How Automation Can Help Avoid Next Generation Sequencing Errors Amid “The Great Resignation”

Concerns about manual sequencing and reproducibility challenges come up in scientific and popular press. There are many contributing factors and affected disciplines within science, but one that needs critical attention is reducing human error as a factor in obtaining high-quality next generation sequencing (NGS) research data.

NGS library prep – the process of creating barcoded DNA fragments from a sample for sequencing – is labor intensive, and prone to error when performed manually, not to mention the potential for burnout of lab staff. The complexity and exacting nature of preparing NGS libraries is underscored by the resources devoted to their QC: every few steps, it seems, you are checking nucleic acid concentrations, yield, fragment size and purity.

What are some of the errors that automation helps overcome?

The ability to manually handle liquids in a library prep context with any degree of consistency takes practice and patience. Even then, it is not easy to draw and accurately dispense small liquid volumes of different viscosities, to mix detergent-containing buffers without making bubbles, and to wash microscopic beads repeatedly but not so much that they wash away.

I’ll never forget my first experience with library prep. My supervisor was doing ChIP-Seq experiments and asked me to help. Since I had done hundreds of PCR and cloning experiments, I was confident in my ability to follow the protocol on my own, yet my supervisor wanted us to prepare a set in parallel: the ultimate test! Despite my experience, I can still hear her gasp as I washed the bead pellets a little too vigorously. She started watching me more closely and pointing out various faults – from the way I leaned over the reagents, which were very expensive, to the way I ejected pipette tips, which could have contaminated the whole third floor! Finally, we checked our progress on a Bioanalyzer instrument. To my total embarrassment, half of my samples were completely gone, and those remaining were full of suspiciously sized fragments. This was a fast lesson in the value of automation!

Even for those most experienced with library prep, the sheer number of steps in a prep, multiplied by the number of preps done in a week, amounts to a statistical guarantee that mistakes will be made. My boss was no exception.

Automating library prep in a foolproof, easy-to-use way, however, is about more than just liquid handling. It requires workspace planning as well as a strategy to help eliminate another common error: cross-contamination. Watch experienced technicians perform a library prep and you’ll notice that first they arrange the labware and reagents within their workspace to minimize chances of contamination. Then watch as they carefully maneuver their pipette tips over and around the workspace to keep any accidental drips from contaminating clean tubes below.

We designed the Biomek NGeniuS Next Generation Library Prep System* with this sort of careful workspace management in mind.  We developed a carefully laid out deck, along with an optical analytics system called Dynamic DeckOptix. Combined with a head-up display on the back inside wall of the instrument, the system provides users with real-time feedback on labware placement as they set up a batch to run.

How can NGS library prep remain flexible enough to work well with different library prep kits and still be fool-proof?

Before we introduced the Biomek NGeniuS System, it was hard to find the automation “sweet spot” for NGS research library prep. For those willing to sacrifice protocol flexibility, there were NGS-specific automation tools available, but they tended to lock you into one specific chemistry or method of library prep. If you wanted to maintain the flexibility to use different library prep chemistries and methods, you had to sacrifice ease of use to create a custom automation workflow using all-purpose liquid handling systems which require extensive automation expertise.

In addition to labware placement verification, the DeckOptix system provides other guardrails to help ensure successful preps. For example, it checks for lids, ensures labware inventory needed to execute the demonstrated method, and automatically selects the right tip for the volume. My favorite fool-proofing feature, however, is its ability to read reagent labels, including most hand-written labels. Users simply load the reagent carousel and let the system identify them. Each reagent is verified to match the selected batch protocol and is automatically maintained at proper temperature. It is this feature that gives the Biomek NGeniuS system the flexibility to work with most commercial library prep kits and methods.

This feature also helps take the guesswork out of troubleshooting. If you’ve ever had to troubleshoot a failed prep and wondered if you used the wrong enzyme, or if your sample was ruined due to improper storage, this might be your favorite feature too.

How can automating library prep help us navigate the Great Resignation and boost lab morale?

Labs of all sizes and disciplines have struggled to maintain productivity during the pandemic. Social distancing requirements and facility closures forced lab staff, who were used to working elbow to elbow, to adopt shifts and do whatever aspects of the work they could from home. There is no doubt the pandemic drove interest in remote automation.

The Biomek NGeniuS system is designed for remote operation of one or more instruments simultaneously once loaded. With temperature-controlled reagent storage, this system can run overnight. It also features an integrated thermocycler to help extend walk-away time for those prep protocols that require it.

Scientists and technicians are passionate about improving global health and well-being, and are motivated to see the promise of research on personalized medicine fulfilled. While there is much appreciation for automation’s capacity to greatly reduce library prep errors, perhaps the greater appreciation is the extra time it allows them to focus on research, design new methods, or develop new biomarker panels.

Bringing automation to labs that do a lot of manual library prep can create a positive boost in morale and employee retention by allowing them to focus on the research, not the research workflow. 

*Biomek NGeniuS Next Generation Library Prep Systems are not intended or validated for use in the diagnosis of disease or other conditions. In development. Performance characteristics have not been validated.

Each app template for use in the Biomek NGeniuS Next Generation Library Prep System has been demonstrated but has not been validated by Beckman Coulter. Beckman Coulter makes no warranties of any kind whatsoever, expressed or implied, with respect to app templates, including, but not limited to, warranties of fitness for a particular purpose or merchantability or that app templates are non-infringing. All warranties are expressly disclaimed. Your use of any app template is solely at your own risk, without recourse to Beckman Coulter.    

Products and demonstrated applications are not intended or validated for use in diagnostic procedures.   

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