Next-Generation Sequencing (NGS) is a high-throughput DNA sequencing technology that allows the simultaneous analysis of…
A lot is said about nucleic acid extraction and rightly so. It is defined as the “first step of any amplification experiment, no matter what the amplification is used to detect a specific pathogen.”
An article by JH Shin in The National Center for Biotechnology Information, goes further and stresses that it is a “crucial preanalytical step in the development and performance of any successful molecular diagnostic method and ensure a reliable result.”
The key word being “crucial” as once extracted, nucleic acids go through amplification and such methods include Next Generation Sequencing and qPCR. These are particularly sensitive techniques and to ensure a reliable result, it is critical that any variations and other errors are eliminated otherwise issues such as cross-contamination, loss of time, increase in costs and invalid results start to creep in.
Manual Extraction Issues
The issues of manual extraction are plentiful and include:
- Manual errors
Errors such as cross-contamination can abound in a manual workflow. Irrespective of any protocols in place or indeed any training given, errors will still happen as factors such as tiredness and stress cannot be fully eliminated. Moreover, the more the touches, the greater the risk of errors occurring.
- Time limitations
As errors occur, so too does the loss of time and time, unfortunately, is not something we can ever get back. Workflows might have to pause (or labs shut down completely). This in turn leads to poorer efficiency levels and an increase in costs. You should consider the opportunity cost here as well. What value-adding activities could be undertaken instead of having to do a manual extraction?
- Scaling issues
Scaling up using manual extraction is a challenge. There is only so much your staff can do. They can’t work continuously or at least without getting fatigued and making errors. Moreover, tube format protocols limit the number of tubes that team members can process simultaneously in a centrifuge and other necessary equipment. Using smaller batches to process large sample numbers is a common workaround, but it is slow and requires a lot of manual effort. Therefore, it is not a viable option for scale.
The Benefits of Automating Your Nucleic Acid Extraction
With the challenges of manual extraction laid out, there are a number of significant advantages in regards to automating nucleic acid extraction.
- Less touches = less errors
Automation allows for less touches in the lab. Less touches equate to less opportunities for errors (e.g., pipetting errors) as well as reduced chances of cross-contamination. We noted earlier that current amplification processes such as NGS & qPCR are sensitive so any slight variations can negatively impact on the result. An automated solution allows therefore for greater consistency and reproducibility. Moreover, such solutions typically use pre-filled reagent kits which further simplifies the workflow and removes an additional potential error waiting to happen.
- Time for value-adding activities
Manual extraction doesn’t allow for a walk-away solution. Automation, on the other hand, does permit as much and the time saved can be used for more value-adding activities that are critical to the well-running of a lab and indeed to the overall engagement of team members.
- Improved efficiency & productivity
Unlike manual extraction, automated nucleic extraction does not require specially trained staff. Automation solutions don’t tire either and larger number of samples can be processed at significantly greater speed more efficiently and with the ability to scale accordingly.
- Cost savings
The cost of running a workflow cannot be ignored. There are misconceptions, and at times guesses, as to how much it actually costs to run a manual extraction versus an automated solution. The cost of labor and the cost of repeating runs for example are typically not fully considered and assumptions are made as to the cost of automation without considering break-even points or indeed the cost-savings it can generate. The Return on Investment Calculator highlights as much as well as the expected break-even point.
If you’re considering an automated nucleic acid extraction solution or if you would just like to have more info at this point, get in touch with us. We’d be more than happy to help.