Next-generation sequencing (NGS) is a staple technique in genomics research, and has enabled numerous discoveries that would not otherwise have been possible. High-throughput genetic sequencing can provide a complete overview of an entire genome in a fraction of the time of previous methods, often at a far lower cost. However, despite these benefits, NGS can incur several unexpected – and often significant – expenses at various stages of the workflow, and this additional financial investment can be a strain on lab budgets.

In this article, Arto Klug, Director of Field Applications at Beckman Coulter Life Sciences, discusses how the right combination of cleanup method, automation platform, reagents, and supplier can enable faster and more cost-effective NGS workflows tailored to the specific requirements of each lab.

The hidden costs of NGS library cleanup

RNA and DNA purification for NGS involves the targeted removal of impurities – for instance, enzymes, adapters, and primer dimers – that can create background noise and interfere with sequencing. Accurate and reliable results therefore depend on precise and effective sample preparation, making efficient cleanup of libraries with minimal loss of genetic material vital, especially where the input material is low.

Inadequate removal of these contaminants can lead to poor data and experiment reruns – if additional sample material is available – increasing the overall time and financial costs of NGS workflows. In addition, commercially available NGS nucleic acid extraction kits can be a large and ongoing drain on a lab’s allocated budget, especially when experiments have to be repeated several times due to sample contamination.

SPRI technology is an advanced method that selectively and reversibly binds nucleic acids to paramagnetic beads based on their type and size. The technique offers high-performance isolation, purification, bead cleanup, and size selection of nucleic acid samples. SPRI beads have a uniform bead size for highly reproducible results, show a high binding capacity – with a low rate of non-specific binding – and enable rapid purification, supporting a more efficient workflow and higher throughput.

We have developed a range of genomic reagents based on SPRI technology, offering efficient DNA and RNA extraction from a range of typical and more challenging sample types. SPRI bead-based cleanup can also be easily automated on liquid handlers, without the need for prior centrifugation or filtration, providing optimum performance, flexibility, and scalability.

Automated NGS library preparation

Creating libraries for NGS is a tedious process that can take several days to complete, hindering lab throughput and productivity. Pipetting each sample and reagent by hand can also lead to pipetting inconsistencies, ultimately negatively affecting end results and possibly leading to costly repeats.

NGS library preparation automation can help labs to reduce hands-on time for higher throughput, and avoid manual errors for more reliable and robust data. Automated sample preparation may also be used as a key part of an effective cost reduction strategy, as it can lower the need for experiment reruns and the corresponding high reagent consumption.

Unfortunately, many automation platforms require large dead volumes of expensive reagents than when performing library preparation by hand. In addition, processing partial plates usually results in a higher cost per sample than full plates, as the same dead volume is typically required for automation, regardless of the total batch size.

Our robust automated liquid handling platforms standardize the steps involved in NGS library preparation, helping to eliminate manual errors for more consistent results. They cater to a wide range of sample types, volumes, and batch sizes with minimized reagent usage, helping to reduce library preparation costs and providing more hands-free time for greater lab productivity.

The Biomek NGeniuS Next Generation Library Prep System provides flexible processing of four to 24 samples per run, with automated reagent aliquoting and plate handling – plus an on-deck thermocycler – to increase walk-away times for lab personnel and eliminate human errors. The system’s pre-programmed protocols streamline library preparation, with a straightforward reagent identification system to prevent loading errors.

We also offer Echo Acoustic Liquid Handlers that facilitate miniaturization of reaction volumes through nanoliter- and sub-microliter-scale non-contact liquid transfers, drastically reducing reagent consumption and the associated costs, especially for lower-throughput experiments. The contactless any-well to any-well nature of the Echo Acoustic Liquid Handler facilitates rapid equimolar pooling and normalization, all with a straightforward software interface.

Our experienced Application Scientists calculate exact dead volume requirements to provide an accurate cost to customers, and our portfolio of genomic reagent kits incorporate redundant material to factor in the additional dead volume needed for automation. These kits can therefore be used for both manual and automated workflows to help minimize reagent waste and avoid hidden costs further down the line.

Customizing NGS workflows

Tailoring the combination of cleanup methods, platforms, and reagents to each lab’s existing infrastructure and requirements plays a large part in reducing unexpected and unnecessary NGS costs. Partnering with a reliable and expert supplier that understands how to customize workflows to fit with existing laboratory practices is also a crucial aspect of developing a robust and future-proof cost reduction strategy for DNA and RNA sequencing.

We work together with our varied customers to determine the specific equipment, software and lab set-up they need to optimize their results and avoid unnecessary expenses. Contact us to find out how we can support you in designing an efficient and more affordable NGS workflow.