DOI

10.17077/etd.kppqwd7f

Document Type

Thesis

Date of Degree

Fall 2016

Degree Name

MS (Master of Science)

Degree In

Biomedical Engineering

First Advisor

Terry A. Braun

First Committee Member

Thomas L Casavant

Second Committee Member

Michael J Schnieders

Abstract

One of the tools a clinician has in disease diagnosis and treatment is genetic testing. To generate value in genetic testing, the link between genetic variants and disease must be discovered, documented, and shared within the community. Working with two existing genomic variation tools, Kafeen and Cordova, a new set of features referred to as Variant-Curation and Database Instantiation (Variant-CADI) was identified, designed, implemented and integrated into the existing Cordova system to unite data collection, management and distribution into one cohesive tool accessible through user interfaces. This eliminates the user needing specialized knowledge of the underlying implementation, data pipeline or data management to collect desired disease specific genetic variations. Using this tool, new disease-specific variation database instances have been initialized and created as demonstrations of the utility of these applications.

Public Abstract

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.

Keywords

Cordova, Disease Specific Genetic Variation, Genetic Variation Database, Kafeen, Variant-CADI, Variation Annotation

Pages

viii, 57 pages

Bibliography

Includes bibliographical references (pages 55-57).

Copyright

Copyright © 2016 Andrea Rae Hallier

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