Introduction

Next-generation sequencing (NGS) technology has become a valuable approach in life science, fundamentally transforming the kinds of questions scientists can ask and answer.¹ With the ability to sequence large numbers of samples at higher depth and lower cost, it has become a common tool in a researchers’ arsenal. ²

But as sequencing has grown in popularity, so has the demand for samples. With more experiments, comes the need for more NGS library prep, which is a complex and costly process that requires substantial time, resources, and reagents. For many projects, the total costs associated with library prep can rival costs associated with sequencing itself. As a result, it is natural that users are motivated to find ways to reduce the cost of preparing samples for sequencing, much in the same way that multiplexing economizes the use of the sequencer.

Hidden Costs of NGS Library Prep

NGS library prep is a tedious process that is often deemed the “bottleneck” of DNA sequencing.¹ The costs incurred during library preparation derive from laboratory equipment, trained personnel’s hands-on time and reagent cost. The relative impact of library preparation on overall sequencing cost varies. While this cost may be insignificant for whole genome sequencing (WGS) of human DNA, it can be a key factor for WGS of extensively multiplexed bacterial samples.²

Typically, when users and labs are considering approaches to scale their library prep, there is a tendency to focus solely on the cost of buying the library construction kits without considering other hidden expenses such as:

• Plastics Use: Gone are the days of reusable glass pipettes and culture dishes – disposable plastics are now considered convenient and cost-effective.³ From pipette tips to microplates and cell flasks, every day thousands are discarded after a single use, only to be incinerated or sent to a landfill. This adversely contributes to the elevated levels of plastic pollution with a negative impact on the environment.⁴
•  Miniaturization and Optimization: While miniaturization of reagent volumes reduces costs for kits, it still uses the same number of tips/plastics in most instances. Miniaturization also can require the use of specialized liquid handling equipment, which can mean additional costs.
• PCR Workflows: PCR is a critical component of library prep and yet cross-contamination of samples can be a major issue that is challenging to detect. With PCR, even small errors can be quickly amplified leading to skewing your library. These types of errors can add unnecessary cost to what is already an expensive process. ⁵
• Lack of Workflow Evaluation: Frequent assessments of workflows, reagents, and techniques is critical if you want to save time and money. For instance, your lab’s sample throughput may have increased over time to the extent that automation is now advisable, even if it wasn’t last year.⁶
• Manual Process: Using a manual process requires additional work to prepare reagents, and is repetitive as well as error-prone, leading to both time and cost inefficiencies for clinical genetics laboratories.

Keeping Costs of Library Prep Down

seqWell’s prep methods use significantly lower amounts of plastics and pipette tips, potentially saving users several dollars per batch of samples, while also reducing the amount of plastics waste produced in the lab.

Designed to solve many of the difficult challenges that NGS users face when approaching medium- to large-scale multiplexed library preparation, our plexWell NGS library preparation technology enables efficient, cost-effective preparation of libraries from multiple samples for sequencing in a single run.²

Our plexWell libraries are conveniently prepared in a single tube after a single tagging step, reducing associated labor, consumable and library QC costs by more than 10-fold. Researchers can eliminate costly and error-prone normalization steps, as plexWell library prep kits normalize for a wide range of DNA input amounts and deliver uniform read count and insert size distributions across multiple samples in a single library. ²

Conclusion

Researchers need to think differently about the costs of NGS library prep.  It is imperative to look beyond just the price of a kit and factor in other variables. Selecting the right library prep method for your specific downstream application and technology can be a simple way to help reduce overall NGS costs.⁵

With seqWell’s plexWell library prep kits, you can save money and reduce your environmental impact with fewer pipette tips required for your process.

References

1. https://www.illumina.com/science/technology/next-generation-sequencing.html
2. http://seqwell.com/wp-content/uploads/2019/06/TDS_plexWell_v20181106.pdf
3. https://www.sciencedirect.com/science/article/pii/S0734975020300343
4. http://seqwell.com/wp-content/uploads/2019/06/TDS_plexWell_v20181106.pdf
5. https://www.tecan.com/blog/100-dollar-genome-real-cost-ngs/
6. https://www.biocompare.com/Editorial-Articles/580896-Tips-on-Keeping-NGS-Costs-Down/