window. Burroughs said seamless movement of graphical images was important to them.

What users see, in part, is a graphical representation of what is happening in each of the DNA replication wells (the machine has 96 individual wells). As DNA strands are doubled, the lab technician can view progress on a graph, compare information, and can zoom in and out to see patterns

The GUI is powered by a 1.3 GHz, single core APU, and Burroughs says it was critical to their success. Its unprecedented level of graphics integration, power efficiency and small form factor met the requirements for xxpress and could also serve well in a variety of other imbedded applications requiring strong graphics and an intuitive UI.

Maximizing Throughput

xxpress provides users with a personal storage and security key and automatically stores their preferences, profiles and results. The data key also enables the GUI to be run remotely on PCs, so additional experiments can be designed and analyzed away from the machine, which helps maximize machine throughput.

With cycle times of less than 10 minutes, as many as five experiments can be completed per hour, or more than 40 on a single day shift. With lab technicians being able to plan and analyze experiments remotely on PCs, the thermal cycler provides greater availability and outstanding return on investment (ROI).

In fact, the xxpress design enables all-around time savings—from its GUI to its processes. In DNA analysis, time savings can greatly benefit patients.

For instance, MRSA (Methicillin-Resistant Staphylococcus Aureus) is a dangerous infection that can have devastating consequences when it turns up in environments such as hospitals, where it can spread among the patient population.

By being able to move DNA testing close to the patient—and by speeding up the process with xxpress—clinicians can envision testing for MRSA in less than 15 minutes. The patient could then be tested as they are admitted or even in an ambulance en route to the hospital. A positive result would enable the hospital to implement isolation procedures to protect other patients and staff, while still providing the critical care required.

Speedier DNA testing also opens the doors for timely testing for diseases and other health problems in third-world countries where patients may have to travel a long way to see the doctor. Testing could be provided in the field, at the point of need, where there are no central labs and refrigeration of samples is not often possible. The xxpress unit is small enough to be portable, and could even be powered by batteries charged by solar energy. Test results can be completed while the patient waits and treatment given before they endure the often arduous trip home.

BJS Biotechnologies will begin delivering its xxpress units in Europe this fall and to North America by mid-2013.

For more information, please visit http://www.xxpresspcr.com/.

Kelly Gillilan has worked extensively in embedded applications for most of the past decade. He currently is the Product Marketing Manager for the AMD Embedded Solution division, overseeing worldwide marketing strategy and activities. He holds a degree in Computer Engineering and is fluent in Mandarin Chinese.