Automation can simplify some sequencing steps and make the process more robust. In preparing samples for next-generation sequencing (NGS), adding a robotic instrument makes sense for many labs—decreasing cost and increasing output, as well as improving reproducibility. How does a lab manager know when adding automation make sense?
“Nearly all reagent handling is amenable to automation—from isolation to library prep,” says Andrew Gane, product strategy and technology manager at GE Healthcare. “Automation is highly desirable in the majority of workflows for several reasons—throughput is an obvious one, but when dealing with large numbers of samples, manual processing is a real bottleneck and automation allows scientists to deploy their time on more demanding tasks.”
Charles Cowles—senior research scientist, protein and nucleic acid, Promega—adds, “The most common steps to automate include nucleic-acid extraction, quantification/quality control, library prep, library quantification, and normalization.”
The decision to add automation to NGS sample preparation, though, is not always easy.
Making a move to automation
The genomics core at Louisiana State University Health Shreveport “is a part of an academic research institution and most of our business comes from internal investigators,” says research specialist Camille Abshire. “We offer a variety of genomics services, but we do not have the level of NGS business that commercial sequencing companies have.” So, this core does not automate NGS sample preparation.
“The number of NGS samples we process a month varies, depending on how many investigators want to sequence and when their samples are ready,” Abshire says. “I typically process samples in batches by the investigators’ experiments, only one experiment set at a time.” One experiment from an investigator at LSU usually includes 12–40 samples for sequencing. Usually, Abshire processes 20 samples at a time, with 60 being the most that she’s ever processed at once.
When asked when she might consider making a change, she says, “If I was consistently processing 60 samples at a time, automation would be something our core would consider.”
Other experts agree that turning to automation depends on throughput, and more. “Decisions on when and how to automate are based on a number of parameters, such as cost, budget, resource availability, space, and timing, but it needs thought and planning to make it work for the user,” Gane says.
According to Henry Shu, product manager at Agilent Technologies, “Customers seek out automation for a variety of reasons.” As an example, he says that “some labs with large sample throughput are looking to save time and make their workflows more efficient.” In research labs, “reproducibility, consistency, and walk-away time are considered very valuable,” Shu says. “These labs will also probably be interested in an open and flexible platform that can handle a variety of reagents and protocols.”
Image: The Bravo NGS Workstation comes preconfigured for library prep and enrichment when using next-generation sequencing protocols. Image courtesy of Agilent.
Automation, though, isn’t only for big labs sequencing many samples. As Cowles says, “For laboratories working in a lower throughput range, automating key routine steps, such as sample extraction, can go a long way in preventing upfront bottlenecks and ensuring consistency and quality of input DNA.”
Pick a platform
Scientists can consider automating various sample-prep steps in NGS, such as the reagent handling. “Magnetic bead-based approaches are great in this respect,” Gane says. “For example, nucleic-acid purification is easily automated on many platforms, and the output can feed into the library-prep process. Library preparation is also largely automatable with magnetic bead-based approaches for size selection and PCR clean-up, as well as library enrichment, using our Sera-Mag Select and Sera-Mag Streptavidin beads, for example.”
Among these reagents, Gane notes the key options for users. “We have the Sera-Mag and SeraSil-Mag magnetic beads for NGS kit developers as well as end user–ready solutions such as Sera-Mag Select for PCR clean-up and/or size selection in NGS and Sera-Xtracta for gDNA and cell-free DNA isolation.”
In considering steps for NGS sample preparation that can be performed on a complete platform, Shu points out a few options. Customers often use “the Agilent Bravo NGS Platform and Bravo NGS Workstation for the library prep and enrichment parts of the NGS workflow,” he says. “Some customers also use these instruments for nucleotide extractions.” He adds, “Specific steps that are commonly automated include PCR setup, hybridizations, ligations, normalizations, and sample clean ups.”
When asked about the most recent benefits from Agilent platforms, Shu says that an adapter on the Bravo NGS platform helps users “who are shearing their DNA using a different system—for example, a prep system from Covaris can directly place their plate on the Bravo deck to continue their workflow.”
Plus, this platform provides sample-number flexibility. “The Bravo can handle isolated wells, columns, and rows, and also a full plate of 96 wells,” Shu says. “This provides customers the ability to reliably scale the number of samples without dramatically increasing costs or having concerns about significant sample loss.”
Some vendors develop platforms and chemistries. As an example, Cowles discusses Promega’s Maxwell RSC for benchtop sample extraction. He adds, “We have been expanding the number of extraction chemistries for the Maxwell RSC 48 and MaxPrep mid-throughput liquid handler.” In addition, Cowles says, “We recently have developed several products under the ProNex brand that exclusively address critical NGS sample prep steps, all of which may be automated, such as using the ProNex Size-Selective Purification System for NGS library clean up and size selection.”
Image: Scientists can automate sample-preparation steps for next-generation sequencing with various platforms, including the Maxwell RSC 48. Image courtesy of Promega.
Thinking about the time
Time—both in hours and years—can play a part in the decision to automate NGS sample preparation or to keep it manual. In some cases, it might seem too complicated to make the switch to automation, but Cowles says, “Field technicians really make automation possible for those who find it too daunting to go it alone.” Some of the decision also depends on who is doing the sample preparation. As Abshire says, “I’m fairly young and do not have issues multi-channel pipetting my day away.” Nonetheless, if the throughput did increase, she says that “the bead clean-up part in our protocols is time sensitive, and it would be hard to do this in a timely fashion, as it involves a lot of pipetting and resuspension.”
Abshire’s experience shows the sort of considerations that a scientist must make with NGS. In some labs, the throughput can force the need to automate the sample preparation, but at lower levels of samples, a scientist might find the decision more complicated and probably dependent on the most common workflows and their complexity. In cases when automation makes sense, there’s no doubt that it increases the speed of preparing samples for NGS. The automation also makes the steps easy and more accurate. It’s all a matter of time—and money—in picking the best option in a particular lab.