The success of next-generation sequencing (NGS) experiments is dependent on precise library preparations. Manual preparation is error-prone due to its intricate steps that require delicate handling and concentration. However, the utilization of automation has enabled researchers to prepare samples both efficiently and accurately.
Our understanding of genomes, transcriptomes, and epigenomes has been significantly advanced due to the employment of NGS. This technology is instrumental in critical research fields such as oncology. In particular, methods like single-cell sequencing have offered novel insights into the heterogeneity within the tumor microenvironment. Additionally, NGS has been pivotal in precision medicine, identifying disease-associated genetic variants, and providing personalized treatment strategies. During the recent pandemic, NGS played a crucial role in monitoring the spread of SARS-CoV-2, demonstrating its rapid and comprehensive capabilities. Each of these applications underscores the importance of precise and accurate results generated by NGS.
In the past, detailed laboratory workflows, such as NGS library preparations, were strictly performed manually. Even with extensive lab experience and meticulous attention to detail, this type of manual procedure is more susceptible to human error. Mistakes during any library prep stage can lead to sample loss or, even worse, yield inaccurate data.
Completing a library prep can often take multiple days and common steps like diluting, pooling, and normalizing samples require intense focus, especially for larger sample sets. Multichannel pipettes and repeat pipettors take off some of the strain from manual preparations; however, they still require high levels of concentration to avoid mistakes. Manual pipetting also creates variability as individual techniques differ among researchers. These variations can compromise the results and are further exacerbated when handling viscous liquids like magnetic beads, a commonly used reagent for library cleanup steps. Incorrect bead-to-sample ratios can also cause significant sample loss.
Other major challenges of manual preparations include a higher likelihood of introducing contamination. The frequent opening and closing of tubes and pipetting across microwell plates make contamination nearly inevitable. In addition to these concerns, manual prep, as the name suggests, requires repetitive manual actions that can cause physical strain or even injuries over time.
Among the commonly used automation systems, there are many different types of liquid handlers tailored to perform library preparations. When choosing a liquid handler, users should consider sample throughput, volume range, labware compatibility, desired automation level, and the user interface's intuitiveness for creating or modifying methods. While some systems might require hands-on adjustments for certain stages of the library prep, they typically manage most liquid handling, incubation, and magnetic bead separation steps. In some cases, the PCR steps using a thermocycler are completed off-deck, while others utilize an on-deck thermocycler. The ideal automated liquid handler can offer assistance throughout the library preparation process, regardless of the prep kit used. From common DNA library prep workflows to custom-targeted preps, these instruments are capable of generating high-quality libraries.
When selecting an automated liquid handler, it’s important to consider one that can not only assist with the entire experimental workflow, but also offers the versatility to automate everyday liquid handling tasks. This encompasses tasks such as nucleic acid extractions, library preparations, sample normalization, post-preparation procedures, as well as serial dilutions and plate reformatting. Automation proves particularly valuable for critical steps like qPCR quantification of libraries, due to its enhanced precision and accuracy.
Automating library preparations offers benefits beyond simply reducing hands-on time. With the time gained from automating their tasks, researchers can concentrate on other responsibilities, thereby increasing productivity and lab output. As scientists transition from manual to automated methods, they can easily increase the scale of their experiments. Despite the higher throughput, automation reduces mental and physical fatigue as well as exposure to contaminants.
This shift from manual work also promotes standardized preparations, ensuring reproducibility. The advanced robotics within these liquid handlers maintain consistent pipetting for all experiments, even for minute volumes. This consistency translates to cost savings by reducing errors and preventing costly mistakes, as well as ensuring optimal reaction conditions, which reduces waste and preserves valuable lab resources. Adopting automation for library preparations is essential for overcoming the traditional challenges posed by manual work.
The transition to automation is simplified, especially for new users, with the epMotion® liquid handler. Eppendorf's epMotion 5073 and 5075 provide advanced, all-in-one solutions for automating NGS library preparation. Engineered for precision and ease, these automated liquid handlers seamlessly integrate into laboratory operations, ensuring streamlined NGS workflows from start to finish. Unlike many other liquid handlers that can be challenging to use and demand automation experts, the epMotion is designed with scientists in mind.