Genomics Workshop Sparks Students’ Interest in Research
| This spring break about 40 students from across Arkansas passed on the beach and instead advanced their scientific knowledge. Those attending the free workshop at UAMS gained experience with third-generation sequencing, which helps scientists understand the type of genetic information carried in DNA.
Tristan Eoff of Little Rock, a high school student at Arkansas School for Mathematics, Sciences and the Arts in Hot Springs, was one of 38 enrolled in the March 18-20 workshop of lectures and hands-on computer work presented by UAMS and the University of Arkansas at Little Rock (UA Little Rock).
“I’m interested in pursuing a degree in research, especially biomedical,” Eoff, 16, said. “I learned a lot about the sequencing technology and using the software from this experience.”
David Ussery, Ph.D., director of the Arkansas Center for Genomic Epidemiology and Medicine at UAMS and professor in the UAMS College of Medicine Department of Biomedical Informatics, recruited other lecturers and helped develop much of the curriculum. Ussery also lectured during the workshop, now in its third year. Elizabeth Pierce, associate professor and chair of the Department of Information Science at UA Little Rock, initiated the workshop and organized it along with Ussery.
“We’re giving the students experience with analyzing large volumes of data, known as big data, and getting them interested in the science and technology of it,” Ussery said. “We’re trying to deepen their interest in genomics.” Genomics is the study of all the genetic material of an organism.
Ussery presented a lecture on biological information, including DNA, RNA, proteins and an introduction to bioinformatics, which uses computational methods to study biological information from DNA, RNA and proteins. Genome sequences can be used in clinical diagnostics as well as modeling complex biological systems.
Joanne Huh, 15, and a 9th-grader at Central High, was one of the 38 attendees of a recent workshop where students learned about biological information, including DNA, RNA, and proteins. The students also practiced analyzing the date sequenced, comparing their sequences to known genomes in a huge DNA database.
Students were divided into groups of about 10 and given a demonstration of flow cells — small, ‘disposable’ third-generation DNA sequencing machines. They were given unidentified DNA samples they loaded onto flow cells using devices plugged into laptops.
Students practiced analyzing the data sequenced, comparing their sequences to known genomes in a huge DNA database. Their samples of unknown DNA from safe bacteria were grown in the lab but included some surprises.
“We gave the students an ‘unknown’ that contained purified DNA extracted from elephant feces that has bacterial DNA from many different organisms in it,” Ussery said. “So all of a sudden, there isn’t just one correct answer but instead a mixture.”
To keep the class on their toes, the organizers also threw in some unknown yeast and viruses.
“It’s been really cool to see what all you can do with all this information and being exposed to it,” said Matthew Thompson, 21, of Jackson, Mississippi, a junior at Harding University in Searcy. “It’s been awesome to see the technology and use real data to make graphs. It has confirmed that this is something that I’m really interested in, not just something I think I am.”
Six faculty members were also enrolled in the workshop, including Thompson’s biology professor, Rebekah Rampey, Ph.D.
“Dr. Ussery had emailed me about collaborating on this because of my background in genetics,” said Rampey, chair, Department of Biology at Harding. “But my focus is more classic genetics and very much one-gene focused, and this workshop has allowed me to think more about genomics in larger scale sequencing. I’ve really enjoyed this experience.”
Don Catanzaro, Ph.D., a research assistant professor in the Department of Biological Sciences at the University of Arkansas in Fayetteville, also attended the workshop.
“There’s a high school student here which is fantastic,” he said. “I didn’t have opportunities like that when I was a kid.”
Catanzaro who, studies tuberculosis, says he works closely with genomics.
“But I’m the interface between the physician, microbiologist and genetic people so I have to learn what they’re doing so I can talk to all sides.”
The workshop was supported by the Arkansas IDeA Networks of Biomedical Research Excellence (INBRE). Arkansas INBRE is led by Lawrence Cornett, Ph.D., UAMS associate vice chancellor for research. Bioinformatics uses computational methods for the study of biological information that flows from the decoding and analysis of DNA, RNA and proteins.
“Information science focuses on the processes for collecting, storing and working with information, especially scientific or technical,” Pierce said, “Bioinformatics is a great partner discipline for us because it specializes in working with complex biological data such as genetic codes that has applications for areas ranging from waste management and agriculture to insect, animal and food studies as well as biomedical applications, which are especially useful for medical students.”
“Each year, new resources and advanced technology enhance this workshop,” Ussery said. “The disposable flow cells we used this year cost $500 each. The newest version of them just released are $100 and we can put 10 samples on them so it’s just $10 a sample. With these portable sequencers, we can get the first read within 15 minutes.”
In the workshop, the students ran the sequencers for about 15 to 20 minutes, then stopped them to analyze the data. All four groups correctly identified their samples, just from a short time sequencing.
“In the past, a lot of time was spent getting the computational software installed on the student’s computers, but now students work on Jupyter notebooks that they can log in to from the internet. Using the new tools, the students can do a full comparison of their set of genomes in about one hour, instead of the 16 hours (four hours a day over four days) it used to take in previous workshops.”
“Back in 1995, it cost a million dollars and took 100 people more than a year to complete what we can now do in one afternoon with one high school student using a disposable sequencer,” Ussery said.