Blogcritical consideration for DNA extraction

You’ve secured funding. You have lab space. Now, your research starts. Likely, one of your first steps will be collecting samples and extracting viable DNA for your downstream processes. Before you do, here are 5 things to consider.

DNA extraction is a crucial first step necessary for many downstream applications. In this article, we cover some of the considerations beyond the monetary cost that researchers and lab managers need to consider when starting a DNA extraction project.

Of course, your budget and funding will likely be the primary driver behind any DNA extraction project decisioning. We’ll cover that first before diving into the other avenues to consider the “cost” of a DNA extraction project.

What is the Cost of DNA Extraction?

The cost of DNA extraction projects depends on a variety of factors. These factors include:

  • Sample type: Some samples are easier to extract DNA from. Some are harder. Depending on the type of sample you’re working with, the process may take more time and cost more money. It may require special instrumentation or expertise to get the right protocol in place to ensure the best possible DNA quality.
  • Sample prep: Depending on the type of sample and the quality of that sample, there may be preliminary steps needed to prep the sample for a successful DNA isolation. These steps will take more time and likely add to the cost of outsourcing the project.
  • Timeline: If you need to get your samples processed fast, you’ll either need to dedicate extra lab time if you’re doing it yourself or you’ll need to possibly pay rush fees when working with an outsourced provider.
  • Extraction quality: The quality of DNA required depends on your downstream applications. Some, you might be able to get away with a quicker, less expensive, lower-quality extraction. For others, high-quality DNA is a must, and you’ll likely have to pay for that quality.

Now that we’ve explored the monetary considerations let’s dig into the other types of costs and tradeoffs associated with DNA extraction decisions.

5 Critical Non-monetary Cost Considerations for DNA Extraction

Consideration #1: Automation or Manual Extractions

There are many ways to extract DNA. The broadest way to break down is manual and automatic processes.

Within automated and manual DNA extraction protocols, there are countless workflow protocols and instruments designed to extract DNA and RNA from a wide variety of samples.

The main thing you must consider here is which of these two routes to follow.

Manual extraction processes are much cheaper; however, the consistency and quality of the extracted sample may suffer.

On the other hand, an automated instrument will be consistent in giving you a high-quality sample. They work by handling that sample from start to finish, adding the right amount of additives and chemical reagents thanks to predetermined protocols and pre-measured consumable chemistry kits.

Automated instruments can be a significant investment upfront. They take up valuable lab space, and unlike humans, if something goes wrong, they can’t think or operate with nuance.

If you plan to extract DNA and RNA at scale, then instrumentation may be a wise investment.

Consideration #2: Instrumentation

If you’ve decided on the automation route in your lab, then you’ll need to consider which extraction workflows to invest in.

You can start to narrow down your search by understanding your needs in the critical features:

  • Throughput capacity: You should consider instruments that can not only process the number of samples you have now, but ones that can scale to meet anticipated future need.
  • Protocols: Compatibility with a variety of sample types and extraction protocols is crucial to address diverse research needs.
  • Precision: Instruments that can precisely and reliably handle samples while preventing contamination and ensure consistent results.
  • User interface: How easy is the instrument to use? Will it require training or is the interface intuitive and user-friendly?
  • Compatibility: Make sure the extraction instrument and protocols are compatible with your LIMS software and any other internal system you use to track samples, labeling and data.
  • Instrument upkeep: Consider maintenance requirements, the need for technical support, and instrument uptime. These are vital for minimizing disruptions and can wreak havoc on your budget past the initial investment.

Lastly, the system’s data management capabilities, including integration with LIMS and data security protocols, play a key role in maintaining traceability and compliance.

Consideration #3: Personnel

Once you’ve decided on a protocol, another cost to consider is personnel. To start exploring whether you will need to hire or train lab techs, ask questions like:

  • What prior skills and training do they need to have to complete the protocol correctly?
  • Have they operated automated extraction instruments in the past?
  • How long will the protocol take?
  • Are there other tasks they can do while the automation is running?

These questions and your funding will help you make informed decisions about the personnel running these extractions should you decide to do it yourself.

Consideration #4: Sample Storage

How will you store your samples?

Depending on the type of samples you’re collecting and extracting from, proper storage can be critical. You need to make sure that you have a way to optimally store samples beforehand. That means space, infrastructure, and electricity costs.

For example, whole blood samples should ideally be stored in a deep freeze at -80°C. Saliva samples on the other hand are much easier to store.

Keeping samples in a deep freeze is costly in terms of equipment and energy. Ideally, whole blood samples should be processed as soon as possible because DNA can be stored at a much more reasonable temperature for much longer while also taking up less space than a standard blood sample tube.

So, no matter your sample, if you’re extracting DNA, you need to take the time to think through the needed storage for those samples. When stored improperly it can compromise your entire study.

Consideration #5: What if extraction goes wrong?

DNA extraction is a crucial first step that can determine the quality of your study or clinical research.

So, consider the worst-case scenario. What happens if something goes wrong? What does it cost you in terms of money, time, and the ability to complete your research?

Extracting DNA is a routine step in research, but it can go wrong in many ways. Suboptimal storage can degrade your sample or extracted nucleic acid. Mislabeled samples can lead to bad data, null results and wrong outcomes and conclusions.

Sample collection and processing can take weeks or months. Going back to get samples can set your critical research back. Not to mention, if you’re studying vulnerable populations or the time progression of disease, it may not be possible even to go back to collect samples from your selected population.

It’s imperative to think DNA extraction through entirely.

Conclusion: Consider Outsourcing Your Extraction Projects

Extracting usable DNA may be a basic laboratory process, but there are still plenty of nuances to consider when optimizing the process to fit the needs of your study, your budget, and your resources.

If you want to do it right, sometimes outsourcing to an extraction lab is the best solution. Not only do you avoid the upfront investment of instrumentation and storage, but you may also get better results that will improve the quality of your study. Plus, you’ll save your team time and allow them to focus on other core competencies.

Don’t just go with any outsourced lab services provider. For you to reap these benefits, you need to find the right partner. When vetting potential DNA extraction providers, it’s important to prioritize communication. Make sure that they keep in consistent contact at every step of the process. And when you call, a person should answer. That person should have full knowledge of your project and be equipped to answer any questions clearly and with transparency.

Whether you’re purchasing instrumentation or looking for a reliable DNA extraction outsourcing partner, talk to AutoGen. We’ve got DNA and RNA extraction experts on hand to answer your questions.