Sanger Sequencing Initiative Offers In-House Alternative For Sample Testing
Mar 01, 2023 — Atlanta, GA
Most biological research is grounded in DNA sequencing, a way to determine the order of organic molecules in DNA. The process is typically conducted by large-scale biotech companies, but the drawbacks can be time, cost, and environmental impact.
“What makes a researcher or a lab want to switch over to us? We provide the same if not superior-quality data to them,” says Nicole Diaz, SSI’s founder and manager, and a fourth-year student in the Wallace H. Coulter Department of Biomedical Engineering at Georgia Tech and Emory University. “We use an optimized process that is less industrialized. And the service we offer is more personal, so if researchers have any issues, we are able to be a lot more flexible than the big companies.”
Launched in 2020, SSI has evolved into a full-fledged, student-run program to collect and process samples for research labs.
Researchers can submit samples in drop boxes at one of six locations in the BioQuad – Krone Engineered Biosystems Building, Molecular Sciences And Engineering, Ford Environmental Science & Technology Building, Marcus Nanotechnology Research Center, Cherry L. Emerson Building, and the Parker H. Petit Institute for Bioengineering and Biosciences at Georgia Tech.
Samples are charged at $5 per tube for less than 20 samples. That price is reduced to $4 per tube with more than 20 samples. After 96 samples are processed, the price goes down to $3.50 per tube.
And with just three billing cycles based on the academic calendar—fall, spring, and summer—labs can easily reach the lowest discounted price for all samples by the end of the semester regardless of how many samples are submitted at a time, Diaz says.
Turnaround time is within three days.
The added benefit of working directly with SSI is its commitment to providing a sustainable sampling process.
“The carbon footprint is lowered by keeping samples local instead of shipping them across the country to have them sequenced,” Diaz says. “So, researchers have access to dropboxes just outside the door of their lab in the buildings here in the BioQuad.”
Lab technicians are culled from federal work study, student assistants, student volunteers, or those seeking internship credit.
“It’s great to have a foundation and building blocks where I won’t be nervous when I encounter this down the road,” says, Aaron Kent, a first-year chemical engineering student.
SSI not only services labs at Georgia Tech, but it can also support labs for institutions in the Georgia Research Alliance, a consortium of public and private universities in Georgia including Emory University, Morehouse School of Medicine and the University of Georgia.
A Novel Idea During Covid-19
Sanger sequencing has been conducted in the Molecular Evolution Core (MEC) since 2018 under the direction of research technologist Naima Djeddar. Anton Bryskin, Regents researcher and MEC technical director, wanted to expand the mission of the MEC and tap into an undervalued resource on campus—undergraduate students.
“I knew that undergraduate students at Georgia Tech are very special,” Bryskin says. “It was never thought that undergraduate students might do a part of the work typically done by researchers or technicians.”
With support from M.G. Finn, professor and chair in the School of Chemistry and Biochemistry and chief advisor of the MEC, the Sanger Sequencing Initiative (SSI) was launched in 2020. The height of COVID-19 proved to be a valuable time for the program. Between sample processing sessions for Tech’s COVID-19 surveillance testing program, student workers were pulled to process sequencing samples for SSI.
“It was great because these students had already been trained on clinical practices,” Diaz says. “So, we didn't have to go back and train them on what it would be like in the lab because they already had the maximum training that was necessary.”
Diaz joined the Initiative in its inception as a federal work study student. Since then, she’s led the growth and development of SSI, from processing samples to marketing to hiring to building out a lab management system for operations alongside operations manager of the MEC TipCycling program and fourth-year biomedical engineering student Helya Taghian.
Not only have undergraduate students gained valuable lab experience, Diaz said, but SSI has become a multidisciplinary effort. The staff is composed of students from biomedical, industrial, and chemical and biomolecular engineering, as well as computer science and design majors.
“We have a stacked team,” she says.
Diaz says the team is working to incorporate more automation into the process, including tracking metrics for sample processing and developing a bioinformatics solution to optimize workflow and data quality. Third-party app integration to centralize the SSI workflow was tackled by the MEC web development team—comprised of computer science (CS) undergraduates led by fourth-year CS student Bakr Redwan—whom devised a custom Laboratory Information Management System (LIMS). This LIMS system will serve as SSI’s hub for all operations including processing, billing, inventory, and communications.
SSI currently process samples for several labs across campus, including for Finn, Chemical and Biomolecular Engineering Professor Mark Styczynski, and newly elected National Academy of Engineering Professor Mark Prausnitz, and hopes to expand to more labs in the future.
“We want to be an example program for other universities to use, implement in different capacities, and offer the same opportunities to their undergraduate students,” Diaz says.
To learn more about the Sanger Sequencing Initiative, including how to submit samples or join the program, visit their website.
Author: Kelly Petty