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University of Southern California
1.
He, Lijun.
The role of genetic ancestry in estimation of the risk of
age-related degeneration (AMD) in the Los Angeles Latino
population.
Degree: MS, Biostatistics, 2014, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/457444/rec/7225
► 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…
(more)
▼ 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.
Advisors/Committee Members: Azen, Stanley P.Marjoram, Paul (Committee Chair), Gauderman, William James (Committee Member).
Subjects/Keywords: ancestry analysis; Latino population; AMD
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APA ·
Chicago ·
MLA ·
Vancouver ·
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APA (6th Edition):
He, L. (2014). The role of genetic ancestry in estimation of the risk of
age-related degeneration (AMD) in the Los Angeles Latino
population. (Masters Thesis). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/457444/rec/7225
Chicago Manual of Style (16th Edition):
He, Lijun. “The role of genetic ancestry in estimation of the risk of
age-related degeneration (AMD) in the Los Angeles Latino
population.” 2014. Masters Thesis, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/457444/rec/7225.
MLA Handbook (7th Edition):
He, Lijun. “The role of genetic ancestry in estimation of the risk of
age-related degeneration (AMD) in the Los Angeles Latino
population.” 2014. Web. 02 Mar 2021.
Vancouver:
He L. The role of genetic ancestry in estimation of the risk of
age-related degeneration (AMD) in the Los Angeles Latino
population. [Internet] [Masters thesis]. University of Southern California; 2014. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/457444/rec/7225.
Council of Science Editors:
He L. The role of genetic ancestry in estimation of the risk of
age-related degeneration (AMD) in the Los Angeles Latino
population. [Masters Thesis]. University of Southern California; 2014. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/457444/rec/7225

University of Southern California
2.
Dong, Cheng.
Capture and analysis of circulating tumor cells in patients
with hepatocellular carcinoma: analysis of a pilot study.
Degree: MS, Biostatistics, 2014, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/444458/rec/1226
► Hepatocellular carcinoma (HCC), which we can also call malignant hepatoma, is a primary liver cancer and a major cause of cancer morbidity and mortality all…
(more)
▼ Hepatocellular carcinoma (HCC), which we can also call
malignant hepatoma, is a primary liver cancer and a major cause of
cancer morbidity and mortality all over the world. According to
Zhang Y, Li J, Cao L, Xu W, and Yin Z (2012), circulating tumor
cells (CTCs) reflect the information of HCC metastasis or
recurrence. This makes CTC as a useful biomarker of HCC. The
popular standard method based on immunomagnetic binding of
epithelial cell adhesion molecules (EpCAMs) cannot be used to
collect CTC of HCC because HCC cells rarely express EpCAM. However,
Dr. Amir Goldkorn solved this problem by developing a parylene–C
slot microfilter platform. So a total of 170 HCC patients are
planned to be recruited to analyze CTC in HCC. For now, only 93
patients are enrolled to this program and the study is still in
process. The hypothesis in this study to be tested are (1) Patients
with advanced disease stage will have more CTCs. (2) The numbers of
CTC are decreased after treatment.
Advisors/Committee Members: Gauderman, William James (Committee Chair), Groshen, Susan L. (Committee Member), Stram, Daniel O. (Committee Member).
Subjects/Keywords: HCC; CTC
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APA (6th Edition):
Dong, C. (2014). Capture and analysis of circulating tumor cells in patients
with hepatocellular carcinoma: analysis of a pilot study. (Masters Thesis). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/444458/rec/1226
Chicago Manual of Style (16th Edition):
Dong, Cheng. “Capture and analysis of circulating tumor cells in patients
with hepatocellular carcinoma: analysis of a pilot study.” 2014. Masters Thesis, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/444458/rec/1226.
MLA Handbook (7th Edition):
Dong, Cheng. “Capture and analysis of circulating tumor cells in patients
with hepatocellular carcinoma: analysis of a pilot study.” 2014. Web. 02 Mar 2021.
Vancouver:
Dong C. Capture and analysis of circulating tumor cells in patients
with hepatocellular carcinoma: analysis of a pilot study. [Internet] [Masters thesis]. University of Southern California; 2014. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/444458/rec/1226.
Council of Science Editors:
Dong C. Capture and analysis of circulating tumor cells in patients
with hepatocellular carcinoma: analysis of a pilot study. [Masters Thesis]. University of Southern California; 2014. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/444458/rec/1226

University of Southern California
3.
Weaver, Garrett M.
Disparities in exposure to traffic-related pollution sources
by self-identified and ancestral Hispanic descent in participants
of the USC Children’s Health Study.
