Fine-Mapping Tools : an interactive framework for dissecting disease-associated genetic loci with functional genomics data
Author(s)
Nguyen, Peter H. T. (Peter Hung Trung)
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Alternative title
Interactive framework for dissecting disease-associated genetic loci with functional genomics data
Other Contributors
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science.
Advisor
Manolis Kellis.
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Metadata
Show full item recordAbstract
Fine mapping causal SNPs from GWAS summary statistics is hard. Although many frame- works exist to support fine mapping, some of which leverage epigenomic contexts to increase predictive power, they fail to provide interactivity. Here, we introduce Fine-Mapping Tools (fm-tools), a framework for doing interactive and iterative fine mapping. Fm-tools provides a harmonized data store and implements a number of algorithms for fine mapping -- one of which is the custom RiVIERA-mini, an efficient Bayesian inference framework -- and exposes them via a rich API that can be plugged into a variety of services (e.g., web applications for visualization). Most importantly, fm-tools allows scientists to interactively and iteratively explore dynamically generated hypotheses, as demonstrated by a case study for celiac disease. In summary, fm-tools standardizes the way fine mapping is done, reduces the overhead of fine mapping for scientists and of algorithm development for researchers, and paves the way towards achieving real-time personalized medicine.
Description
Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2017. This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. Cataloged from student-submitted PDF version of thesis. Includes bibliographical references (pages 57-58).
Date issued
2017Department
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer SciencePublisher
Massachusetts Institute of Technology
Keywords
Electrical Engineering and Computer Science.