UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN
Omics Data Platform Investigator Portal
Time Period: May 2022 – Present
Ongoing
Omics Data Platform Investigator Portal
Background
Next Generation Sequencing (NGS) is a technology used to identify DNA variations in the human population. It is used by clinicians and researchers to find potential causes for inherited disorders or cancer mutations [1]. NGS data is large and expensive to store, so it is becoming increasingly common for hospitals to house NGS data in cloud-based solutions [2].
Problem
Currently, accessing large sets of NGS data from the cloud requires specialized training. Many clinicians and researchers rely on bioinformaticians to retrieve data and initial insights. Researchers and healthcare providers need user-friendly tools that enable them to select, retrieve, and display the specific data that answers their research or clinical question. How to best empower users to ask specific questions of the data and to explore and interpret the information that is retrieved is an important UI/UX challenge.
Solution
In this project, we are developing an Investigator Portal for the genomic data stored on the Google Cloud-based Mayo Clinic Omics Data Platform (ODP). This portal allows users to search and filter their data (e.g., formulate queries) to look across and access the vast amount of knowledge in these genomic datasets.
Contribution
With our experience in building clinical user interfaces, we designed, developed, and released a web applicationMayo researchers query their genomic datasets. The application fits seamlessly into Mayo’s current clinical and research ecosystems, since we applied the UI/UX style guide our group previously developed for Mayo Clinic.. For the next phases of this project, our goal is to foster new collaborations between researchers across Mayo Clinic. Our designs will allow researchers to run queries across multiple datasets at once, providing a way for researchers and clinicians to share their data.
Collaboration
Drs. Sekulic, Olson, and Klee from the Mayo Clinic provide expert guidance and feature prioritization for the tool’s interface capabilities and design. The Mayo development team creates and tests the primary backend services which retrieve and display the cloud genomics data requested by user queries.
The user can monitor the status of all of their queries while they wait for the results to be retrieved from the cloud.
Lower right: The ODP Investigator Portal enables users to sort and filter data (e.g., build a query) from cloud-based genomics datasets.
Lower left: Users can also integrate annotation fields from several different catalog databases.
When the results are ready, users can explore the variants discovered by their query (rows) with the different annotations that they requested (columns).
VA Participants
Charles Blatti, Product Manager
Jessica Saw, Clinical Content Specialist
Lisa Gatzke, UI/UX Lead Designer
Fangyu Zhou, UI/UX Designer
Chad Olson, Frontend Development
Matt Berry, Application Development
Sara Lambert, Application Development
Jonathan Kim, Application Development
Our Collaborators
Erik Klee, Director of Bioinformatics, Center for Individualized Medicine, Mayo Rochester [profile], Product Sponsor
Aleksandar Sekulic, Associate Director, Center for Individualized Medicine, Mayo Phoenix [profile], Product Owner
Rory Olson, Mayo Rochester, Advisory Panel
Mark Heggestad, Mayo Jacksonville, Project Manager
Eric Winter, Mayo Rochester, IT Tech Specialist
Corey Carlson, Mayo Rochester, Programmer
Laura Lo, Mayo Rochester, Business Analyst
Kiran McCombs, Mayo Rochester, Quality Assurance
Megan Williams, Mayo Rochester, IT Manager
Related References
Project Contact:
Charles Blatti
Research Scientist
blatti@illinois.edu
Funding agency:
Mayo Clinic Center for Individualized Medicine
