How Automation Saves You Time & Money in NGS Library Preparation

Next-generation sequencing (NGS) is a massively parallel sequencing technology that holds huge promise for genomic research, rare disease diagnostics, and personalized medicine¹. Despite its potential, NGS comes with considerable challenges, many of which are associated with the error-prone, lengthy, and cost-inefficient NGS library preparation stage.

However, these challenges can be overcome by integrating advanced automated liquid handling into library preparation pipelines. The I.DOT Liquid Handler represents a game changer for NGS library preparation workflows (Fig. 1). Here, we explore how the I.DOT Non-contact Dispenser can streamline processes to save time and money in NGS library preparation. 

Figure 1. Workflow schematic showing where the I.DOT Liquid Handler and G.PURE NGS Clean-up Device fit into the NGS library preparation workflow.

Saving Money with the I.DOT

While significantly cheaper than traditional Sanger sequencing, NGS is still relatively expensive when all costs are considered², limiting its use in many labs¹. The main costs associated with NGS library preparation are equipment costs, labor costs, and reagent costs³, all of which can be reduced considerably by automating up to 80% of the library preparation process. 

Reducing Reagent Costs

Minimizing dead volume is crucial in reducing reagent use, especially when dealing with expensive reagents. Miniaturizing reaction setups through the use of microplates or microfluidic systems significantly decreases the required volume of reagents and samples, thus reducing dead volumes and associated costs⁴. 

The I.DOT Non-contact Dispenser facilitates miniaturization, supporting accurate dispensing volumes as low as 8 nL through volume verification technology and requiring a dead volume of only 1 µL (Fig. 2). With the I.DOT users can scale NGS reaction volumes as low as one-tenth of the manufacturer’s recommended SOP without compromising data quality. This reduces costs significantly and is especially useful when working with precious, unreadily available samples like patient samples⁵. 

Figure 2. DropDetection enables the detection and counting of every droplet released during a dispensing run, ensuring robust and accurate dispensing of low liquid volumes. 

Reducing Labor Costs

Automating the NGS library preparation workflow significantly enhances experiment throughput. This automation allows multiple samples to be processed simultaneously with minimal manual intervention, effectively decreasing the number of experiments that need to be performed manually. This reduction in hands-on time leads to considerable savings in labor costs, making it an economically beneficial investment. 

Automation has also been shown to reduce the risk of human error and contamination, which can lead to costly and time-consuming repeats of experiments⁶. The precision and reproducibility offered by automated systems ensure high-quality data, reducing the need for complex data filtering and unnecessary repeats and lowering labor costs⁷.

Reducing Equipment Costs

Given the initial expenses associated with automated devices, many people believe that automating workflows leads to higher equipment costs. However, when estimating NGS costs, it is important to consider many factors, including instrument purchase, cost per sample (consumables, reagents, and labor inclusive), data analysis and storage, and training costs². When this is evaluated fully, lab managers frequently find that the long-term benefits far outweigh the initial equipment costs, primarily through enhanced operational efficiency, reduced labor costs, and lower consumable expenditures. The I.DOT Non-contact Dispenser enables tipless reactions, which saves money on consumables while also supporting labs in sustainability efforts, which are becoming increasingly important requirements of lab operations^8,9.

Saving Time with the I.DOT

In addition to its high costs, NGS library preparation is also highly time-consuming. Manual library preparation requires up to eight hours of hands-on time and can take up to a full day for DNA libraries and two days for mRNA libraries. Aside from the labor costs incurred, this is highly inefficient, and the potential for error increases exponentially with increasing time and steps. Automating processes can significantly reduce turnaround times by increasing throughput, reducing manual steps, and minimizing unnecessary replicates¹⁰. 

Increased Throughput

Automated liquid handling facilitates a significant increase in the throughput of NGS library preparation by enabling batch sample processing. This means that multiple samples can be processed simultaneously rather than sequentially, a common limitation in manual or less advanced automated systems¹¹. Liquid dispensing and cleaning with automated systems is also markedly faster than traditional methods. This rapid processing capability not only speeds up the entire workflow but also minimizes the downtime that typically occurs between steps in manual handling, resulting in a substantial reduction in NGS library preparation turnaround times.

Fewer Manual Steps & Repeated Experiments

Automation with the I.DOT system drastically reduces the need for manual intervention during the NGS library preparation process. In traditional library prep, manual steps not only waste time but also introduce variability and errors, such as pipetting inaccuracies, which are avoided with automated liquid handling. 

Additionally, the I.DOT’s non-contact dispensing technology plays a crucial role in preventing cross-contamination between samples (Fig. 3), which represents a significant concern in NGS workflows as it can compromise the integrity of the sequencing data, invalidating data and requiring re-runs. With automation, integrity is maintained, meaning that each sample is more likely to be used as a valid data point, thus reducing the frequency and need for costly and time-consuming repeats due to errors or contamination⁶.

Figure 3. The I.DOT employs a non-contact dispensing mechanism, which eliminates the risk of cross-contamination while also supporting tipless dispensing. 

Conclusion

Integrating advanced automation technologies into NGS library preparation workflows presents an effective solution to cost and time efficiency challenges. By minimizing manual interventions and reducing the consumption of valuable reagents and labor, automation enhances operational efficiencies and lowers the overall costs associated with NGS. It not only expedites the library preparation process through increased throughput and reduced manual steps but also mitigates the risks of error and cross-contamination. This highlights the cost-effectiveness of investments in automation technology, yielding significant long-term benefits in NGS workflows.

Ready to streamline your NGS library preparation and free up resources for what matters most? The I.DOT Liquid Handler is your key to efficiency and cost-effectiveness. Book a demo today and see for yourself!

References

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