9 The truth about NGS and library prep: find out what is inflating your costs

Typical manual library prep workflows require a lot of hands-on time Since the majority of library prep workflows can now be automated, too much time is spent doing manual work. This time could and should be better spent on more intellectually demanding tasks, like results interpretation or planning the next important experiment. Other wastes of time in the lab include, for example, the need to order reagents and consumables from multiple vendors and having to find the correct reagents and consumables in the lab before starting library preparation.

Training is a hassle Whether preparing libraries manually or with an automated system, an excessive amount of time is often spent on training. This can have a big negative impact on productivity, especially in labs where there is a high staff turnover. In cases where automated library prep is not user friendly, or requires some level of programming skills, many labs will hand over day-to-day management and running of the system to a dedicated expert. However, this can be a costly option, not to mention a waste of valuable expertise.

Errors are more likely Any steps that require manual intervention are opportunities for human error, and potential sources of variability. Lots of replicates and boring, repetitive tasks like pipetting are a recipe for mistakes because it’s easy to lose concentration. Errors and variability often translate into poor quality or invalid results, in which case the experiment must be repeated. Not only can this cause an expensive delay, there may not even be enough sample remaining to enable a repeat experiment, for example, if it was a very rare patient sample, you might only have one shot. Even when library prep is automated, it can take far too long to set up and optimize the scripts Many automated workflows still involve a lot of time-consuming activities that could be further simplified and streamlined. For example, how much time are your lab members spending making up master mixes, ensuring the workdeck is configured properly and reconfiguring protocols for their specific applications? Do you need to get help from a programmer every time a new application comes along or even to make a simple script change? This is not uncommon.

Manual processing increases the risk of variability In particular, library prep involves numerous pipetting steps, which increases the likelihood of errors, sample carry-over, contamination and operator variability.

Lack of standardization can have a big impact Use of standardized procedures and protocols is essential to ensure consistent results, yet this is a source of variability that is often overlooked. Problems can arise when there are inconsistencies or unplanned changes in the library prep kits and protocols being used, the quality or source of reagents, the standard to which incoming staff are trained and so on.

Variability in the amount of input DNA or RNA Nucleic acid variability is another common culprit that can affect NGS library reproducibility, particularly if the kit you are using is not designed to tolerate a broad input range or variable sample volumes.

Lab work is demanding at the best of times, but stress levels can go through the roof when staff are burdened with many mind-numbing and time-consuming tasks that don’t seem to add much value. In addition to compromising the quality of their work, this situation can cause ill health, job dissatisfaction and, ultimately, a higher than average attrition rate. Don’t let it get to that point!

The bottom line is that while the cost of sequencing has plummeted over the years, a lot of labs are still spending far more than they should on NGS. Many hidden costs of NGS can be traced back to the upstream steps of sample and library prep. Over time, the cost of errors or poor quality in library prep is often higher than investing in a streamlined library prep workflow. Any time spent doing something a robot could do or figuring out how to operate the robot – if there is one – is a total waste of resources. Likewise, having to hire or train dedicated experts is an unnecessary expense if you can source equipment and reagents designed to minimize complexity and maximize ease of use. Until recently, labs running NGS at low throughput, or only infrequently, have tended to suffer the most from these sorts of issues because library prep solutions are typically designed with higher throughputs in mind. Fortunately, for labs such as these, Tecan is working with them to uncover hidden costs that make NGS and automated library prep a more feasible solution even at low throughputs.