6 Powerful Ways to Automate Your Next-Generation Sequencing Lab

For low-throughput labs, manual processing might be the simplest and best way to operate. But for high-throughput labs, automation is the key tool needed to boost speed and efficiency.

Every process you currently perform manually is an opportunity for incremental improvement. So, it makes sense to automate as many processes as possible once your monthly throughput exceeds a certain threshold. We’ve talked about this before in our post on scaling throughput, but we think it bears repeating. If you want to scale, automation is critical.

There are other significant benefits, too. Automation using robots and code that operate according to defined algorithms can also help the lab achieve a greater degree of reproducibility and accuracy. It can also result in fewer human errors and boost the morale of your highly qualified lab technicians.

Here are six ways your lab could begin to take advantage of this important capability.

1. Instruments integrated with the LIMS & the LIS

A simple way to add automation to your lab is to facilitate data transfer between your LIMS and analytical instruments. For next-generation sequencing (NGS) labs, this means integrating polymerase chain reaction (PCR) instruments, sequencers, and quality control instruments with your laboratory information management system (LIMS). This will reduce the amount of time your lab technicians spend recording data, freeing them up to do the more hands-on work with samples and instruments.

2. Integrated software

Clinical NGS labs generally use a number of different types of software, including electronic health record (EHR) or electronic medical record (EMR) systems, laboratory information system (LIS), order management, and other enterprise software. When you integrate these systems, you can avoid the risk of duplicated data and errors that can occur when data is transferred between systems manually.

3. Automated liquid handlers

Automated liquid handlers are frequently used in NGS labs performing DNA/RNA extraction and purification. The benefits of these devices include:

  • Automated indexing and multiplexing. For instance, the liquid handler transfers a specific barcode from the reagent plate to the destination plate that contains the sample, providing reproducibility.
  • Automated failure handling and error prevention. This is enabled when you integrate the liquid handler with the LIMS, and includes a “pre-flight check” to make sure the plates are ready and in the right positions. The liquid handler doesn’t proceed until the check is complete and everything has passed. After the LIMS goes through a checklist, the robot performs its operations and then reports if there are any issues.
  • Post-step error reporting. When the liquid handler is finished, it notifies the LIMS that it has completed that step in the protocol. If the liquid wasn’t transferred because a tip was loose, volume-sensing robots can tell the LIMS which wells need to be reviewed.

4. Custom applications to automate lab processes

If your lab wants to take automation a step further, custom applications can help you automate processes such as importing manifests, accessioning, clinical reporting, and order management. For an example, you can read about how we helped a lab streamline a spreadsheet manifest import with an automated data import solution.

5. Custom LIMS workflows

If your lab has a LIMS, it probably came with a set of preset protocols. But these presets might not accurately reflect your lab’s protocols, be optimized for efficiency, or work with your automated liquid handlers to compute and send custom instructions based on data tracked in the LIMS. Custom workflows might be a better solution because they can incorporate scripts to automate processes such as decision-making (including quality control pass/fail decisions and re-queues), file generation, file parsing, calculations, and synchronization with another service.

6. Automated software testing

A final area of automation that labs frequently overlook is automating software testing. Automated tests that are built into your software will ensure the systems are performing as expected, further reducing the risk of errors or even downtime. They also enable your team to make changes to existing software with confidence, as the automated tests can help ensure there are no unintended consequences.

Other things to think about

When you’re considering all the ways you can automate your lab, there are a few caveats. Automation does not mean the lab will operate flawlessly with 100% efficiency all the time. But any time you add automation, you should expect to see incremental improvements in speed and efficiency overall.

Another thing to consider is that automating one part of the process might cause a bottleneck further down the line. Planning ahead can help you avoid this. One option is to partner with an experienced consultant with the right domain and systems knowledge. At Semaphore, we know what to look for and how important it is to get things right the first time, so your lab can focus on delivering the medical breakthroughs that are so important for patients and their healthcare providers.

Check out our service areas—many of them are related to automation. Contact us if you have any questions or want to talk about how to automate your lab.

Prior to joining Semaphore, Shahriar was a LIMS product specialist and field implementation specialist for Genologics and Illumina. As Senior Product Owner at Semaphore, he is passionate about translating the complex needs of all stakeholders into highly functional software.