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Alleviating the Burden of NGS Library Preparation

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Next-generation sequencing (NGS) has undoubtedly revolutionized the genomics field and thanks to technological advances in recent years, laboratories around the globe are now applying NGS to a wide variety of applications. However, library sample preparation remains a key bottleneck and researchers are now looking to adopt automation solutions to alleviate this pain point, streamlining genomics workflows.

Technology Networks recently spoke with Paul Lomax, product manager at SPT Labtech to hear about the fields benefitting from NGS and learn more about firefly®, the company’s new liquid handling platform for NGS library preparation.

Laura Lansdowne (LL): NGS has become an integral technology for many research fields, can you highlight some of the areas benefitting most from this approach?

Paul Lomax (PL): NGS is a technique that has spread rapidly across many different areas of research, such as genetic testing, personalized medicine, crop science, and so on. Perhaps the first area that springs to mind is the use of NGS in the surveillance of infectious diseases. That's obviously become a critical tool worldwide for identifying and surveying SARS-CoV-2 variants. As we all know, there's been an explosion in the number of test samples that labs have been processing since the start of the pandemic. But the demand is huge and growing in other areas too.

Personalized therapeutics, for example, are now a reality, especially within oncology. Genomic profiling is supported here by NGS, where genomic testing of new medicines is carried out to identify whether they're suitable for a specific patient. There are also many new research efforts coming to fruition right now, such as biomarker-driven clinical development, which is becoming increasingly mainstream. Sequencing plays a vital role in the diagnosis of rare and suspected genetic conditions.

Looking ahead, the growth in multiomics research for drug discovery looks very promising, with researchers going beyond the genome to capture data on the transcriptome, proteome and metabolome. It's exciting, and the rate of new breakthroughs is increasing. Sequencing is getting faster all the time. Labs can now sequence a human genome in a single day. And the process is getting cheaper too: if it isn't here already, we'll soon hit that $100 genome milestone.

LL: SPT Labtech has produced an industry report “Shaping a new era of genomics liquid handling” that discusses the future of genomics liquid handling and provides insights from NGS customers about their library preparation experiences. Could you share some of the key points discussed in the report?

PL: Our report covers several recent liquid handling trends we've been seeing in genomics labs. Many are now using automation solutions to accelerate their NGS library prep. A key takeaway of the report is the dramatic increase in efficiency you get from automation. Automated NGS applications are driving massive improvements in terms of reliability, accuracy and throughput. Labs can now easily set up complex experiments using multi-well 96- and 384-well plates with multiple reagents. Thanks to intelligent and accessible automation, they can do so while reducing costs at the same time. The cost factor plays an important role in accelerating wider research output. A compact, all-in-one solution like our firefly gives labs cost-effective and accessible options to take their first steps into NGS automation or enhance their existing workflows. Multi-functional technologies with a more compact footprint than single-task instruments offer numerous benefits in the area.

In the report, we also set out why in the modern genomics lab, automation is quickly becoming accessible for all. You don't need external automation experts anymore – we're seeing a definite shift away from labs having to rely on instrument vendors when developing and running new protocols. And easy-to-use software is clearly key when it comes to empowering all lab staff. Because, ultimately, that's the goal: labs want to make the best use of their highly skilled people, making sure their scientists can spend more time analyzing results and designing reliable experiments, with less of their valuable time spent on repetitive manual workflows or managing large, complex equipment that doesn't give them the versatility and agility they need.

LL: What would you consider to be the key challenges faced by researchers during NGS library preparation, and how does firefly help to alleviate some of these issues?

PL: There are many steps in NGS and PCR protocols, and so there's an enormous potential for streamlining your workflows, reducing reagent volumes, and limiting tip consumption. firefly combines highly accurate pipetting in the 0.5 µL to 125 µL volume range with non-contact dispensing. This means you can transfer samples, run bead clean-ups, and do your mixing with firefly's dispensing head while managing all your other protocol steps with firefly's dispense head. Along with this, you have integrated incubating and shaking technologies and a plate gripper to move labware between firefly's decks and heater/cooler plate.

Genomics workflows require reliable and accurate pipetting and dispensing of challenging liquids such as enzymatic reagents and beads – often at very low volumes. Miniaturization is, therefore, a key challenge, especially if you're dispensing low-volume viscous reagents. In this regard, firefly is a real gamechanger by supporting 200 nL non-contact dispensing.

Credit: SPT Labtech. 

Going back to what I was saying before, powerful, user-friendly software is almost as important as the liquid handling platform itself. If you consider the challenges faced by researchers today – with labs facing a real and immediate need to scale up – liquid handling software needs to be intuitive for researchers to use. You don't want to be battling complex programming steps. And so we're extremely proud and confident that firefly's software sets a new industry standard for the years to come. Protocols can be built remotely on a PC by lab users at all levels via simple drag and drop. The software has 'presumptive intelligence' in that it anticipates many standard and common assumptions. It's also fully application-ready with pre-validated protocols for library prep kits, such as NEBNext Ultra II and Illumina DNA Prep. Advanced users have the option to fine-tune with extended features. And the protocols are then easily accessible to everyone in the lab via the inbuilt tablet.

The other big challenge I touched on is the space constraints in modern genomics labs. firefly's compact, all-in-one design gives you a very small footprint, especially considering all the functionalities you're getting. Because of its integrated workflows, you don't need to take up additional bench space with single-task instruments. firefly frees up that space for you and gives lab leaders that ROI they're looking for – productivity and instrument uptime.

LL: Could you tell us more about firefly’s complementary first-in-class peer-to-peer cloud-based network and how this functionality is encouraging collaboration and innovation?

PL: Yes, absolutely. We're proud to be pioneering this new opportunity for online collaboration with firefly. There's no doubt that cloud-based collaboration is going to be a part of the future of genomics research. With firefly, researchers can share custom protocols and quickly validate steps via SPT Labtech's validation tools. Facilitating collaboration in this new way really goes to the heart of what scientific research has always been about – collaboration between researchers leading to bigger and faster breakthroughs. And so we're very much looking forward to seeing how cloud-based collaboration will shape genomics research in the future.

Paul Lomax was speaking with Laura Lansdowne, Managing Editor for Technology Networks.