Degree: MS, Applied Biostatistics and Epidemiology, 2014, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/439655/rec/2040
► Significant evidence has accrued that air pollution negatively impacts respiratory health and other health outcomes. The USC Children’s Health Study has also demonstrated a link…
(more)
▼ Significant evidence has accrued that air pollution
negatively impacts respiratory health and other health outcomes.
The USC Children’s Health Study has also demonstrated a link
between increasing levels of air pollution, at both regional and
local levels, and reductions in lung development in children.
Within Los Angeles and other large urban cities, studies have
investigated whether air pollution exposure differs by ethnicity.
Preliminary results from these studies suggest that certain ethnic
groups, such as Hispanics, may be exposed to higher levels of air
pollution compared to non‐Hispanics. We aim to further determine
whether a disparity exists in local air pollution exposure between
Hispanic white (HW) and non‐Hispanic white (NHW) children of
Southern California. Among Hispanic white children, we also intend
to test whether children with a higher percentage of Native
American are more exposed to local air pollution sources as well. ❧
From the Children’s Health Study cohort, we identified 4,279 NHW
and 4,138 HW children with sufficient data to calculate local
pollution exposure levels. Among this sample, 2,571 NHW and 2,767
HW children had genetic ancestry data available as well. Multiple
linear regression and logistic regression were used to test the
association between Hispanic‐descent and two measures of local air
pollution, distance from freeways/major roadways (m) and Caline4
predicted estimates of NOx levels (ppb). Differences between the
groups were determined both in the overall sample and within each
of the 14 communities at baseline entry into their respective
cohorts. ❧ HW children were found to live, on average, 139 m closer
to freeways and 55 m closer to major non‐freeway roads in the
overall sample compared to NHW children (p < 0.0001).
Additionally, HW children with 50% or more Native American ancestry
(More-NA HW) lived 244 m closer to freeways compared to NHW
children (p < 0.0001) and 143 m closer to freeways than Hispanic
White children with less than 50% Native American ancestry (Less-NA
HW) (p = 0.003). For major non‐freeway roads, More‐NA HW live 89 m
and 44 m closer to a major road compared to HW children and Less‐NA
HW, respectively. Based on the secondary outcome measure, HW
children had an estimated freeway Caline4 estimates that are 13%
(95% CI: 8%-17%) higher than NHW children. The major non‐freeway
road NOx exposure is also estimated to be 16% (95% CI: 12%-19%)
higher in HW children compared to NHW children. Among children with
ancestry data, freeway Caline4 estimates were 20% and 14% higher
for More‐NA HW compared to NHW children (p < 0.0001) and Less‐NA
HW (p < 0.0001), respectively. Additionally, major non‐freeway
road Caline4 estimates were 27% and 14% higher for More‐NA HW
compared to NHW children (p < 0.0001) and Less‐NA HW (p =
0.0001), respectively. Lastly, the odds of HW children being within
500 m of a freeway or 75 m of major non‐freeway road is 1.34 (95%
CI: 1.18–1.51) and 1.39 (95% CI: 1.21–1.58) times that NHW
children, respectively. Within HW, the odds of those with…
Advisors/Committee Members: Gauderman, William James (Committee Chair), Berhane, Kiros T. (Committee Member), McConnell, Rob (Committee Member).
Subjects/Keywords: freeway; Hispanic; Latino; Native American; pollution; traffic; ancestry; genetic
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Weaver, G. M. (2014). Disparities in exposure to traffic-related pollution sources
by self-identified and ancestral Hispanic descent in participants
of the USC Children’s Health Study. (Masters Thesis). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/439655/rec/2040
Chicago Manual of Style (16th Edition):
Weaver, Garrett M. “Disparities in exposure to traffic-related pollution sources
by self-identified and ancestral Hispanic descent in participants
of the USC Children’s Health Study.” 2014. Masters Thesis, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/439655/rec/2040.
MLA Handbook (7th Edition):
Weaver, Garrett M. “Disparities in exposure to traffic-related pollution sources
by self-identified and ancestral Hispanic descent in participants
of the USC Children’s Health Study.” 2014. Web. 02 Mar 2021.
Vancouver:
Weaver GM. Disparities in exposure to traffic-related pollution sources
by self-identified and ancestral Hispanic descent in participants
of the USC Children’s Health Study. [Internet] [Masters thesis]. University of Southern California; 2014. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/439655/rec/2040.
Council of Science Editors:
Weaver GM. Disparities in exposure to traffic-related pollution sources
by self-identified and ancestral Hispanic descent in participants
of the USC Children’s Health Study. [Masters Thesis]. University of Southern California; 2014. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/439655/rec/2040

University of Southern California
4.
