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How NGS Workflow Automation Can Benefit Labs of Every Size
Unlocking Universal Access to Genomic Sequencing
Discussions surrounding the need to expand access to NGS-based genomic testing beyond large academic medical institutions and advanced labs continues to build momentum. As it becomes clearer that NGS testing insights can be game-changing for cancer treatment approaches and for our understanding of genetic conditions, we must proactively work to increase this technology’s accessibility. Bringing NGS capabilities to smaller community hospitals and clinics can empower providers to dive even deeper into their patients’ care and overcome many logistical limitations patients face in seeking testing elsewhere.
What steps can we take to bring NGS testing capabilities to smaller hospitals and clinics? While automated NGS workflows may sound unnecessary outside of a massive, advanced laboratory, smaller clinical care settings shouldn’t be discounted. Automation of NGS workflows can take many forms, and its advantages are not limited to labs handling hundreds or thousands of samples daily. For a smaller hospital or clinic implementing NGS capabilities, considering automation can make workflows more feasible and approachable by increasing precision, reducing the need for advanced expertise and saving time.
This piece will discuss the benefits of automating components of NGS workflows as well as some tips for evaluating approaches to automation in labs of any size. Additionally, it will share the implications of automation for the future of NGS-based diagnostics and its role in bringing valuable health insights to more patients than ever.
Why Automate NGS Workflows?
Automation presents an opportunity to overcome many of the limitations that smaller hospitals and clinics face in implementing NGS in the first place. Many facilities whose patients would benefit from NGS-based testing lack the lab personnel with the necessary expertise to process samples, perform sequencing, and analyze sequencing data. Automation of steps in the process can lower this barrier to entry; with more streamlined “plug and play” processes in place, lab technicians will not need advanced or specialized education to perform NGS, meaning that more hospitals and clinics likely already have the necessary manpower in-house. Additionally, if tedious and repetitive steps in NGS workflows are automated, lab technicians can spend that valuable time completing other tasks, increasing overall productivity.
Beyond ease of use, automating steps in NGS-based testing can reduce human errors. Automating sample tracking from collection through processing and analysis can ensure sample integrity from start to finish. Additionally, by automating repetitive tasks including serial pipetting during DNA extraction or library prep, a lab can minimize mistakes, reduce between-user variability, and maintain processes in a more controlled environment. This is particularly critical during early steps such as nucleic acid extraction and NGS library prep, as errors in these phases compromise the process.
How Smaller Labs Can Approach Automation
Automation of NGS workflows doesn’t have to be a “one size fits all” decision. Different clinics and labs have different priorities that can be considered when approaching automation. For example, a clinic processing 20 samples each day doesn’t need to have a massive, fully automated liquid handling system that would be suitable for a lab processing hundreds or thousands of samples each day. However, the clinic can still benefit from automated NGS library prep, which can give the technician valuable time to attend to other tasks.
In considering NGS workflow automation, a lab can evaluate a few broad factors: which steps to automate relative to their individual needs and the abilities of technicians; how automated those steps should be (i.e., how much “walk-away” time it produces for a technician); and what types and quantities of samples are being processed. Additionally, labs should consider the requirements for reagents and other supplies needed for automation techniques when making this decision. For example, some automated liquid handling methods use mass quantities of pipette tips and stocks of reagents that would be untenable for smaller groups. While staying open to the idea of automating workflows, clinics can also be strategic and realistic about which automation approaches best fit their needs.
Moving the Field Closer
While implementing NGS-based testing is possible for smaller clinics and hospitals, further technologies will make automated NGS workflows more feasible and suitable for groups of this size. Newer, low-cost sequencing equipment with smaller footprints and scalable operational workflows can help overcome financial and spatial constraints to NGS-based testing. Additionally, the development and approval of NGS-based IVD tests with clear, binary outputs is a step towards the automation of data analysis. Currently, clinical NGS results often require interpretation by a molecular pathologist, which increases the time from sample to results and excludes facilities without such an expert on staff from implementing NGS-based testing. NGS-based diagnostics that produce quick, clear results can offer insights and guide treatment decisions that cannot and should not wait.
Expanding smaller clinics’ access to NGS-based genomic testing is more complicated than simply getting sequencers into facilities– considerations such as enabling workflows that are efficient, minimizing errors, and ensuring ease of use throughout the entire process are all key factors as well. While automating NGS workflows in labs new to sequencing in general may seem like a step too far ahead, automation can be the right investment for data integrity and simplified workflows that will increase value for all parties involved.
Jason Myers brings over 20 years of experience in the genomics industry. Prior to Genapsys, he was co-founder and CEO of ArcherDX, continuing his track record of successful technology development and enterprise value creation. Before that, Jason led platform and sequencing application development for Ion Torrent™ where his leadership contributed to its acquisition by Life Technologies.