Introducing PromethION24: the newest machine to join the Genomics Sequencing Center
November 9, 2020
According to Greek mythology, a titan named Prometheus once stole fire from the gods and gave it to humanity, thus granting them the gift of civilization. Because of his heroic deeds, Prometheus is often referred to as the Titan god of fire and the author of the human arts and sciences.
Fast forward to today, and you will find that the titan is the namesake for the Genomics Sequencing Center’s newest genomics sequencing machine from Oxford Nanopore Technologies: the PromethION24.
Song Li, an associate professor in the School of Plant and Environmental Sciences, and Rich Helm, an associate professor of Biochemistry and the director of the Fralin Life Sciences Institute’s Genomics Sequencing Center, have received funding for the novel machine through a competitive grant process, which will allow researchers to couple the technologies of today with agricultural science and create a unique link from the farm to the lab bench.
“If there is a pathogen that starts to spread into Virginia, we will be able to monitor that and be able to quickly determine its spread, permitting the design of strategies to eradicate it, just by having this tool available,” says Song Li, the principal investigator of this effort and an affiliated member of the Fralin Life Sciences Institute.
Oxford Nanopore Technologies is world-renowned for creating innovative technologies that are able to “read” short or long sequences of DNA from an organism's genome, a process called genomic sequencing. The data that is generated from the reads can be used for pathogen identification, detection, and more.
The new genomics sequencing machine will be housed within the Genomics Sequencing Center in Steger Hall and will provide genomic data for 18 research groups with diverse research interests including, but not limited to, plant microbiology, plant disease detection, plant genomics, animal genomics, water quality, and food safety.
The machine was acquired through the Equipment Grant Program of the United States Department of Agriculture’s (USDA’s) National Institute of Food and Agriculture. The USDA’s equipment grant program seeks to strengthen the quality, and expand the scope, of fundamental and applied research at eligible institutions by giving them the opportunity to obtain one major piece of equipment that supports their research, training, and extension goals.
Their proposal, titled “Acquisition of long read, high-throughput sequencing device for food and agriculture research at Virginia Tech,” was one of 17 that survived a national competition where only ten percent of the submitted proposals were funded.
“If you think about it, the acquisition of new pieces of equipment is a grassroots effort. In this case there was a group of over 15 investigators that identified a common instrumentation need, but did not have the time or resources to manage it properly, let alone train others to use it,” said Rich Helm, who is also an affiliated member of the Fralin Life Sciences Institute.
“Song Li and I worked out a usage plan, and then all the investigators contributed to the writing of the proposal. This effort ended up demonstrating not only the need for the equipment but also the breadth of Virginia Tech’s research portfolio.”
The remarkably small and powerful machine is a high throughput, long read sequencing machine that operates using flow cells, which are like microscope slides that are composed of fluidic channels. Each flow cell can sequence up to 220 billion nucleic acids, which is equivalent to sequencing a human genome 30 times over.
“The workflow has always been that we would prepare our samples, send it to the facility, and after two or three weeks we would get something back. For this type of machine, you can put samples in and the readings can be seen on your screen in real time. And you can see the readings from any computer. Providing real-time sequencing results is essential for both rapid response situations as well as for teaching students the power of genomics,” said Li.
Not only does PromethION24 produce fast results in real time, it also maximizes the efficiency of running samples. The machine has the ability to stop sequencing when the data reaches a certain goal or threshold, allowing more time for other samples to step off the sidelines and be processed. “It fundamentally changes the workflow of how sequencing is done,” added Li.
The Genomics Sequencing Center will serve as a centralized facility for the machine, providing research faculty the ability to conduct large scale experiments, while giving them the comfort that they will have one less machine to maintain in their already crowded laboratories. Instead, the experts at the Genomics Sequencing Center will maintain the equipment and, perhaps most importantly, keep costs low.
“We are setting up a proposal process where investigators on campus can submit a proposal and have access to the flow cells we have on hand at no charge. If they have the funds for their own flow cells and reagents, with proper training, researchers can have access to the instrument at no cost,” said Helm.
This acquisition comes at an opportune time as the Fralin Life Sciences Institute is developing a robust increase in core services support, investment in other state-of-the- art equipment to support a staff that can deliver excellent customer service.
“Due to the expansion of Core Services in Steger Hall, we are currently hiring a core facilities manager to oversee the Core Service operations within the Institute,” said Matt Hulver, executive director of the Fralin Life Sciences Institute. "The person will ensure efficient and effective operations of the core services and regularly interface with faculty and students so we can evaluate and meet the changing needs of the Virginia Tech research community.”
Li and Helm have proposed to use the new technology within the Virginia Tech College of Agriculture and Life Sciences’ SmartFarm innovation network, a decentralized network of interconnected research centers across the commonwealth of Virginia. With samples that have been collected across the entirety of the network, they will be able to generate a map of how pathogens are distributed across the state.
Part of this proposal also involves Virginia Tech’s Advanced Research and Computing (ARC). With the help of Bob Settlage, a computational scientist, a pipeline will be set up so that newly generated data goes straight to the ARC, where it can be processed and closely monitored from sample prep to data output.
Of the 10 surrounding universities in Tennessee, North Carolina, and Maryland, Virginia Tech will be the only one with access to a PromethION24. In the long run, Li and Helm will be able to offer this instrumentation to institutions beyond Virginia Tech, further developing regional collaborations.
Written by Kendall Daniels