Inhouse genetic analysis

We ask for insight into the successful instrument development collaboration that has resulted in the recent launch of a single base resolution capillary electrophoresis (CE) instrument for low-throughput DNA separation and analysis.

Q: What were the main design and development drivers behind this instrument?

Philip: Our collaborative goal was to produce an affordable instrument that could perform both fragment analysis and Sanger sequencing with high quality. The Spectrum Compact CE System needed to be easy to learn and use, and flexible to adapt to any user’s workflow. It had to be highly reliable with no interruptions to operation, and ideally would have a small footprint with no special infrastructure required in a customer’s lab. Finally, we wanted related consumables that were easy to use and change out when necessary.

Gabriela: Genetic analysis methods have become essential in many labs. Short tandem repeat (STR) analysis, for example, was most often used in forensic and paternity analyses. However, STR analysis can also support non-forensic applications such as cell line authentication and mixed-sample genotyping. Researchers are turning to these methods to verify cell line origins, detect sample contamination and track genetic changes. Similarly, Sanger sequencing by capillary electrophoresis (CE) is the gold standard for DNA sequencing, even with the advent of next-gen sequencing (NGS). The current best practice in many labs is to confirm NGS results with Sanger sequencing, and Sanger is the most cost-efficient method for sequencing single samples.

This single base resolution capillary electrophoresis Instrument is low-throughput by design. We have heard from many scientists who don’t process enough samples to justify purchasing a higher-throughput instrument, so this instrument was engineered to meet those specific needs. The new system is an automated, 4-capillary electrophoresis instrument that processes up to 32 samples in a single run.

From a business standpoint, it was important that the relationship produce a win for both companies. With any collaboration, building a good relationship is an important first step, and our face-to-face meetings went a long way towards building that relationship

Q: How did the two companies collaborate?

Philip: We leveraged each organisation’s respective expertise. Promega brought decades of experience with reagents and sample analysis, as well as a strong understanding of customer needs for support. Hitachi, in contrast, offered expertise in both instrumentation and software.

Gabriela: Ultimately, both companies had the same vision. During development, our project partners had a team of hardware and software engineers who routinely came to our headquarters to work with our specialist team of reagent experts. In turn, our service engineers travelled to their headquarters to gain insight on supporting the instrument. We also worked closely on verification and validation efforts, as well as working through the logistics for global customer service.

I believe we developed a deep respect for each other’s knowledge, experience and capabilities. On top of that, this collaboration helped us to grow our understanding of global customer needs and how those needs differed in unique ways

Q: How has the hardware been optimised?

Philip: This solution is smaller than traditional instruments with similar capabilities, allowing scientists to do DNA analysis right on their benchtop. The separate consumables give customers maximum flexibility.

Gabriela: The plug-and-play consumables make it extraordinarily simple to set up and run. Installation is simple and the format prevents contamination and spilling. Every single person who touched the instrument during internal training has made the comment, “Wow, the consumables really are easy to install!”

Q: How has the software been optimised?

Philip: Any scientist in the lab, regardless of skill level or expertise, can use this system with minimal training. Scientists can take analyses into their own hands and perform CE applications in their own lab. Labs can also get results on their own timeline without having to wait to batch samples or send them to an outside lab. This makes it easier to avoid delays and scheduling headaches.

Gabriela: In the past, many labs have relied on sending samples to core labs for analysis. Limited or rare samples had to be packaged and sent out of the lab, results could take any amount of time, and researchers had little or no control over the workflow. Our instrument allows labs to keep these applications in-house, reducing cost-per-sample and maintaining control of timelines.

Additionally, with the Remote Access software users are not tied to the lab. This interface allows users to check the instrument status and access data remotely from any browser on the same network. This means you can enter sample information, monitor runs, review alerts, consumables and data, and even set up your next run while the instrument is still running.

Q: Were there lessons learned from this collaboration?

Philip: From a business standpoint, it was important that the relationship produce a win for both companies. With any collaboration, building a good relationship is an important first step, and our face-to-face meetings went a long way towards building that relationship. Future collaborations will expand the software to add important functions and flexibility to this product.

Gabriela: Given our different areas of technical expertise, we both learned a lot from each other throughout the process. I believe we developed a deep respect for each other’s knowledge, experience and capabilities. On top of that, this collaboration helped us to grow our understanding of global customer needs and how those needs differed in unique ways.

Authors: Dr Philip Hargreaves is Head of Strategic Marketing and Business Development and Gabriela Saldanha is Sr. Product Manager, Sample Analysis. Both work at Promega Corporation: promega.co.uk