In this interview, Dr. Dagmara Lewandowska, Product Manager for NGS at INTEGRA Biosciences, talks to NewsMedical about innovations in magnetic bead-based extraction and genomics automation.
Please introduce MAGFLO™ NGS magnetic beads.
INTEGRA is built on decades of liquid-handling expertise, combining MAGFLO NGS magnetic beads for size selection in NGS library prep with protocols that can be performed on the MAG module.
MAGFLO NGS beads incorporate three key features that set them apart from alternatives. Firstly, the beads remain stable at room temperature for 12 months, whereas magnetic beads from other suppliers typically need to be kept in the fridge and equilibrated to room temperature before use to ensure consistent liquid handling parameters.
Since MAGFLO NGS beads are room temperature stable, labs can avoid equilibration delays and reduce variability in their bead-to-sample ratios. Our beads are also RNase free, so they can be used to handle RNA, and QC verified, meaning every batch is qualified for use in size-selection protocols before it's released for sale. MAGFLO NGS beads are therefore a cost-effective, 3-in-1 magnetic bead solution.
Explain how MAGFLO NGS beads integrate with liquid handling solutions in a genomics workflow.
MAGFLO NGS beads were designed to pair seamlessly with INTEGRA’s range of pipetting instruments, which can be configured based on specific workflow requirements. They are also compatible with our MAG and HEATMAG modules for fast bead collection with minimal loss and bead carryover.
Unlike traditional ring magnets, which create a ring pellet around the well that requires precise pipette handling and upright tip alignment to avoid disturbing the beads, the MAG modules conveniently collect the pellet in one corner of the well by vertically moving the magnetic rods. This enables easier, more reliable pipetting without bead loss, leading to more reproducible results.
The HEATMAG module goes one step further by combining this innovative magnetic separation with heating capabilities, providing the perfect set-up for heated lysis during nucleic acid extraction, or for optimizing elution conditions to increase yields.
These modules can be used as standalone units for manual processing, or combined with a variety of INTEGRA pipetting platforms for semi- or fully automated workflows. For example, pairing a MAG or HEATMAG with a MINI 96, VIAFLO 96, or VIAFLO 384 pipetting platform will enable users to simultaneously process entire 96 or 384 well plates – or 24 tubes at a time – significantly boosting lab productivity.
When used in combination with the ASSIST PLUS pipetting robot and a VIAFLO or VOYAGER multichannel electronic pipette, the MAG modules provide fully walk-away magnetic bead-based purification without the need for costly grippers and robotic arms. The D-ONE single channel pipetting module can also be mounted onto the ASSIST PLUS for normalization and pooling after library prep.
From the outset, INTEGRA developed MAGFLO NGS beads to offer customers a tested and calibrated end-to-end package of instrumentation and reagents for NGS, ready to use, all from one trusted supplier.
What are the main workflow challenges that MAGFLO NGS beads and MAG modules are designed to address in NGS library prep?
Firstly, reproducibility. Automating sample transfer, for instance, on the ASSIST PLUS with a MAG module, improves liquid handling consistency compared with manual methods, leading to more reproducible results. Parameters such as incubation times and magnet height can be quickly programmed using our VIALAB software to ensure liquid is handled in exactly the same way each time.
As I mentioned before, another major challenge our beads address is the need to equilibrate refrigerated beads to room temperature before use to maintain consistent pipetting parameters and bead-to-sample ratios. MAGFLO NGS beads are stable at room temperature, so they do not need to be refrigerated and equilibrated, saving cold chain storage space and preparation time.
Another benefit of our magnetic bead solutions is that the MAG module magnets move up and down, while the plate itself stays in place. This means the modules have a compact footprint, saving valuable deck space and making the modules easier to handle and integrate with other platforms.
What applications can magnetic beads be used in? How does using integrated liquid handling solutions help to scale NGS workflows?
Magnetic beads are typically used for NGS library prep, PCR clean-up, and genomic DNA extraction. Labs commonly adopt magnetic beads to scale up their throughput, improve result reproducibility, and gain more walk-away time. Some groups would also like to move away from traditional spin column extraction and introduce more automation, bypassing the centrifugation step and avoiding tedious manual processes. To support these workflows, we launched the Clean Blood and Tissue DNA Kit (CleanNA) specifically to cover an extraction step, which can be automated on an INTEGRA benchtop device equipped with a MAG module for walk-away extractions.
Describe a typical NGS workflow from start to finish and explain how different liquid handling products can be used in each step.
INTEGRA’s solutions support every stage of low to medium throughput NGS workflows. Following sample collection, the first step is extraction and isolation, including aliquoting/re-formatting and nucleic acid extraction, which can be performed using the ASSIST PLUS, VOYAGER, and HEATMAG module.
Next comes library preparation, including fragmentation, size selection/clean-up, and NGS library generation. The SWITCH hybrid pipette can be used for fragmentation, and the ASSIST PLUS and VOYAGER pipettes can also be used with the MAG module for the remainder of the tasks involved in stage 2. The MIRO CANVAS can be used for assay miniaturization.
Finally, there is sequencing ready, from quantification and normalization to pooling. The ASSIST PLUS can be mounted with the VOYAGER for quantification, and with the D-ONE single channel pipetting module for normalization and pooling. After this, the sample should be ready for sequencing.
