The Complete Guide to Automated Sample Preparation for NGS

Due to advances in scientific research, such as next-generation sequencing (NGS), increasingly complicated experimental workflows are becoming more common. NGS is a high-throughput DNA and RNA sequencing method that has now overtaken Sanger sequencing in popularity due to its cost-effectiveness and high sensitivity¹. NGS has widespread use, leading to a large impact on research and healthcare, including identifying disease-associated genetic mutations². The requirement for accuracy and reproducibility in achieving successful NGS experiments³ has led to automated sample preparation gaining popularity. 

In this article, we explore what the key challenges in the NGS workflow are and how automated sample preparation can overcome these challenges to improve lab efficiency.

Overcoming Challenges in NGS Workflows

NGS sample preparation is a laborious process, requiring repeated wash steps, consistent pipetting, and the handling of many samples. Errors in this process, such as sample contamination⁴, are therefore extremely common and can result in incorrect or biased results or can ruin an entire day’s work – both of which require experiments to be unnecessarily repeated, leading to wasted time, money, and resources^5,6.

Sample preparation is a time-consuming process and can form a workflow bottleneck due to difficulty achieving high-speed manual sample preparation⁵. Researchers carrying out these experiments must spend much of their day laboriously pipetting instead of having the time available to carry out innovative work⁵. In addition, any differences in technique between researchers, such as pipetting technique⁷, can cause a batch effect between experiments and lead to incorrect conclusions⁸. Fortunately, automated sample preparation can be used to overcome these challenges.

Read our dedicated article on overcoming challenges in NGS workflows through the use of automated sample preparation to learn more.

Optimizing Lab Efficiency

Optimization of lab output is becoming more difficult due to increasingly complex workflows. Manual workflows slow down output, have a high risk of error, and can introduce researcher-to-researcher variability resulting in batch effects⁸. The removal of manual processing through the use of automated sample preparation decreases human error and environmental exposure, therefore improving the accuracy and precision of the results and reducing the risk of contamination⁹. In addition, automated sample preparation reduces the length of time taken to complete the preparation, enabling the whole NGS process to be completed faster and researchers to use their time more effectively⁵. The experiment-to-experiment consistency achieved through the use of automated sample preparation alleviates any batch effects and enables experiments to be scaled up to large projects and clinical applications¹⁰.

Automated sample preparation further enhances lab efficiency by making NGS experiments more cost-efficient – minimizing reagent and consumable use and reducing human-error-induced repeated experiments¹¹. Use DISPENDIX’s G.PREP ROI calculator to see how much your lab could save through using automated sample preparation. The versatility of automated sample preparation enables its use in multiple areas of experimental workflows and different types of experiments (Fig. 1.) 

Figure 1. NGS workflow schematic demonstrating the multiple areas of the workflow that can be automated using DISPENDIX’s I.DOT Liquid Handler.

To learn more about how automated sample preparation can optimize lab efficiency, read our dedicated article.

Streamlining NGS Automation

Manual NGS sample preparation involves long periods of hands-on work, limiting efficiency and increasing the likelihood of human error⁵. Automated sample preparation streamlines NGS by enhancing precision, increasing throughput, reducing human error (such as contamination), and improving reproducibility. To effectively integrate NGS automation into lab workflows, researchers should consider key lab needs, such as throughput requirements, accuracy requirements, and sample volume requirements¹². These will change system to system, so they must be thought through before choosing a system to introduce to the lab. Further consideration should be given to whether the automated sample preparation system will be compatible with the existing lab equipment (Fig. 2.)

Figure 2. The automated sample preparation systems produced by DISPENDIX, such as the I.DOT Non-Contact Dispenser and G.PURE NGS Clean-Up Device are designed to work effectively with each other and with a wide range of other lab equipment and labware.

Read our dedicated article to learn more about how to streamline NGS automation and incorporate it into your lab workflows.

Conclusion

The complicated workflows involved in NGS, particularly in sample processing, result in a time-consuming process with multiple steps and make it vulnerable to human error. Errors, such as contamination, can lead to inaccurate results and incorrect conclusions. In addition, the requirement for consistency in the experimental setup is paramount, as any researcher-to-researcher differences can lead to bias and inaccurate conclusions. These challenges complicate NGS, reducing the effectiveness of this popular sequencing technique.

Automated sample preparation is, therefore, a key tool for use in NGS, providing accuracy, consistency, speed, and reproducibility. These features not only improve experimental efficiency but can also lower experimental costs by minimizing reagent and consumable use and reducing unnecessary experiment repetition. Automated sample preparation can be streamlined by carefully assessing key lab needs before deciding on which automation system to choose.

To learn more about how DISPENDIX’s G.PREP NGS Automation can optimize your NGS sequencing, download the brochure and take the next step in transforming your workflows!

References

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