Chiam, Jenn Rong.
Association testing of polymorphisms in the vitamin D
metabolism and signaling pathway with multiple sclerosis across
multiple populatuions.
Degree: MS, Biostatistics, 2012, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/42097/rec/966
► min D is an environmental factor known to protect against multiple sclerosis (MS). Furthermore, it has also been shown to influence activities of immunological genes…
(more)
▼ min D is an environmental factor known to protect
against multiple sclerosis (MS). Furthermore, it has also been
shown to influence activities of immunological genes such as the
HLA-DRB1*1501, which have found to be associated with this
autoimmune disease. Genes controlling the metabolism and signaling
functions of vitamin D are also likely to be MS susceptibility
regions. ❧ In this thesis, we examined the association between nine
genes of the vitamin D pathway and MS. The functional relevance of
significantly identified single nucleotide polymorphisms (SNPs) as
they contribute to MS was also explored. After conducting a
meta-analysis, we found rs928329 from CYP27B1 to be significantly
associated with MS (meta p < 0.0002) while all other vitamin D
genes did not yield significant associations. ❧ Significant
interactions between RXRB and HLA-DRB1*1501 identified in this
thesis indicate the importance of complex gene-gene interaction in
MS. Given the importance of vitamin D as an immune-regulator and
the important role of immunity in MS, future investigation of
interaction between vitamin D and other immune-related genes will
likely reveal important biological mechanisms that cause
MS.
Advisors/Committee Members: Mack, Thomas M. (Committee Chair), Gauderman, William James (Committee Member), Islam, Talat (Committee Member).
Subjects/Keywords: multiple sclerosis; vitamin d genes; CYP27B1
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
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APA (6th Edition):
Chiam, J. R. (2012). Association testing of polymorphisms in the vitamin D
metabolism and signaling pathway with multiple sclerosis across
multiple populatuions. (Masters Thesis). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/42097/rec/966
Chicago Manual of Style (16th Edition):
Chiam, Jenn Rong. “Association testing of polymorphisms in the vitamin D
metabolism and signaling pathway with multiple sclerosis across
multiple populatuions.” 2012. Masters Thesis, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/42097/rec/966.
MLA Handbook (7th Edition):
Chiam, Jenn Rong. “Association testing of polymorphisms in the vitamin D
metabolism and signaling pathway with multiple sclerosis across
multiple populatuions.” 2012. Web. 02 Mar 2021.
Vancouver:
Chiam JR. Association testing of polymorphisms in the vitamin D
metabolism and signaling pathway with multiple sclerosis across
multiple populatuions. [Internet] [Masters thesis]. University of Southern California; 2012. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/42097/rec/966.
Council of Science Editors:
Chiam JR. Association testing of polymorphisms in the vitamin D
metabolism and signaling pathway with multiple sclerosis across
multiple populatuions. [Masters Thesis]. University of Southern California; 2012. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/42097/rec/966

University of Southern California
5.
Lin, Pi-Chu Kaylene.
Genetic variation in inducible nitric oxide synthase
promoter, residential traffic related air pollution and exhaled
nitric oxide in children.
Degree: MS, Applied Biostatistics and Epidemiology, 2013, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/303576/rec/3012
► Background: Fractional concentration of nitric oxide in exhaled air (FeNO) is a biomarker of airway inflammation. Nitric oxide synthase 2 (NOS2) in airway epithelium has…
(more)
▼ Background: Fractional concentration of nitric oxide
in exhaled air (FeNO) is a biomarker of airway inflammation. Nitric
oxide synthase 2 (NOS2) in airway epithelium has been recognized as
the major source of NO in exhaled breath. Earlier work has shown
that common promoter haplotypes in NOS2 and total length of local
roads around homes, a metric of residential traffic related
pollution, affect FeNO level in children. ❧ Aims: The aims of this
study were to examine the joint associations of NOS2 promoter
haplotypes and length of local roads around homes and FeNO and to
assess the influence of asthma on these associations in children. ❧
Methods: The study included 2,457 (7 to 11 year-old) children of
the
Southern California Children’s Health Study. FeNO was measured
at school during 2005-2006. Lengths of local roads within circular
buffers (50m, 100m and 200m) around the participant residence were
estimated using GIS methods. Two common promoter haplotypes in NOS2
that have been associated with FeNO, asthma and lung function
growth in children were selected. Linear regression was utilized to
examine the independent and joint associations of NOS2 promoter
haplotypes and road length measures on FeNO. ❧ Results: We observed
joint effects of length of local roads within 100m and 200m buffer
and the most common haplotype for FeNO (P-values for interaction
≤0.03). In children who had ≤250m of road within 100m buffer around
home, those with two copies of the haplotype had significantly
lower FeNO (adjusted mean FeNO=10.71ppb; 95% confidence intervals
(CI): 9.10-12.61) than those with no copies (adjusted mean FeNO
14.18ppb; 95% CI: 13.09-15.36). This protective effect of the
haplotype was not observed in children who had >250m road
lengths within 100m buffer. Similar joint effects of this haplotype
and road lengths within 200m buffer on FeNO was observed. These
joint effects were not influenced by asthma. ❧ Conclusion: Our
results indicate that the protective effect of a common NOS2
promoter haplotype on NO synthesis in the airway is not evident in
children who live near higher levels of local
traffic.
