Variant-curation and database instantiation (Variant-CADI): an integrated software system for the automation of collection, annotation and management of variations in clinical genetic testing

One of the tools a clinician has in disease diagnosis and treatment is the evaluation of DNA sequences for changes that may cause disease. Changes in DNA sequence can be valuable for the diagnosis of disease, consideration of treatment, and understanding the pathophysiology of disease. Tools to share the link between disease phenotypes and observed DNA changes can be valuable to the research and clinical communities. This thesis describes extensions to software tools (Cordova and Kafeen) that are used to aggregate data for the evaluation of pathogenicity of DNA sequence variants. Kafeen is a data collection pipeline that searches public repositories for both pathogenic and non-pathogenic variations. It assembles this data and calculates an overall pathogenicity prediction for each variation found. Cordova is a web template suited to management of genetic variation data. Cordova is available to the research community for the deployment of disease-specific genetic variation databases. New functionality was identified, designed, implemented and integrated along with Kafeen into the Cordova system to automate collection, management and distribution of genetic variation data within the Cordova software system. Using this tool, new disease-specific variation database instances have been initialized and created as demonstrations of the utility of these applications.