The Mayo Clinic and Illinois Alliance offers innovative educational programs that bring University of Illinois at Urbana-Champaign students together with Mayo Clinic researchers and clinicians to address big data challenges in healthcare. The Technology-Based Healthcare Research Fellowship program is designed to leverage Illinois’ technological expertise with the medical informatics and clinical practice expertise of Mayo Clinic for biomarker discovery, systems medicine analysis, and more. To get the most from the experience, fellows are encouraged to spend one year at Illinois and one year at Mayo Clinic.
Dan Wickland recently completed his Technology-Based Health Care Research Fellowship and earned his doctorate in bioinformatics. Wickland spent the last two years working with Mayo Clinic and Illinois researchers to analyze genomic sequencing data of more than 10,000 cases and healthy controls from the Alzheimer’s Disease Sequencing project (ADSP). While his interest in biology and the brain drew him to the field of neuroscience as an undergraduate, he switched to a different type of biology in his graduate program—crop sciences—after learning he did not enjoy working with animal models.
As a doctoral student, Wickland joined crop sciences professor Matthew Hudson’s lab to map a gene in soybeans that controlled plant height and internode length. Early in the project, the team discovered the software they were using was not accurately identifying differences between soybean genomes. While seeking a solution, Wickland developed GB-eaSY, a program that dramatically increased the accuracy, speed, and simplicity of genotyping-by-sequencing data analysis.
When Hudson encountered a similar need in the research he was involved with at the National Center for Super Computing Applications (NCSA), he immediately thought of Wickland. Hudson had been working with Liudmila Mainzer, Ph.D., senior research scientist at NCSA, and Yan Asmann, Ph.D., associate professor of biomedical informatics at Mayo Clinic, to improve genetic variant calling software for human genomics targeted at Alzheimer’s disease. The collaborators had been using Blue Waters, NCSA’s petascale computer, to perform a vast number of comparisons to troubleshoot the huge amount of genome data that Mayo Clinic was analyzing on Alzheimer’s.
“As a result of Dan’s prior work on variant calling software, and his interest in neuroscience from his undergraduate days in the Illinois Neuroscience Program, I thought he would be an excellent candidate for this project. Although soybeans and humans are very different, the bioinformatics problems involved were closely related,” said Hudson.
Eager to tackle this ambitious project, Wickland made another big leap. Hudson recalls, “Although Dan had already pretty much completed the work necessary for a Ph.D. in crop sciences, he enthusiastically agreed to transfer to this project, move his Ph.D. to the informatics program, and spend two years between the Mayo Clinic campus in Florida and NCSA working on human genome variant calling.”
His advisors were impressed with how quickly Wickland was able to master the complex workflows on Blue Waters necessary to analyze the data in several ways to determine the source of inconsistencies they found. “He was ultimately able to determine that in this case, the problem did not lie in the software itself but in the discrepancies between the data generated at the different participating institutions in the Alzheimer’s Disease Sequencing Project,” said Hudson. The team is now working on a joint paper that characterizes the batch effects and study design biases in the data sets.
Wickland credits the fellowship for his growth as a researcher. Wickland spent the first year of his fellowship at NCSA, developing skills in high-performance computing and workflow programming. He explained that, over two years, this project used more than 600,000 node hours on Blue Waters, which is equivalent to a single server running continuously for almost 100 years. “These intensive computing needs could not have been met without a resource like Blue Waters at NCSA. In addition, feedback and ideas from my Illinois advisors, Dr. Hudson and Dr. Liudmila Mainzer, were critical to the success of this project.”
For the second year, Wickland worked at the Mayo Clinic campus in Florida. “There I received invaluable guidance from my Mayo Clinic advisor, Dr. Yan Asmann, and very helpful feedback from renowned Alzheimer’s researchers regarding interpretation of my results. Working in these two environments exposed me to different methods and ideas that strengthened my skills as a researcher.”
Wickland will soon join Mayo Clinic’s Department of Health Sciences Research as a research associate where he will continue to work with Dr. Asmann on a project with Mark Sherman, M.D., professor of epidemiology and laboratory medicine and pathology at Mayo Clinic, that focuses on breast cancer immunogenomics. Dr. Asmann looks forward to having Wickland join her team. “Dan has great analytic skills and is intellectually curious with an inquisitive mind. I am very proud of Dan and happy that he decided to accept the job offer from Mayo Clinic.”
Illinois faculty were thrilled to hear the news of Wickland joining the Mayo Clinic research team. Professor Hudson reflected on watching Wickland defend his doctoral dissertation, “a process which was extremely enjoyable for me as his advisor as there was no doubt about his passing and gaining a doctorate.” He has the utmost confidence that Dan will be an asset to the Mayo Clinic team.
Bryan White, Ph.D., director of the Mayo Clinic and Illinois Alliance, was also happy to hear the news. “We are excited and pleased that Dan will be joining Mayo Clinic. We have already had three former University of Illinois graduate students hired by Mayo Clinic. Dan is our first student hired to work at the Mayo Clinic campus in Florida. The continued pipeline of University of Illinois graduate students to the Mayo Clinic workforce builds on the long history of educational programs that the Alliance has supported,” said White, referring to the Technology-Based Healthcare Research Fellowship program, as well as the Summer Undergraduate Research Fellowship program, the Information Technology Internship program, and the Computational Genomics short course. “We are hopeful that this pipeline will continue to grow and provide new educational and employment opportunities in technology-based healthcare for University of Illinois students at Mayo Clinic.”