System for Interpretation of Personal Genomes

Genomics is undergoing a revolution sparked by higher throughput and cost effective DNA sequencing technologies. Sequencing has become a ubiquitous tool with varied inputs, scopes, techniques, technologies, and purposes. There is potential for the development of software systems that assist in translating raw sequence data into actionable information that helps improve disease assessment, detection, and treatment so that individuals who are or may be affected by genetic conditions are treated with an unprecedented level of precision and predictiveness. This new kind of medicine informed by personal genomic interpretation promises to have immense medical and economic benefits. Despite the capacity of new sequencing technologies to generate huge volumes of raw sequence data, it remains a substantial informatics challenge to efficiently analyze it. HTS technologies produce data at a rate that exceeds Moore's Law, creating enormous technical and usability issues. Freely available tools that are both powerful enough to be efficient and user-friendly enough to be used by genomic researchers without informatics expertise are scarce. Notwithstanding a few exceptions, users are often forced to choose between powerful, specialized software that needs to be run on the command-line or alternatives that are less specialized but are graphical and user-friendly. This thesis presents two software platforms that combine techniques from various domains of computer science, most notably data structures, databases, algorithm design, data visualization, user interface design, and user experience design, that together form a highly integrated system for interpretation of personal genomes that is both powerful and easy to use.Ph.D