Veterinary college lab leads exploration of DNA sequencing advances
August 29, 2023
The ability to examine up to 2 million DNA bases instead of just a few hundred in a single read and get results in under two weeks instead of months with a device costing about $1,000 instead of 100 times as much would certainly seem like a win-win-win proposition.
The Virginia Tech Animal Laboratory Services (ViTALS) within the Virginia-Maryland College of Veterinary Medicine has secured a $200,000 grant from the National Animal Health Laboratory Network (NAHLN) to develop further expertise internally on nanopore-based genome sequencing for pathogen detection and disseminate that acquired knowledge to other laboratories.
Nanopore technology leader
“At the veterinary college, we have been working the last seven or eight years to develop expertise in deep sequencing, especially with this nanopore technology,” said Kevin Lahmers, clinical professor in anatomic pathology at the veterinary college and head of research and development at ViTALS. “And we are recognized as one of the leaders in that area in veterinary diagnostics.”
Nanopore sequencing is a technology in which DNA is fed through microscopic holes along with electrical current. Computer algorithms detect changes in the electric current which can be interpreted as one of the four bases in DNA, establishing the sequence.
More cost effective, efficient
Most DNA sequencing now is by synthesis, Lahmers said, a more complex process in which nucleotides are matched up with a single strand of the double-helix DNA, and those nucleotide additions are detected by color or changes in acidity or electrical charge.
Nanopore sequencing can be performed on equipment “the size of a stapler, costing $1,000,” Lahmers said, whereas synthesis requires larger equipment costing around $100,000. Only about 350 bases at a time can be detected by synthesis, often taking several weeks to complete the analysis, whereas “if you can be gentle enough with the DNA” up to 2 million DNA bases can be read by nanopore sequencing, results ready in 1 to 2 weeks.
While much of the grant focuses on training for more individuals within the veterinary college and further study of how nanopore sequencing works with known pathogens, another purpose is to spread the knowledge that is obtained to other laboratories, including a cloud-based workspace to share information on bioinformatics and sequencing processes.
The end goal is to increase the pool of individuals and laboratories capable of using nanopore sequencing technology to identify emerging pathogens and connect DNA sequences found in lesions to those pathogens through a process called in-situ hybridization.
“What we are proposing is to share what we've learned and what we've developed with the veterinary community, potentially having people come to Virginia Tech to train, so that we have more people with that expertise,” Lahmers said. “It's great to be a leader. But if it's just one group doing this, then that's not really efficient. Part of this is to disseminate knowledge, so that more labs are capable of doing this.”