Time Period: Spring 2019 – Spring 2020
As exome-wide and genome-wide genomic sequencing tests become increasingly common in healthcare, clinical specialists need tools to assess and verify the quality of the test results and
record any clinically significant impacts.
Genetic variations as assessed by sequencing tests are becoming a larger part of clinical care. Traditional software systems have had difficulties in handling the data from these technologies. These sequencing tests are susceptible to experimental error, and strict controls over the quality of the sample results need to be monitored and maintained before passing the variants on to genetic counselors and consultants to assess the clinical impact. The original tools used to assess this type of information were not built to scale, and therefore there was a need for a tool that would provide quality assessments of sequencing results for all genes or for the entire genome.
The VA Group worked with Mayo Clinic developers to create the Coverage Utility, a specialized tool for evaluating the depth of sequence coverage in regions of interest from the results of a single sample sequencing test. This interface allows users to review the coverage quality information in tabular or graphical interfaces with low coverage regions flagged for follow up. Reviewers are able to closely examine these low coverage events within the sample, compare to historical results for the related test, and decide which course of action is needed to address the issue.
VA developed the visualization and interactions of this interface from understanding user’s difficulties and the limitations of the existing tools. We focused on allowing users to prioritize events in an order that they preferred and enabled many different navigation shortcuts to allow them to move between events and to modify the status of each event.
In this project we worked alongside sequencing pipeline, data storage, and clinical application developers. Their input into the requirements of the user interface, as well as their expertise in integrating it into their Repository of Quality Control and Metrics application were invaluable.
Charles Blatti, Product Architect
Peter Groves, Backend Development
Matt Berry, Lead Developer
Colleen Bushell, MFA, Design Consultant
Lisa Gatzke, UI/UX Design
Kaveh Karimi, Frontend Developer
Alice Delage, Project Manager
Nate Mattson, IT Lead Analyst, Mayo Clinic
Jennifer Skierka, IT Application Architect, Mayo Clinic
Jenny Benson, IT Lead Analyst, Mayo Clinic
Eric Winter, Developer, Mayo Clinic
Paris Hare, Developer, Mayo Clinic
Center for Individualized Medicine, Mayo Clinic