How INTEGRA liquid handling solutions can support each step of the NGS workflow. Image Credit: INTEGRA Biosciences
What feedback have customers provided regarding the MAGFLO NGS beads so far?
The feedback we’ve received has been very positive. Customers are pleased with the high quality of our beads and find them to be comparable to the current industry gold standard. They also note that the beads yield highly reproducible sequencing results and appreciate the ability to quickly prepare samples in an automated, hands-free manner.
A third-party lab has performed beta testing on the MAGFLO NGS beads, using them for size selection and library clean-up. Liquid handling was carried out using an ASSIST PLUS paired with a 12 channel VIAFLO electronic pipette, and the workflow's magnetic separation steps were performed twice: once using a standard magnetic plate and once using a MAG module.
The lab found this set-up to be extremely versatile, as it could be applied across numerous labware formats and adapted to specific protocols without extensive programming skills, thanks to intuitive user interfaces and pipette automation software. It was much easier for the team to adjust and optimize the workflow than the more complex programming often required for full workflow automation, providing full control while enhancing time efficiency. The lab also discovered that automating certain time-consuming components of NGS library preparation accelerated repetitive liquid handling tasks, giving staff more walk-away time and improving sample-processing capacity.
Crucially, the combination of MAGFLO NGS magnetic beads with the MAG module achieved the tightest size selection and the least size variation of all the options trialed in this beta test. In addition, the fragments produced were, on average, closest to the target size of 750 bp across all tested set-ups. The workflow also produced the highest library concentration and the least variation in concentration of all trialed combinations, demonstrating its reproducibility. Sequencing results showed that the set-up also produced more reads and less variation between read values than the lab’s existing method, and results were more reproducible and less variable than manual NGS library preparation and size selection.
Looking ahead, how do you see solutions such as MAGFLO NGS beads and liquid handling automation shaping the future of genomics workflow design?
INTEGRA always endeavors to innovate and develop high-quality alternatives to existing solutions, providing added value to customers. Our magnetic bead kits meet this brief, as they are compatible with and verified for use with our liquid-handling instruments, enabling convenient and accurate magnetic bead extraction workflows. We are excited to establish ourselves further in the growing NGS market and continue meeting the needs of our customers in the genomics space through further innovations.
We took a major step in this regard by acquiring Miroculus, the developer of MIRO CANVAS, a microfluidics-based, fully walk-away library prep instrument, in 2022. To further support high molecular weight (HMW) sequencing workflows, we launched an innovative in-tip DNA shearing application using the SWITCH hybrid pipette. The SWITCH combines manual pipetting with electronic repeat dispensing in a single device, and now also includes reproducible HMW DNA shearing capabilities, so users do not need an additional dedicated platform. We plan to build on this foundation by continually investing in other solutions and reagents for the diverse sequencing technologies and genomics workflows that are constantly emerging.
Where can readers find more information?
To learn more about MAGFLO NGS magnetic beads, please visit: www.integra-biosciences.com/en/ngspcr-purification/magflotm-ngs
Read about the SWITCH hybrid pipette here: www.integra-biosciences.com/en/switch-hybrid-pipette-now-hmw-dna-shearing
To find out how INTEGRA’s solutions support NGS workflows, please visit: www.integra-biosciences.com/en/application-type/next-generation-sequencing-ngs
About INTEGRA
INTEGRA Biosciences (www.integra-biosciences.com) is a leading provider of high quality laboratory tools and consumables for liquid handling. The company is committed to creating innovative solutions that meet the needs of its customers in research, diagnostics, and quality control across the life sciences and medical sectors. INTEGRA's portfolio also encompasses next generation sequencing (NGS) solutions, with automated workflows and magnetic bead-based reagents for reliable NGS sample preparation. INTEGRA's engineering and production teams in Zizers, Switzerland, and Hudson, NH, USA, strive to develop and manufacture instruments and consumables of outstanding quality. Today, INTEGRA's innovative laboratory products are widely used all around the world, where they help scientists accelerate scientific discovery. INTEGRA is an ISO 9001-certified company.
About Dr. Dagmara Lewandowska
Dagmara obtained her PhD in viral metagenomics from the Institute of Medical Virology at the University of Zurich and has gathered experience with NGS sequencing and lab automation during her career. She joined INTEGRA in 2022 and is now the Product Manager for the company’s NGS portfolio. In this role, Dagmara is responsible for launching new reagents and products for NGS applications, such as the MAGFLO NGS beads.
About INTEGRA Biosciences
INTEGRA provides innovative solutions for liquid handling and media preparation applications that serve the needs of its customers in research, diagnostics, and quality control laboratories.
The company's instruments and plastic consumables are developed and manufactured in Zizers, Switzerland, and Hudson, NH, USA. To remain close to its customers, INTEGRA maintains a direct sales and support organization in several North American, European, and Asian countries, as well as a network of over 100 highly trained distribution partners worldwide.
In recent years, INTEGRA has focused on developing a new and technologically advanced range of lab devices that are simple to use and meet the ergonomic needs of its customers.
Today, INTEGRA is proud to offer the widest range of electronic pipettes on the market, covering everything from single channel pipettes to 384 channel benchtop instruments.
INTEGRA's PIPETBOY GENIUS provides superior ergonomics and liquid control for cell culture