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APPLICATION OF BAYESIAN METHODS IN ASSOCIATION MAPPING
by
Keyan Zhao
A Dissertation Presented to the
FACULTY OF THE GRADUATE SCHOOL
UNIVERSITY OF SOUTHERN CALIFORNIA
In Partial Fulfillment of the
Requirements for the Degree
MASTER OF SCIENCE
(STATISTICS)
May 2007
Copyright 2007 Keyan Zhao
Object Description
| Title | Application of Bayesian methods in association mapping |
| Author | Zhao, Keyan |
| Author email | kzhao@usc.edu |
| Degree | Master of Science |
| Document type | Thesis |
| Degree program | Statistics |
| School | College of Letters, Arts and Sciences |
| Date defended/completed | 2007-04-01 |
| Date submitted | 2007 |
| Restricted until | Restricted until 23 Apr. 2009. |
| Date published | 2009-04-23 |
| Advisor (committee chair) | Sun, Fengzhu |
| Advisor (committee member) |
Goldstein, Larry Zhou, Jasmine |
| Abstract | There is great interest in the use of computationally intensive methods for fine mapping of marker data. This thesis proposed a method to analyze diploid phase-unknown data using ideas derived from Bayesian spatial statistics. We use spatial clustering of haplotypes as a low-dimensional surrogate for the unobserved genealogy underlying a set of genotype data. In doing so we hope to avoid the computational complexity inherent in explicitly modelling details of the ancestry of the sample, while at the same time capturing the key correlations induced by that ancestry at a much lower computational cost.; We benchmark our methods using both the Cystic Fibrosis dataset and the simulated GAW 14 data. For the GAW 14 dataset, we used 100 replicates of 4 phenotypes to indicate the power of our method. When a functional mutation relating to a trait is actually present, we find evidence for that mutation in 97 out of 100 replicates, on average. Results show that our method has the ability to accurately infer the location of functional mutations from unphased genotype data. This shows the promise of integrated approach in fine mapping this kind of genetic data. |
| Keyword | association mapping; Bayesian methods |
| Language | English |
| Part of collection | University of Southern California dissertations and theses |
| Publisher (of the original version) | University of Southern California |
| Place of publication (of the original version) | Los Angeles, California |
| Publisher (of the digital version) | University of Southern California. Libraries |
| Type | texts |
| Legacy record ID | usctheses-m454 |
| Rights | Zhao, Keyan |
| Repository name | Libraries, University of Southern California |
| Repository address | Los Angeles, California |
| Repository email | http://www.usc.edu/isd/libraries/services/ask_a_librarian/email/ |
| Filename | etd-Zhao-20070423 |
| Archival file | uscthesesreloadpub_Volume26/etd-Zhao-20070423.pdf |
Description
| Title | Page 1 |
| Full text | APPLICATION OF BAYESIAN METHODS IN ASSOCIATION MAPPING by Keyan Zhao A Dissertation Presented to the FACULTY OF THE GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE (STATISTICS) May 2007 Copyright 2007 Keyan Zhao |
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