NIH grant helps teens perform genome sequencing

Stephen T. Koury, research associate professor of biotechnical and clinical laboratory sciences, has been awarded a $1.3 million grant that will allow high school students and teachers the opportunity to perform genome sequencing of bacteria.

“The Metagenomics Education Partnership: Harnessing the Power of Microbial Genome Sequencing and Big Data with High School Students and Teachers” is the title of the Science Education Partnership Award, which is supported by the National Institutes of Health.

The new grant continues a partnership between the Department of Biotechnical and Clinical Laboratory Sciences in the Jacobs School of Medicine and Biomedical Sciences, the New York State Area Health Education Center System, UB’s Center of Excellence in Bioinformatics and Life Sciences (CBLS) and the Buffalo Niagara Waterkeeper with schools across a 14-county region of Western New York.

The project, which was delayed a year due to COVID-19, is finishing the first year of the five-year grant.

Participants are among the first high school students and teachers to use third-generation Oxford Nanopore MinION sequencing technology.

Teachers and students from two schools — Research Laboratory High School for Bioinformatics & Life Sciences in the Buffalo Public Schools and Le Roy High School in Genesee County — took part in pilot training sessions in the summer of 2021. Kira Mioducki and Dawn Weihrich are the Research Laboratory teachers, while Michael Chiulli, a New York State Master Teacher, is the Le Roy teacher.

Students from Research Laboratory collected water samples at Broderick Park in Buffalo.

“They differentially filtered the samples to collect bacteria and they extracted the metagenomic DNA,” Koury says. “They determined what combination of genus and species bacteria were in the water by doing the sequencing analysis on that sample.”

The Le Roy students collected their samples at Oatka Creek, a tributary of the Genesee River.

“Oatka Creek runs through a lot of dairy farmland, so there may be some nitrogen runoff there. The idea is to look at the species that are there and try to correlate it with what’s known about the geology and the chemistry of those bodies of water,” Koury says.

The grant was to run through 2025, but due to the pandemic, Koury will apply for a no-cost, one-year extension.

“The idea was we would do the pilot teachers first and get the procedures in place, and in the next four years we would have different teachers from different schools,” Koury says.

He hopes to have 10 teachers per year take part, with each teacher bringing along 10 students. That means 100 students a year and 500 total will be able to take part.

“It’s hands-on experience — it’s real science. The students don’t know what they’re going to find,” Koury says. “It’s kind of special because at least at the time we wrote this proposal, there was no other high school experience that was going to be able to use this technology to sequence a whole genome and have the ability to do the analysis.”

Allison Brashear, vice president for health sciences and dean of the Jacobs School, praises Koury and all those associated with the award. “This program will give hundreds of high school students the opportunity to perform high-level research,” Brashear says “It can provide the spark needed to get students in Western New York high schools to pursue careers in research science.”

Two training sessions are scheduled this summer: June 27 through July 1 and Aug. 1-5.

Norma J. Nowak, professor of biochemistry and executive director of the CBLS, is co-investigator on the grant.

Others from the CBLS contributing to the project are Jonathan E. Bard, senior programmer and bioinformatics analyst; Sandra K. Small, science education manager; and Natalie Anne Lamb, project programmer/analyst.

Khaled ElShorbagy, who earned a master’s degree in biotechnical and clinical laboratory sciences in 2021, and Xinyi Yu and Zilin Lu, undergraduate supervised research students in biotechnical and laboratory sciences, have also contributed to the project.