In advanced gene sequencing, scientists are always searching for improvements. This can include better accuracy, higher throughput, as well as reduced cost. In many cases, automation delivers on all of those levels. Nonetheless, most labs lack access to automated methods, but that is changing.
As Will Canine, cofounder of Opentrons, explains, “90% of labs don’t have access to automation today.” Although steps in sequencing require scientists to move tiny amounts of liquid in very precise ways, most of that gets done by hand. “It’s a real problem,” Canine says. “Society and scientists would be better served by having researchers doing more thinking and less pipetting.”
According to Canine, “sequencing costs have been going down orders of magnitude year after year, and we’re at the point where sequencing capacity is not the bottleneck—it’s doing the sample prep to get samples on a sequencer.”
Many scientists agree on the benefits of automating such processes. Scientists from Complete Genomics and BGI-Shenzhen, for instance, described a long-fragment read technology, which is a preprocessing step in genome-wide haplotyping with whole genome sequencing (WGS). The researchers noted: “This method can be employed either manually using hand-held micropipettors or in the preferred, automated manner,” which relies on liquid-handling robots. “Automating the method limits the amount of hands-on time and allows significant reduction in reaction volumes.”
To make it possible for more labs to benefit from sequencing, automation needs to be more easily and inexpensively available.
Don’t break the bank
To bring automated liquid handling to more scientists, Opentrons developed its pipetting robot. “It’s 10 times cheaper than the next cheapest lab robot,” Canine states. An Opentrons robot with a single-channel pipette costs just $4,000. Labs that need a multichannel pipette can get that system for $4,500. Despite being inexpensive, these robots perform many tasks. “It will do all of the library prep,” Canine adds.
Plus, scientists can customize this platform. A 4–95°C temperature block can be added to the deck of this robot to keep samples at a desired temperature. A magnetic module can also be added to engage and disengage bead-based samples.
This robot can be used in many ways, Canine says. “This can be used upstream of NGS to isolate the genomic data that you want to sequence from a cellular or tissue sample and for clean up during library preparation after amplification.”
Image: Zane Colaric, a research technician in Erez Aiden’s lab at the Baylor College of Medicine, works with the Opentrons OT2 robot. Image courtesy of the Aiden lab.
With all of these features and potential applications, how can Opentrons keep the price so low? “We’re using a different supply chain than typical lab automation,” Canine explains. “It’s only been available in the past five years, and it comes from the same motors and electronics used in a desktop 3D printer.” So, Canine and his colleagues repurposed the 3D printer supply chain for lab automation. Plus, Opentrons does the robot manufacturing in-house.
With all of this—low price and high performance—it might seem like something must be problematic with these platforms. For example, maybe it takes more skill to use them. Canine disagrees. When asked if it takes more user experience to run these robots, he says, “It takes significantly less.” Opentrons provides a library of protocols on a website. For the most popular NGS library-preparation kits, users can download the protocol to use with an Opentrons robot. Even more, Canine notes: “We leverage the community to share their protocols.” Plus, users can develop their own protocols, which Canine calls “pretty easy.”
Adapt the fit
Other vendors also focus on personalizing the automation platform to specific lab needs. Hamilton Robotics, for example, offers three automation platforms. These were created to tailor-fit any sample throughput and workflow needs, especially in upstream sequencing preparation steps,” says Sha Liao—senior market segment leader for genetic screening at Hamilton Robotics.
“Our open and flexible platform format and wide-reaching assay chemistry partnerships mean that customers can continue to use their preferred sequencing assay chemistry in a Hamilton solution without time-consuming method development.” Precision dispensing and liquid level sensing, especially at very low volumes, helps to effectively use or conserve precious and expensive reagents, according to Liao.
“Hamilton liquid-handing workstations feature dynamic Y-axis movement to allow direct loading of NGS reagent-containing tubes without risk of evaporation or unnecessary reagent transfer steps,” Liao adds. “This also allows easy cherry picking for pooling libraries.”
One of the newest tools from Hamilton is the Microlab VANTAGE liquid-handling system. This platform plus its INSTINCT V software “automatically transports labware without additional programming and also manages all consumable calculations, such as the number of tips and tip racks along with reagent and buffer volumes,” Liao explains. “Any inter-assay reloading is automatically planned and communicated to the operator in a dynamic visual Gantt chart.”
Image: Sequencing requires considerable liquid handling, which must be automated for accuracy and throughput. Image courtesy of Hamilton Robotics.
This automation platform from Hamilton Robotics and others aim at easy adaptation. “This includes accommodating a wide variety of different sample types, from formalin-fixed paraffin-embedded to liquid biopsies and many more,” Liao says. Keeping on the flexibility pathway, Hamilton collaborates with other companies to provide more ways to use its technology. We “routinely partner with leading chemistry providers to optimize automated workflows as their expertise in even the most subtle nuances of their chemistries can make a big difference in process,” Liao says. “This includes scripting or pre-programming steps and integrating third-party devices, such as thermal cyclers on the platform deck.” As an example, she notes that the Nextera Flex for Enrichment Kit from Illumina is specifically optimized for use on Hamilton Robotics’ automated platforms.
A zoo of opportunities
Erez Aiden, assistant professor of genetics at Baylor College of Medicine, “does a lot of 3D mapping of genomes, lots of straight-up DNA sequencing of samples.” To do that, Aiden and his colleagues use an Opentrons robot for automated liquid handling, including pipetting, incubation, washes, and size selections.
His lab also runs the DNA Zoo, which is an effort to sequence the genomes of many species. Currently, the team is assembling over 1,000 species and cultivars. Most important, Aiden and his colleagues want to do the sequencing and assembly in an open-source way. “We want it to be the case that if a high school student wants to sequence a pet dog, you should be able to do it,” he says.
So, the DNA Zoo team wants to build a robot that fully automates all of the experiments for sequencing and assembling a genome. As Olga Dudchenko, a postdoctoral student in Aiden’s lab and the primary lead of DNA Zoo, says, “We are excited about the opportunities that automation brings to the DNA Zoo effort!”
“We want to democratize sequencing,” Aiden says. “All of our software is open source and so are our experiments.” This could help bring automated sequencing to many more labs.