Dynamic software design for clinical exome and genome analyses: insights from bioinformaticians, clinical geneticists, and genetic counselors

J Am Med Inform Assoc. 2016 Mar;23(2):257-68. doi: 10.1093/jamia/ocv053. Epub 2015 Jun 27.


Background: The transition of whole-exome and whole-genome sequencing (WES/WGS) from the research setting to routine clinical practice remains challenging.

Objectives: With almost no previous research specifically assessing interface designs and functionalities of WES and WGS software tools, the authors set out to ascertain perspectives from healthcare professionals in distinct domains on optimal clinical genomics user interfaces.

Methods: A series of semi-scripted focus groups, structured around professional challenges encountered in clinical WES and WGS, were conducted with bioinformaticians (n = 8), clinical geneticists (n = 9), genetic counselors (n = 5), and general physicians (n = 4).

Results: Contrary to popular existing system designs, bioinformaticians preferred command line over graphical user interfaces for better software compatibility and customization flexibility. Clinical geneticists and genetic counselors desired an overarching interactive graphical layout to prioritize candidate variants--a "tiered" system where only functionalities relevant to the user domain are made accessible. They favored a system capable of retrieving consistent representations of external genetic information from third-party sources. To streamline collaboration and patient exchanges, the authors identified user requirements toward an automated reporting system capable of summarizing key evidence-based clinical findings among the vast array of technical details.

Conclusions: Successful adoption of a clinical WES/WGS system is heavily dependent on its ability to address the diverse necessities and predilections among specialists in distinct healthcare domains. Tailored software interfaces suitable for each group is likely more appropriate than the current popular "one size fits all" generic framework. This study provides interfaces for future intervention studies and software engineering opportunities.

Keywords: clinical; cognitive science; decision support systems; exome; genomics; medical informatics; software design.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Attitude to Computers*
  • Computational Biology
  • Computer Graphics
  • Decision Support Systems, Clinical
  • Exome*
  • Focus Groups
  • Genetic Counseling
  • Genetics, Medical
  • Genome, Human*
  • Humans
  • Sequence Analysis, DNA
  • Software Design*
  • User-Computer Interface*