Abstract
Routine clinical application of whole exome sequencing remains challenging due to difficulties in variant interpretation, large dataset management, and workflow integration. We describe a tool named ClinLabGeneticist to implement a workflow in clinical laboratories for management of variant assessment in genetic testing and disease diagnosis. We established an extensive variant annotation data source for the identification of pathogenic variants. A dashboard was deployed to aid a multi-step, hierarchical review process leading to final clinical decisions on genetic variant assessment. In addition, a central database was built to archive all of the genetic testing data, notes, and comments throughout the review process, variant validation data by Sanger sequencing as well as the final clinical reports for future reference. The entire workflow including data entry, distribution of work assignments, variant evaluation and review, selection of variants for validation, report generation, and communications between various personnel is integrated into a single data management platform. Three case studies are presented to illustrate the utility of ClinLabGeneticist. ClinLabGeneticist is freely available to academia at http://rongchenlab.org/software/clinlabgeneticist.Electronic supplementary materialThe online version of this article (doi:10.1186/s13073-015-0207-6) contains supplementary material, which is available to authorized users.
Highlights
Molecular genetic testing is playing an increasingly important role in medicine
Under hardware specification described in the software implementation section, it takes less than 10 min for an administrator to upload and annotate one variant file from whole exome sequencing (WES)
Advancement of generation sequencing technologies has provided an unprecedented opportunity in medicine, and we have entered a new era of genetic and genomic testing
Summary
Molecular genetic testing is playing an increasingly important role in medicine. Due in large part to the breakthrough of genome and exome sequencing technologies, the scope of clinical genetic testing has been expanded from its traditional niche in rare Mendelian disorders to a broad application in complex disease and personalized medicine [1, 2]. In order to facilitate the implementation of WES-based genetic testing, an integrative tool is essential to provide a comprehensive data source for variant assessment, and to automate, enhance the efficiency of the process and reduce potential errors that may arise in handling large datasets. We describe a tool named ClinLabGeneticist designed to enable and facilitate WES testing in a clinical genetic laboratory setting.
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