The Mayo Clinic & Illinois Alliance for Technology-Based Healthcare (Alliance) hosted its 12th annual Computational Genomics Course June 24-28, 2024. The strategic alliance between the two institutions encourages a broad spectrum of collaborative research, the development of new technologies and clinical tools, and the design and implementation of novel education programs.
Designed for Mayo Clinic and Illinois affiliated scientists and clinicians, the week-long intensive course covers the basics of computational genomics while integrating the latest technologies and computational methodologies. Since 2013, nearly 900 researchers have completed the Computational Genomics Course. Previously hosted in-person at Illinois and video-conferenced to Mayo Clinic, the course shifted to a 100% virtual format in 2020 due to the pandemic – a format that now makes the course more accessible to a broader audience.
During the course, Illinois faculty and Mayo Clinic scientists and clinicians lead lectures and hands-on lab exercises in a variety of subject areas, including genome sequencing and assembly, polymorphism and variant analysis, clinical variant interpretation, and regulatory genomics. The 2024 schedule included new modules on single cell and spatial transcriptomics and AI.
Several individuals from both world-class institutions are involved in bringing this jointly created course to attendees each year. Co-directors Dave Zhao from Illinois and Eric Klee from Mayo Clinic select content and speakers for the course. Teaching assistants spend weeks testing the lab portions of the course and devote the entire week of the course to assist attendees, troubleshoot problems, or answer questions as they work through the lab exercises. Technical support is provided by the Carl R. Woese Institute for Genomic Biology Computer and Network Resource Group at Illinois.
“Computational genomics is so broad and changes so quickly that it's hard to keep up to date. Our Illinois and Mayo Clinic instructors and staff and IGB's computing group put in a huge amount of effort to rehaul the course,” Zhao said. “We streamlined content, added new lectures and labs on spatial and multiomics single-cell biology, introduced cutting-edge material on artificial intelligence, and re-engineered our technology infrastructure to deliver the hands-on labs over a computing platform that has become a standard in the field.”
Lectures and labs
Following a welcome and introduction to the course, lectures begin with presentations on basic genomic concepts, which are expanded upon throughout the course. Featuring a variety of live, pre-recorded, and on-demand lectures, presentation slides and recordings are available for attendees to revisit content as needed.
Each lecture is followed by related lab exercises, either synchronous or self-paced, providing participants the opportunity to immediately implement what they have learned. Hands-on lab activities empower attendees to use complex software tools they may be unfamiliar with or would like to learn more about. Attendees walk away with new knowledge, tools, and resources pertinent to their research and the ability to apply what they have learned to both their current and more advanced future roles.
Participants
Walter Avila, a 2023 doctoral bridge student in the Fisk-UIUC Training of Underrepresented Minds in Data Science and Quantitative Biology (FUTURE-MINDS-QB) program, where quantitative biology encompasses bioinformatics, computational biology, genomic biology, and biophysics, participated in the 2024 course. As a graduate student studying microbiology, Avila has often struggled with the sheer volume of genetic data and the complexity of tools available to analyze it.
“The Computational Genomics Course made these tools and techniques much more accessible and understandable,” Avila said. “The lessons on statistical models used in GWAS and genomic screening studies have greatly expanded my statistical toolkit. This is invaluable for my growth as a statistician, helping me apply the right methods to make sense of relationships between genomic and phenotypic data in my future research."
Rebecca Bishop is an equine surgeon and postdoctoral research associate in the Department of Veterinary Clinical Medicine at Illinois whose research utilizes high throughput technologies to elucidate mechanisms of gastrointestinal disease in horses. A 2024 course participant, Bishop was excited to learn about the cutting-edge applications of machine learning/AI to human medical research going on at Mayo Clinic before embarking on her first RNA-Seq analysis this fall.
“The lab portions of the course were extremely well organized and easy to run without significant prior knowledge of the coding languages and I look forward to digging into the detailed annotated code provided by course instructors to further my understanding of the methods,” Bishop said. “I would recommend this course for learners who are looking to dip their toes into computational genomics for the first time or expand their genomic tool kits. I hope to take the course again in the future as the field continues to evolve.”
Future courses
The Computational Genomics Course is open to all Illinois and Mayo Clinic faculty, staff, and students. Organizers plan to continue with a mix of basic and clinical or translational-focused topics and are considering an advanced course and an asynchronous version of the course in the future.
Registration for the Computational Genomics Course opens each year in April. Subscribe to the Alliance mailing list to receive announcements about the course, as well as information about educational and networking opportunities, upcoming events and deadlines, and the latest news from this powerful collaboration that is working to solve today’s health challenges.