Next-generation sequencing (NGS) has greatly changed biological study. Since 1964, when Robert Holley made the first-ever attempt to sequence a nucleic acid molecule (Alanine tRNA), the science of studying genome structure and function has come a long way.
NGS allows scientists to analyze genomes and transcriptomes with a high level of detail that was not possible before. Yet, the cost of NGS can be a big problem, especially for smaller labs or those having a limited budget.
One major cause of higher costs in NGS is preparing a library, which means transforming DNA or RNA samples into libraries suitable for sequencing on an NGS platform. Thankfully, some strategies can lessen the cost of NGS library preparation while sustaining data quality.
Optimizing NGS Library Preparation Workflows
Library preparation for NGS often includes different stages, such as cleaning samples, breaking them into fragments, attaching adapters, and choosing size and amplification. The right approach to NGS library preparation demonstrates proficiency in a broad range of sequencing methodologies, enabling it to support the creation of highly reliable and economical automated pipelines for NGS.
Here are some ways to make NGS workflows of library preparation more efficient in terms of cost:
Think About Different Library Preparation Kits
Some companies make general library preparation kits that are usually less costly than those from big sequencing instrument makers. You might need to spend a bit more time doing things with these types of packages, but they can give similar results.
Assess In-House Library Preparation
When a lab has high requirements for NGS library preparation, this method can be cost-efficient. It demands knowledge about molecular biology skills but provides more control over reaction conditions and customization. Still, validating and optimizing properly for data quality and reproducibility is important.
Minimizing Sample and Reagent Usage
The cost of NGS library preparation is affected by the amount of starting material and reagents used. You can lessen this expense through tried-and-true methods, like improving DNA/RNA extraction protocols. Good extraction protocols ensure that many high-quality nucleic acids are removed from starting samples. This allows for using less starting material in library preparation, which can reduce the costs related to both DNA/RNA isolation kits and library preparation reagents.
Also, the shrinkage of library preparation reactions should be considered. A few library preparation kits that you can buy now provide choices for smaller reaction volumes. This method is beneficial when dealing with valuable or small-quantity samples. By lessening the reaction volume, scientists can decrease their use of reagents and the linked expenses.
Try multiplexing libraries, i.e. combining several libraries onto one sequencing lane or flow cell. This approach has a big impact on reducing the cost per sample by using sequencing resources to their maximum capacity. However, proper library normalization and optimization are needed for multiplexing to work well so that every sample gets correctly represented in the final sequencing data.
Automation and Streamlining Workflows
Some labs choose to outsource NGS library preparation to specialized service providers. These providers offer expertise in optimizing protocols, handling diverse sample types, and ensuring high-quality library construction. This outsourcing allows biotech labs to focus their resources on core competencies like data analysis and interpretation while still benefiting from the power of NGS technology.
Automating the NGS library preparation process can bolster efficiency and decrease costs related to labor and mistakes. Here are a few methods to simplify the workflow:
Automated Liquid-Handling Robots
These can help with numerous pipetting tasks in library preparation, boosting capacity and lessening the chance of human mistakes. Though the first expense for automation could be big, savings during future periods especially for labs with large volumes might be significant.
Cleanup Methods Using Magnetic Beads
Magnetic bead-based protocols used for cleaning libraries show clear benefits in terms of quickness and convenience. They are faster and simpler to handle, decreasing the time spent on it and making processes more efficient, which helps in lowering costs.
Choosing the Right Sequencing Strategy
The decision about how to sequence also affects the total price of NGS analysis. For instance, consider sequencing depth. The sequencing depth we want, which is how many reads are made for each sample, will directly impact the cost. Fewer sequencing depths could work for tasks that only need low to medium coverage, like focused resequencing or studying gene expression levels (gene expression profiling).
Keep the read length in mid; longer read lengths give more complete data but cost more per sample. In cases where shorter reads can still answer the research question adequately, selecting shorter read lengths could be an economical choice.
NGS Library Preparation: Cost-Effective Approach for Researchers
While the power of NGS is undeniable, its cost can be a barrier for many research projects. However, by adopting a multi-pronged approach, researchers can significantly reduce library preparation expenses without compromising data integrity. This involves careful upfront planning, streamlining workflows to minimize errors and hands-on time, and making strategic choices regarding reagents and sequencing strategies.
By leveraging a combination of cost-effective methods like generic library prep kits, in-house protocols when feasible, and minimizing sample and reagent usage, researchers can stretch their budgets further. Employing automation tools and magnetic bead purification can enhance efficiency and reduce costs. Ultimately, this thoughtful approach allows researchers to maximize the scientific output of their NGS studies, even within budgetary limitations.
