Genetics and Alzheimer’s researchers at BYU have made far-reaching contributions to their fields through two valuable campus resources: the DNA Sequencing Center (DNASC) and the Office of Research Computing.
These resources generate data that is used by BYU faculty researchers, students and collaborators from other universities in their research.
Although many people approach the DNASC requesting sequencing for family history and genealogy related samples, these services are currently not offered. The DNASC, along with the Office of Research Computing, is centered on the primary focus of providing support for academic research.
DNA Sequencing Center
Inside the Life Sciences Building is a collection of small rooms that make up what is known as the BYU DNASC. This center is vital to researchers and houses DNA sequencing machines that are dedicated to efficiently and economically processing DNA samples.
Edward Wilcox, managing director of the sequencing center, has worked as a full-time research faculty member since 2005. He manages everything from the DNA sequencing machines to student employees who help prepare samples.
The process of preparing DNA samples involves isolating them, shearing them down to the right size, making libraries and cleaning them.
“A library is just pieces of DNA with adapters on the ends,” Wilcox said. “The adapters are what allows us to sequence in since it’s a known sequence. From there, we can sequence into the unknown.”
After the libraries are prepared, they are ready to be placed in the sequencing machines. The DNASC currently has three machines: the Illumina, PacBio I and PacBio II. The 2015 Illumina will retire at some point and be replaced by a new machine called the NovaSeq. This machine will cost about a million dollars but is essential for the work and is expected to generate more data at less of a cost.
Handling all this expensive equipment requires great care. Wilcox admits he may come off as “overbearing” to student employees at times, but that’s because everything needs to be done just right.
“That’s $20,000 of reagent (a substance or compound added to a system to cause a chemical reaction) we’re putting on the machines right now. If we don’t do things right, and the run fails, we’re out $20,000,” Wilcox said. “It’s a little concerning, and we cannot afford to lose a run.”
BYU junior Miranda Johnson has been working at the DNASC since September 2018. The neuroscience major said the job is stressful and requires a lot of multitasking.
“But it’s less stressful than customer service in my opinion,” Johnson said.
The DNASC receives a variety of different samples from all across the United States and the world, including recent samples from Russia, the Czech Republic and Italy. The samples can come from any living organism, including fish, plants, insects, sunflowers and blood.
“It’s pretty random what we get,” Johnson said. “That’s the fun part of the DNA Sequencing lab! It’s familiar enough you don’t get lost, but it’s always a little bit different.”
BYU biology professor and Alzheimer’s researcher John Kauwe said the DNASC is an important resource that nearly everyone doing genetics research at BYU relies on for some aspects of their data generation.
“It’s great to have that resource right down the hall, where we know we can get high-quality data,” Kauwe said.
The Office of Research Computing
The Office of Research Computing is another vital resource for research at BYU. With over a thousand computer servers and 24,000 processor cores, this valuable resource is utilized by hundreds of users, including BYU faculty researchers, students and a few dozen collaborators from other universities.
“Nothing I do would be possible without it,” said Perry Ridge, an Alzheimer’s researcher and biology professor at BYU. “Every analysis that we run for every project is on the supercomputer.”
Research director computing Ryan Cox oversees the entire office, running everything from the servers to the employees. His team does everything from maintaining the hardware and software that researchers use and purchasing new equipment to staying on top of industry trends and helping people with code optimizations.
The servers that make up the supercomputer are located in three separate rooms across the BYU campus, the biggest being in the James E. Talmage Building. Several departments on campus rely on this resource — especially the engineering, physical, mathematical and life sciences colleges.
The DNASC in the life sciences college sends terabyte-sized files to the servers on a weekly basis. Wilcox, the managing director of the sequencing center, said not having enough computer space has been one of their biggest challenges.
“We’re dealing with some big files here,” Wilcox said. “The computer center at BYU limits you to 15 terabytes; that’s a week’s worth of data and it’s hard to distribute everyone’s data in that time.”
Realizing this was an issue, Cox said the Office of Research Computing recently started renting out storage space to accommodate those who need the extra space.
“Some people use 80 to a 100 times more storage than the allocation we give people,” Cox said.
Generally the research computing sources are freely available to everyone, but the limited storage space makes it difficult to satisfy everyone’s needs. But according to Ridge, Cox and his team are always finding ways to accommodate those in the research community.
“The Office of Research Computing is service-oriented and they go out of their way to help faculty and students in doing research,” Ridge said. “ They really make a lot of what we do here at BYU possible, and make it possible for BYU to stand out in positive ways.”
Kauwe agrees and added that these campus resources help him and his colleagues make a positive impact in their fields of research.
“It’s been wonderful coming here and having a DNA sequencing center and a high quality research computing center to analyze the scale of data we’re generating,” Kauwe said. “It’s allowed us to be competitive on a national scale and to make research progress that is meaningful in our field. They are incredible resources that are key to genetics research at BYU.”