How Automation Improves NGS Library Preparations

The accuracy of sequencing data analysis is dependent upon the initial step of preparing high-quality libraries. This first part of the next-generation sequencing (NGS) workflow is critical to ensure the resulting data not only captures the sequences of interest but is also correct and reliable. Library preparations have traditionally presented numerous challenges and limitations, but many have been mitigated with the introduction and adoption of a key advancement—automation.

Hurdles in manual library preparations

While automation has been accepted by many labs, some researchers continue to perform manual library preparations, which delivers various challenges. “Data accuracy and quality are certainly at the top of the list,” explained Kevin W.P. Miller, Ph.D., Director of Marketing & Scientific Engagement at HighRes Biosolutions. “NGS library prep workflows are long and include many pipetting steps and incubation at various temperatures. When performed manually, each of these steps offers an opportunity for performance variability as no two people have identical lab techniques.” This variability can further increase when someone is under stress or even at different parts of the day. Inconsistency with library preps is a major problem for a process such as NGS that requires precision and consistency for accurate results.

In addition to variability, John Fink, General Manager, Automated Liquid Handling at Revvity, noted that another major challenge of manual preps is the cost involved or incurred by errors. “Pipetting or workflow errors can cause the loss of precious samples, and then require re-extraction, new kits, reagents, and time,” Fink stated. Indirect costs are also incurred from training new lab technicians on all the aspects of NGS library prep.

Mike Benway, Senior Field Application Scientist, NGS Automation at New England Biolabs (NEB), noted that “once a technician becomes skilled in manual library preparation, they are automatically in high demand and correspondingly difficult to retain. Sudden loss of key skills can devastate workflows and timelines.” There is already a major shortage of trained lab and medical technicians. Relying on a single person to do high or even low-throughput NGS experiments slows down the system and brings things to a screeching halt when their valuable skills are lost.

Transforming NGS library prep with automation

With many of these reoccurring issues involved with manual preps, the advantages of using automation seem clear. Some of these more obvious benefits include improvements to the accuracy and consistency of the resulting libraries, as well as massive reductions in manual errors and contamination.

Traditional views also suggest that automation is an effective labor-saving device, but Benway explained that this benefit has its limits. “The most valuable benefit, by far, is to expand the productivity of a single working person,” Benway added. He highlights this by describing his own lab experiences where automation did, in fact, free up some of his time. But more importantly, he could operate several machines simultaneously and further increase the lab's output.

Automation also offers several cost-saving advantages. Paul Lomax, Product Manager at SPT Labtech, emphasized that thanks to their precise engineering, automated systems can reduce the size of reactions, conserving reagents and samples. Consequently, this not only lowers expenses but also produces more data without sacrificing accuracy. Lomax added that “By alleviating the need for manual, tedious pipetting steps, automation can improve the working environment and operating conditions of the lab by mitigating the risk of RSI (repetitive strain injuries), as well as minimizing contact with harmful samples or reagents.” Furthermore, he shared that automation can be a great way to create a more sustainable lab. Utilizing non-contact dispensing technology diminishes the need for single-use consumables, lowering the amount of daily plastic waste.

The introduction of automation systems has also improved clinical and diagnostic applications. As Miller explained, “Automated NGS makes non-invasive testing such as liquid biopsies a reality and brings personalized medicine closer to patients and healthcare providers.” This can even be applied to sensitive applications such as forensic and human identification. The employment of automation in these procedures provides timely access to process and sequence these samples to correctly and clearly identify individuals, Miller noted.

Dispelling myths about automation

A vast majority of the NGS community has already recognized that automated library preps are the way to go. In fact, Miller believes that automated NGS library prep methods are the gold standard. “Even those still limited to manual library prep understand the risks that they are taking in terms of increased time, limited throughput, and risks of bias and error,” he noted. Equipped with this knowledge, those handling manual preps might not fully recognize the severity of the risks involved. These risks include producing inconsistent or inaccurate data and making errors that result in rerunning samples, leading to increased costs. In addition to these issues, there are several common misconceptions that have slowed the adoption of automation in many labs.

Myth 1: Automation is too expensive

One common myth about automation is that it's prohibitively expensive. While this might hold true for some small, basic labs, many laboratories can find scalable and cost-effective solutions tailored to their needs. Over time, automation can result in significant savings. “The main cost savings from automating a library sample prep will be a non-linear function of the number of samples run,” explained Benway. “This is more determined by the fixed costs of setting up and monitoring a run that could service a whole plate. Spreading that effort across a full plate reduces the cost per sample.”

“These savings are further accelerated when labs choose to miniaturize their workflows,” added Lomax. “Reactions can be scaled down tenfold, or even further, which results in significant cost savings on reagent use.” But reagents and consumables are not the only expense being reduced. “First and foremost, there is a significant hands-on savings that will reduce direct labor costs,” stated Fink. “Not just pipetting, but all the ‘hands-on’ activities such as moving labware to and from the thermocycler and other peripherals—the automated solution takes care of all of this.”

Myth 2: Automation takes away jobs

While automation does save money on labor, principal investigators and technicians alike have feared that automation will end up stealing jobs. “What is really happening with automation adoption is that this manual, repetitive work is reassigned to a robot so that employees have the ability to focus on work that adds great value to the lab, such as managing the automation, analyzing results, or creating more comprehensive reports from the data yielded,” explained Fink.

Additionally, Benway contended that machines alone can't replace the expertise of a seasoned technician. Successful automation depends on knowledgeable individuals familiar with manual sample processing. Employing effective automated systems requires both flexible error-recovery tools and user understanding of proper sample and reagent handling.

Myth 3: Automation is too complicated or special training is required

Implementing new technologies in the lab always requires some time to learn and integrate them into current workflows. “However, new liquid handlers on the market have been designed specifically with usability in mind, and are operated by powerful, intuitive software that doesn’t require previous programming expertise,” explained Lomax. Some older devices may have required some additional skills to set up, but current devices are easier than ever to quickly incorporate, allowing labs to swiftly adapt and optimize their operations without a steep learning curve.

Myth 4: There’s no room for automation instruments

A more minor but valid concern from researchers is finding the space for new instruments. As Lomax explained, “Adequate lab space can be a challenge when adopting new automated systems. Especially when researchers are looking to automate more than one process, new equipment can quickly occupy a substantial amount of premium lab real estate.” He noted that this is where multi-functional solutions make good use of vertical space. “This versatility means researchers can get a lot of use from a single, compact, benchtop instrument.”

Closing thoughts

Embracing automation for library preparations is essential for overcoming the traditional challenges posed by manual work. Once common misconceptions are debunked, researchers can integrate automation into their own lab and begin to see the full potential of their NGS workflows. The increased introduction of automation in these laboratories will lead to increased efficiencies, precision, and data outputs, potentially leading to more scientific breakthroughs.