Ever think about the kinds of challenges R&D scientists run up against in the course of developing a new product? The development of the Maxwell® RSC ccfDNA (circulating cell-free DNA) Plasma Kit is a particularly interesting example. Its path to commercialization was characterized by a number of unexpected technical hurdles, yet each was overcome through creative troubleshooting and aided by valuable collaborations across departments. All had a hand in finally launching the kit last August.

The product’s launch was an exciting milestone for Promega as research interest in the role of ccfDNA as biomarkers in human disease continues to grow. Elevated levels of ccfDNA have now been reported in patients with cancer, inflammatory disease, infections and cardiovascular disease. In pregnant women, up to 10% of ccfDNA can be attributed to the fetus, so critical fetal DNA analysis can now be conducted through maternal blood samples. There are many advantages in the ability to isolate and analyze ccfDNA, so the development of a kit with high throughput capability was a priority for the Nucleic Acid Purification R&D team.

One of the early technical challenges they faced as they set out to create a technology for isolating ccfDNA from plasma samples was development of an optimal binding matrix. The decision to offer automated purification using the Maxwell System dictated the need for a high performing cellulose-based magnetic resin matrix. This proved to be a hurdle that the Madison, Wisconsin group realized could be best overcome by collaboration with their colleagues at Promega Biosciences (PBI) in San Luis Obispo, California. The team from PBI included Zhiyang Zheng, Ruslan Arbit, John Eckert and Poncho Meisenheimer, or as Madison research scientist Doug White describes them, “some of the greatest particle chemists.”

Yet the expertise required to achieve the goal of creating the most optimal magnetic resin for the kit extended beyond the partnership between the two Promega labs. In the process of testing candidate resins the scientists realized the need to visualize the resin at a much higher resolution in order to pinpoint the morphological differences that seemed to affect performance. One of the scientists in the Madison group, Sarah Mahan, had recently joined the team from the University of Wisconsin-Madison where her research included scanning electron microscopy (SEM). Her scientific ties to former colleagues at the University resulted in the opportunity for Promega scientists to view their experimental resins under a scanning electron microscope. They could finally detect the distinctive granular nature of the material, rather than the round, spherical-shaped particles they were hoping to achieve. This critical information impacted the direction of the project once it was relayed to the PBI scientists.

Zhiyang recalls the work by him and his colleagues at that time. “We put tremendous effort into developing the right resins for this project, and then the process of scaling up was particularly challenging,” he says. “In order to optimize the parameters to make it safe and easy to operate at manufacturing scale, we put another half a year fine tuning the process.” Yet, there is no question that their persistence paid off. “In total they screened close to 70 different resins, and they finally nailed it,” says Doug. It also serves as a valuable example of how teamwork in industry achieves results.

The researchers faced another unexpected roadblock during development when they realized that a significant amount of the purified ccfDNA went “missing” prior to its final recovery. In other words, it was getting lost somewhere in the purification process, and this mystery needed to be solved. In strategic discussions among the group, led by their director Marjeta Urh, they exchanged ideas for how they might best visualize and track down the missing nucleic acid. The solution they arrived at necessitated going back in time to an approach that had long since been retired in their everyday lab practices: using radioactivity. Never expecting they’d find themselves “back in the hot lab,” by labeling the ccfDNA with phosphorus 33 (³³P) they found success. As they had reasoned, the strategy of using radioactivity allowed them to quantitatively measure binding and recovery, and the missing ten percent of ccfDNA was not hung up in the wash steps as hypothesized, it was instead located bound to the resin. This approach helped them all to understand and optimize each step of the protocol, ultimately resulting in an even better product.

The Nucleic Acid Purification team couldn’t be more pleased by what they accomplished in bringing this product to market. In the end, the launch of the Maxwell RSC® ccfDNA Plasma Kit was significantly impacted by a wide range of departments that included R&D, manufacturing, QA & regulatory, and marketing services. And everyone involved is excited about the potential applications of ccfDNA in disease detection and identification of tumor biomarkers. “The oncological potential is there—we are facilitating cancer research with our kit,” says Doug. “These are high stakes research challenges, and that makes this a truly interesting and relevant product.”

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Nicole Sandler

Nicole enjoys being a member of the Promega Connections blog team. A former molecular biologist, she earned her PhD from the University of Pennsylvania but realized that writing about science was a more fulfilling way to apply her knowledge and passion for the field. She's excited that her longtime writing career has now landed her at Promega, a company she once relied on for restriction enzymes and buffers as a research scientist.

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