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

Abstract

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.

Development and user evaluation of a rare disease gene prioritization workflow based on cognitive ergonomics

“…The workflows should also be assessed in terms of (a) performance with diseases that present with heterogeneous, overlapping, or novel phenotypes and (b) incorporation of information beyond gene level. In addition to the scope of the evaluation, the study recruitment was also restricted to medical/biochemical geneticists in order to ensure that participants represent a focused group of users, who would exhibit similar areas of attention/interest when approaching WES/WGS data as well as shared desiderata towards WES/WGS analysis software 37 . Further research should also consider inclusion of other healthcare professionals involved in clinical WES/WGS interpretation (eg, genetic counselors and bioinformaticians) to gain further insights into diverse groups of users and their interaction with different workflows.…”

VarFish - Collaborative and Comprehensive Variant Analysis for Diagnosis and Research

“…This allows an integrated display of QC information suitable for clinicians as suggested by Shyr, c.f. (23) . Finally, the user can consider this information for all samples in a project to evaluate a sample in comparison to similarly processed ones or for a whole cohort.…”

User Testing of a Diagnostic Decision Support System with Machine-assisted Chart Review to Facilitate Clinical Genomic Diagnosis

“…[4,[6][7][8] Diagnostic Decision Support Systems (DDSSs) are a key type of CDS needed in genomics to supplement a shortage of trained clinicians and address the inherent complexity of genomic diagnosis. [9,10] Complexity arises from the heterogeneous nature of genetic diseases, the variable expression in patients, and the degree of overlap in findings (i.e., signs, symptoms and test results) among genetic conditions, sometimes differentiated mainly by onset age of individual findings. [11] Systematic review and position statements note two needs from DDSSs in genomics:…”