Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Evidence-Based Design and Evaluation of a Whole Genome Sequencing Clinical Report for the Reference Microbiology Laboratory

View ORCID ProfileAnamaria Crisan, Geoffrey McKee, View ORCID ProfileTamara Munzner, View ORCID ProfileJennifer L. Gardy
doi: https://doi.org/10.1101/199570
Anamaria Crisan
Dept. of Computer Science, University of British Columbia, Vancouver, BC, CANADA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Anamaria Crisan
Geoffrey McKee
School of Population and Public Health, University ofBritish Columbia, Vancouver, BC, CANADA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tamara Munzner
Dept. of Computer Science, University of British Columbia, Vancouver, BC, CANADA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Tamara Munzner
Jennifer L. Gardy
School of Population and Public Health, University ofBritish Columbia, Vancouver, BC, CANADABritish Columbia Centre for Disease Control, Vancouver, BC, CANADA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Jennifer L. Gardy
  • For correspondence: jennifer.gardy@bccdc.ca
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

ABSTRACT

Background Microbial genome sequencing is now being routinely used in many clinical and public health laboratories. Understanding how to report complex genomic test results to stakeholders who may have varying familiarity with genomics – including clinicians, laboratorians, epidemiologists, and researchers – is critical to the successful and sustainable implementation of this new technology; however, there are no evidence-based guidelines for designing such a report in the pathogen genomics domain. Here, we describe an iterative, human-centered approach to creating a report template for communicating tuberculosis (TB) genomic test results.

Methods We used Design Study Methodology – a human centered multi-stage approach drawn from the information visualization domain – to redesign an existing clinical report. We used expert consults and an online questionnaire to discover various stakeholders’ needs around the types of data and tasks related to TB that they encounter in their daily workflow. We also evaluated their perceptions of and familiarity with genomic data, as well as its utility at various clinical decision points. These data shaped the design of multiple prototype reports that were compared against the existing report through a second online survey, with the resulting qualitative and quantitative data informing the final, redesigned, report.

Results We recruited 78 participants, 65 of whom were clinicians, nurses, laboratorians, researchers, and epidemiologists involved in TB diagnosis, treatment, and/or surveillance. Our first survey indicated that participants were largely enthusiastic about genomic data, with the majority agreeing on its utility for certain TB diagnosis and treatment tasks and many reporting some confidence in their ability to interpret this type of data (between 58.8% and 94.1%, depending on the specific data type). When we compared our four prototype reports against the existing design, we found that for the majority (86.7%) of design comparisons, participants preferred the alternative prototype designs over the existing version, and that both clinicians and non-clinicians expressed similar design preferences. Participants articulated clearer design preferences when asked to compare individual design elements versus entire reports. Both the quantitative and qualitative data informed the design of a revised report, which is available online as a LaTeX template.

Conclusions We show how a human-centered design approach integrating quantitative and qualitative feedback can be used to design an alternative report for representing complex microbial genomic data. We suggest experimental and design guidelines to inform future design studies in the bioinformatics and microbial genomics domains, and suggest that this type of mixed-methods study is important to facilitate the successful translation of pathogen genomics in the clinic, not only for clinical reports but also more complex bioinformatics data visualization software.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted October 06, 2017.
Download PDF

Supplementary Material

Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Evidence-Based Design and Evaluation of a Whole Genome Sequencing Clinical Report for the Reference Microbiology Laboratory
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
Share
Evidence-Based Design and Evaluation of a Whole Genome Sequencing Clinical Report for the Reference Microbiology Laboratory
Anamaria Crisan, Geoffrey McKee, Tamara Munzner, Jennifer L. Gardy
bioRxiv 199570; doi: https://doi.org/10.1101/199570
Digg logo Reddit logo Twitter logo CiteULike logo Facebook logo Google logo Mendeley logo
Citation Tools
Evidence-Based Design and Evaluation of a Whole Genome Sequencing Clinical Report for the Reference Microbiology Laboratory
Anamaria Crisan, Geoffrey McKee, Tamara Munzner, Jennifer L. Gardy
bioRxiv 199570; doi: https://doi.org/10.1101/199570

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (1524)
  • Biochemistry (2479)
  • Bioengineering (1731)
  • Bioinformatics (9663)
  • Biophysics (3895)
  • Cancer Biology (2968)
  • Cell Biology (4188)
  • Clinical Trials (135)
  • Developmental Biology (2624)
  • Ecology (4097)
  • Epidemiology (2031)
  • Evolutionary Biology (6892)
  • Genetics (5204)
  • Genomics (6495)
  • Immunology (2182)
  • Microbiology (6936)
  • Molecular Biology (2751)
  • Neuroscience (17259)
  • Paleontology (126)
  • Pathology (425)
  • Pharmacology and Toxicology (705)
  • Physiology (1056)
  • Plant Biology (2487)
  • Scientific Communication and Education (643)
  • Synthetic Biology (831)
  • Systems Biology (2687)
  • Zoology (429)