Accelerate breeding programmes with high-speed, high-throughput NGS workflows
Designing molecular breeding programmes to screen for desirable traits in plants and livestock can accelerate breeding cycles and enable precise genotype selection. But processing thousands of samples — with potentially complex genomes or difficult sample types — to deliver results within critical breeding windows is a major challenge, while the cost per sample can be prohibitive.
However, new targeted genotyping by sequencing (GBS) solutions are bringing together the benefits of next-generation sequencing (NGS) technology with high-throughput workflows and time frames comparable to end-point genotyping.
In our latest webinar, Toby Sangel from Dynamic Devices discusses how LGC Biosearch Technologies and Dynamic Devices’ partnership of advanced tools for DNA purification and genotyping can help labs, breeders and researchers seeking a flexible, scalable and automated solution to high-speed, high-accuracy genotyping.
Improving the transfer of difficult lysates
Transferring lysates prior to DNA extraction is one of the first critical steps of the genotyping process. This can be challenging for some sample types and pipetting errors can lead to sample testing failures. The Lynx robotic liquid handling platform uses volume verified pipetting (VVP) to increase the accuracy of lysis transfer and reduce the sample failure rate. Sangel explains: “We provide the volumetric data for every single transfer, for every single channel. In addition to having the independent volumes that we can set for each channel, every single channel can report whether it has a clog, clot, empty well, or it's just pipetting air.”
In Sangel’s experience with challenging sample types, root tissue, for example, on other liquid handling systems had a 30 to 40% failure rate when the samples were transferred, due to a lot of particulates leading to clogs. He describes how he implemented the same workflows with the VVP on the Lynx, finding that “the first pass/failure rate dropped from 30 to 40% down to 3% and we didn't have to have a manual inspection or camera inspection, because the data was presented to us.”
Exchanging tools on the fly for superfast, automated DNA purification
The Lynx operates as a set up and walk away platform, thanks to its multi core processing arm (MCPA), which exchanges different tools without interruption. As Sangel explains, “what really makes us unique is, not only can we do this on the fly, we can also incorporate things that are not traditional, such as magnetic rods and a whole suite of other tools.” And because the systems are modular, they can expand as you use them. “So you can start with one tool, and then maybe your workflow changes, where you add various parts to that workflow, or want to automate more of it. So you can add those tools,” he continues, also highlighting the popularity of seed crushing tools, as one example.
The MCPA also helps to increase throughput by enabling multiple stages of the workflow to take place side by side, simultaneously. For example, while the magnetic rods are performing the DNA isolation steps, moving the magnetic beads through the buffers, a dual pipette arm can be preparing the next batch to test. It can add the beads and buffers to the plates and transfer the next set of lysates, ready for DNA isolation.
From lysate to eluate in 5 minutes
Current methods to isolate nucleic acids for sequencing typically involve either crude extraction or labour-intensive and time-consuming purification methods. Combining Biosearch Technologies’ sbeadex Lightning purification kit with the Lynx system now enables superfast, high-quality, high-yield DNA purification.
Using the sbeadex Lightning kit involves only 3 steps, and 5 minutes to complete from lysate to eluate, integrating seamlessly with automated platforms such as the Lynx. Sangel describes the method: “We can use the pipette tool features to add all your beads, binding buffers, wash buffers, and then elution as well. And then once that's done, put the core down, pick up the 96 rod head, and begin the actual process,” as shown in video 1. Sangel adds, “then you will be left with your ready to go purified DNA samples — the normal process takes about 5 minutes.”
Video 1. sbeadex reagents on the Lynx system; Source: Webinar
“It is a very simple protocol. In terms of the sbeadex Lightning – the kit is great because of its simplicity. But then the ability to mix and match the pipetting with magnetic rods in the same system, it really just allows that end to end walk away for the customer and user.”
-Toby Sangel, Sales and applications manager, Dynamic Devices
Simple, cost-effective, same-day sequencing
Bottlenecks and hands-on time in genotyping workflows can reduce throughput and slow down the time to result. Biosearch Technologies’ Amp-Seq technology uses a simple and easy to adopt workflow, with a low number of reaction components, helping to minimise errors and sequencing costs. With this method, thousands of samples are pooled, with up to 5,000 markers per sample.
The Lynx’s VVP platform helps to streamline this process, with rapid pooling and normalisation features for NGS. For Amp-Seq pooling, the Lynx uses a 384 plate and aspirates all 384 samples to pool into a single well of a 96 well plate, as shown in video 2. “But this is where the 96 VVP stands alone. This ability to do this non contact on the fly, dispense and pool all of these samples into a single well, is only something that the VVP is capable of doing,” Sangel enthuses.
Video 2. Amp-Seq pooling on the Lynx system; Source: Webinar
“With Amp-Seq we can do the bead cleanup using the magnetic rods. And so, again, it's a very simple process where we're just doing the binding and then transferring those beads into a downstream plate. It doesn't have to be super complicated, but the fact is that we are able to use multiple tools that can be combined to create a single walk away workflow,” he adds.
One-step targeted GBS launched
We’ve now simplified sequencing further, with Amp-Seq One – the first one-step targeted genotyping by sequencing solution that can analyse thousands of samples across thousands of markers.
Amp-Seq One’s high-speed, high-accuracy workflow can reduce your workflow time to just 120 minutes, enabling same day sequencing. By halving library prep time, it can transform your labs’ genotyping capability, resulting in a higher predictive breeding accuracy and an accelerated time to market for new traits.
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