By Ashesh Saraiya
NGS has transformed genomics research and contributed to breakthroughs in many areas of medical science. At the same time, making NGS robust, reliable and cost-effective can be challenging for many labs. In particular, generating libraries for sequencing is a common bottleneck, especially for labs that are processing low sample volumes or not running NGS on a regular basis. In this article we explore the main challenges that labs need to overcome to make in-house library prep a viable option.
Improving library prep is key to making in-house NGS practical for low-throughput labs.
NGS library prep takes time and effort
Preparing high-quality libraries is essential for accurate and reliable NGS results. Manual library preparation takes between 4 and 8 hours of work. Typically, a full day is required for preparation of libraries for DNA and two days for mRNA sequencing libraries. With long, multi-step workflows, there is always ample opportunity for human error. Both the time required and potential for errors increases as the number of processed samples increases.
A simple mistake, such as leaving ethanol in the sample, can adversely affect the quality of your library. Even if no errors are made, the variation in the way that different people carry out the process of library prep can introduce variability and significantly impact the ability to compare results. For example, pipetting accuracy can vary from operator to operator. This along with slight variations in methodology can affect the sequencing results.
Problems such as these can lead to undesirable variability and could compromise the quality of your research and its reproducibility.
Not only human resources but expertise in library prep is required for reliable, in-house library prep. However, for many smaller labs and research groups, the time and effort required for in-house library prep is simply not available.
In addition, there is often concern about whether investing in an automated solution for NGS library prep would give a good ROI—particularly if your lab often works with low numbers of samples or does not process samples on a regular basis. In such cases many labs consider outsourcing in the first instance.
The cost of outsourcing
Outsourcing your library prep needs is definitely a convenient option. When you outsource, you can rely on the expertise of a larger, more vetted team. It doesn't take valuable time away from your lab technicians and is often cheaper than investing in high-throughput automation. However, outsourcing is not without its drawbacks, and if you frequently ship small batches of samples the costs can quickly add up. But isn’t it still cheaper than doing library prep in-house? Not necessarily. Read on.
Could in-house NGS automation be a practical solution for your lab?
Before we talk about how doing your own library prep can save you time and money, let's take a step back. Automation is problematic for smaller labs in several ways.
Cost is an obvious concern. An automation liquid handling system for NGS library prep is a significant upfront investment, but one that should pay off over time in terms of improved processing efficiency and quality of results—provided that it doesn’t push your processing bottleneck upstream.
For example, if you have an automated library prep solution in-house and are working with a commercial NGS kit designed for 96 samples, but typically receive only 8 samples at a time, you will either have to run them inefficiently (potentially wasting expensive reagents and materials) or wait until you have collected more samples.
Turnaround time is a related factor to consider in academic and clinical research settings. As in the above example, it may be difficult to achieve turnaround targets if your lab is forced to wait until there are enough samples for a cost-efficient run. For many laboratories, waiting to collect samples is simply not an option, as delayed results could lead to a number of consequences.
Expertise can also be a challenge, particularly for smaller research groups. Depending on the automation solution, it may take up a lot of valuable time to train staff on how to create and modify protocols, set up and operate the system, and keep it calibrated and in good working order. Even if you already have a dedicated in-house expert on board, performing library prep in-house often means that this scientist becomes tied up with routine day-to-day operations and is less available for data analysis and interpretation.
To address challenges like these, there have been a number of recent developments to make automated library prep for NGS more cost-efficient, practical, user-friendly and accessible—especially for smaller / lower-throughput labs. In the final installment of this series, we will explore these advances in more detail. To make sure you don’t miss out, sign up for The Blog. Contact us for a virtual demo and be the first one to look behind the curtain.
About the author
Ashesh Saraiya is a senior product manager for Tecan’s NGS library preparation solutions with more than 5 years of experience. He manages Tecan’s broad NGS library preparation reagent portfolio and guides the development of new and innovative NGS library preparation solutions. Ashesh has a Ph.D. in molecular biology from Wayne State University specializing in ribosomal RNA genetics. His postdoctoral work at UCSF examined miRNA and gene translation in protozoan parasites. Ashesh’s industry career began as a Field Application Scientist before moving to product management, where he continues to leverage his experience to help develop novel and innovative solutions to address the challenges associated with NGS sample preparation.