Right here on campus, statistics students are getting the chance to make an impact not only in their own field, but also in medicine and perhaps in the lives of people everywhere.
In late June, researchers from the University of Utah published a groundbreaking study that may further the identification and treatment of rare genetic diseases. As part of the research of Dr. Evan Johnson, of the BYU Department of Statistics, several BYU students were able to make contributions to this publication — combining their knowledge of statistics with new software.
Using only blood samples from a few family members, the authors of the study were able to pinpoint the specific DNA mutation that results in a rare and lethal genetic disease. Tentatively called “Ogden Syndrome,” after the residence of the local family they studied, this disorder results in boys who are born with wrinkled skin, a broad mouth, and big eyes and rarely live more than one year.
Since everyone has many mutations in their DNA, finding what ones lead to health problems is very complex. Modern sequencing technologies read large quantities of cut-up DNA strands, outputting massive sets of data. In order to identify the bases that are potentially disease causing, the small snippets of DNA have to be mapped back to their original order.
Nathan Clement, a former BYU computer science student who is now studying at the University of Texas, worked with Mark Clement and Quinn Snell, from the BYU Department of Computer Science, to develop an algorithm that makes this process possible.
The method uses statistics and high performance parallel computing to probabilistically determine from where the DNA piece had been cut. Then the DNA sequence of a child who has a disorder can be compared with another relative who is healthy, allowing them to find which specific mutation is causing the disease. It was this method that allowed the researchers to find the cause of Ogden Syndrome.
Johnson says that this publication is some of “the first fruits” coming out of Clement’s algorithm. Christa Schank, an undergraduate student currently in Dr. Johnson’s lab, is also contributing to the research by analyzing the data obtained from the algorithm.
“We were able to use it to narrow down a list of thousands of genetic mutations in our patient to the one we believe is causing this disease,” said Schank.
Knowing what effect a mutation has can be the difference between the mysterious and the understood. In the disorder addressed in the study, they found that a single mutation was disrupting the modification of nearly half the proteins in the patient’s body.
“This mutation is going to cause huge problems because it is effectively unmodifying 40 percent of human proteins that should be modified,” Johnson said of the seriousness of genetic disorders.
This publication wouldn’t have been possible without the power of BYU’s supercomputer, Mary Lou. Schank’s involvement on the paper included using Mary Lou’s 360 CPU cores to filter and sequence the data. With this many processors, 1,000 hours of computing time can be accomplished in just three hours.
The opportunity to use a supercomputer for undergraduate research is something unique to BYU.
“We have resources that are better than just about any other place I can think of,” Johnson said. “We have very good computing resources that have been donated for us. They are available to all the students and all the people at the university, and that’s not typical.”
Johnson makes involving students in real research a priority because it helps them expand beyond what they know. While Schank admits that research can be difficult, learning on the job has been a good experience.
“The programming experience and the experience in a biology applied setting will impact the career decisions I make,” she said. “BYU just makes research a lot more accessible for undergraduates. From what I hear from my friends at other universities, it’s really hard to get a research job. [BYU] professors just seem interested in you.”
Learn more about the other applications of this research from Dr. Johnson: