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THE
ROLE
OF
GENETIC
ANCESTRY
IN
ESTIMATION
OF
THE
RISK
OF
AGE-‐
RELATED
DEGENERATION
(AMD)
IN
THE
LOS
ANGELES
LATINO
POPULATION
by
Lijun
He
A
Thesis
Presented
to
the
FACULTY
OF
THE
USC
GRADUATE
SCHOOL
UNIVERISTY
OF
SOUTHERN
CALIFORNIA
In
Partial
Fulfillment
of
the
Requirements
for
the
Degree
MASTER
OF
SCIENCE
(BIOSTATISTICS)
August
2014
Copyright
2014
Lijun
He
Object Description
| Title | The role of genetic ancestry in estimation of the risk of age-related degeneration (AMD) in the Los Angeles Latino population |
| Author | He, Lijun |
| Author email | lijunhe@usc.edu;LijunHe@gmail.com |
| Degree | Master of Science |
| Document type | Thesis |
| Degree program | Biostatistics |
| School | Keck School of Medicine |
| Date defended/completed | 2014-08-08 |
| Date submitted | 2014-08-08 |
| Date approved | 2014-08-08 |
| Restricted until | 2014-08-08 |
| Date published | 2014-08-08 |
| Advisor (committee chair) |
Azen, Stanley P. Marjoram, Paul |
| Advisor (committee member) | Gauderman, William James |
| Abstract | The Latino population is an admixed population. Previous studies indicate the potential role of ethnicity in the risk of AMD. The purpose of this study is to evaluate the effect of population structure on the association between the risk of AMD and Single Nucleotide Polymorphisms (SNPs). ❧ The Los Angeles Latino Eye Study (LALES) is a unique population‐based cohort study designed to explore eye diseases in the Los Angeles Latino population. 1007 Mexican Americans aged 40 years and older, including 490 subjects with AMD and 517 corresponding controls, were selected from the LALES population. DNA was extracted for all subjects using blood cards. Genotyping of these DNA samples was performed using the Illumina HumanOmniExpress BeadChip. Genotypes of 988 HapMap samples and 88 Native American samples were also included in our study as reference groups for ancestry estimation. ❧ The PLINK and R software packages are used for data analysis. Panels with 243 ancestry informative markers, and others with a range of different numbers of randomly selected SNPs, are used to estimate global ancestry. This global ancestry analysis is performed using the software STRUCTURE and EIGENSTRAT. Logistic regression is used to evaluate the effect of the global ancestry estimates on subsequent association testing. The software Haploview is used to demonstrate the results of Genome Wide Association Study (GWAS). Correlation coefficient r² is computed to assess the methods used to estimate the genetic ancestry and the effect of population stratification. ❧ The average genetic ancestry for individuals from the LALES population is around 52.4% European, 43.5% Native American, 3.8% African, and 0.3% Asian. The results from logistic regression and GWAS indicate that there is no effect of population stratification on the relationship between risk of AMD and SNPs. |
| Keyword | ancestry analysis; Latino population; AMD |
| Language | English |
| Format (imt) | application/pdf |
| 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 |
| Provenance | Electronically uploaded by the author |
| Type | texts |
| Legacy record ID | usctheses-m |
| Contributing entity | University of Southern California |
| Rights | He, Lijun |
| Physical access | The author retains rights to his/her dissertation, thesis or other graduate work according to U.S. copyright law. Electronic access is being provided by the USC Libraries in agreement with the author, as the original true and official version of the work, but does not grant the reader permission to use the work if the desired use is covered by copyright. It is the author, as rights holder, who must provide use permission if such use is covered by copyright. The original signature page accompanying the original submission of the work to the USC Libraries is retained by the USC Libraries and a copy of it may be obtained by authorized requesters contacting the repository e-mail address given. |
| Repository name | University of Southern California Digital Library |
| Repository address | USC Digital Library, University of Southern California, University Park Campus MC 7002, 106 University Village, Los Angeles, California 90089-7002, USA |
| Repository email | cisadmin@lib.usc.edu |
| Filename | etd-HeLijun-2795.pdf |
| Archival file | uscthesesreloadpub_Volume14/etd-HeLijun-2795.pdf |
Description
| Title | Page 1 |
| Repository email | cisadmin@lib.usc.edu |
| Full text | THE ROLE OF GENETIC ANCESTRY IN ESTIMATION OF THE RISK OF AGE-‐ RELATED DEGENERATION (AMD) IN THE LOS ANGELES LATINO POPULATION by Lijun He A Thesis Presented to the FACULTY OF THE USC GRADUATE SCHOOL UNIVERISTY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree MASTER OF SCIENCE (BIOSTATISTICS) August 2014 Copyright 2014 Lijun He |