Advisors/Committee Members: Gilliland, Frank D. (Committee Chair), Salam, Md. Towhid (Committee Member), Gauderman, William James (Committee Member).
Subjects/Keywords: CHS; Children’ s Health Study; FeNO; fractional concentration of exhaled nitric oxide; htSNP; haplotype-tagging single nucleotide polymorphism; iNOS; inducible nitric oxide synthase; NO; nitric oxide; NO2; nitrogen dioxide; NOS2; nitric oxide synthase isoform 2; ROS; reactive oxygen species; SNP; single nucleotide polymorphism; TRP; traffic related pollution
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Lin, P. K. (2013). Genetic variation in inducible nitric oxide synthase
promoter, residential traffic related air pollution and exhaled
nitric oxide in children. (Masters Thesis). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/303576/rec/3012
Chicago Manual of Style (16th Edition):
Lin, Pi-Chu Kaylene. “Genetic variation in inducible nitric oxide synthase
promoter, residential traffic related air pollution and exhaled
nitric oxide in children.” 2013. Masters Thesis, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/303576/rec/3012.
MLA Handbook (7th Edition):
Lin, Pi-Chu Kaylene. “Genetic variation in inducible nitric oxide synthase
promoter, residential traffic related air pollution and exhaled
nitric oxide in children.” 2013. Web. 02 Mar 2021.
Vancouver:
Lin PK. Genetic variation in inducible nitric oxide synthase
promoter, residential traffic related air pollution and exhaled
nitric oxide in children. [Internet] [Masters thesis]. University of Southern California; 2013. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/303576/rec/3012.
Council of Science Editors:
Lin PK. Genetic variation in inducible nitric oxide synthase
promoter, residential traffic related air pollution and exhaled
nitric oxide in children. [Masters Thesis]. University of Southern California; 2013. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/303576/rec/3012

University of Southern California
6.
Park, Caron.
DNA methylation of NOS genes and carotid intima-media
thickness in children.
Degree: MS, Biostatistics, 2012, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/207627/rec/2073
► Carotid intima-media thickness, a biomarker for atherosclerosis, is associated with cardiovascular disease risk in adults. Atherosclerosis is a lifelong process that begins in childhood. Nitric…
(more)
▼ Carotid intima-media thickness, a biomarker for
atherosclerosis, is associated with cardiovascular disease risk in
adults. Atherosclerosis is a lifelong process that begins in
childhood. Nitric Oxide (NO) plays an important role in
cardiovascular health by maintaining and regulating vascular tone
and blood flow. It remains unclear as to how the epigenetic
regulation of nitric oxide synthase, the gene responsible for
nitric oxide production, affects carotid intima-media thickness
(CIMT) in children. Data from a subset of 377 participants from the
Children’s Health Study on whom buccal cell DNA and CIMT
measurements were collected were analyzed to determine whether DNA
methylation in NOS genes was associated with CIMT. Results showed
that an increase in DNA methylation of NOS1 was significantly
associated with an increase in CIMT measurements in children. Our
study suggests that DNA methylation of NOS genes is associated with
CIMT in children, which may help to advance the understanding of
biological processes contributing to atherosclerosis even at an
early age.
Advisors/Committee Members: Breton, Carrie (Committee Chair), Gauderman, William James (Committee Member), Siegmund, Kimberly D. (Committee Member).
Subjects/Keywords: CIMT; DNA methylation; nitric oxide synthase
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Park, C. (2012). DNA methylation of NOS genes and carotid intima-media
thickness in children. (Masters Thesis). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/207627/rec/2073
Chicago Manual of Style (16th Edition):
Park, Caron. “DNA methylation of NOS genes and carotid intima-media
thickness in children.” 2012. Masters Thesis, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/207627/rec/2073.
MLA Handbook (7th Edition):
Park, Caron. “DNA methylation of NOS genes and carotid intima-media
thickness in children.” 2012. Web. 02 Mar 2021.
Vancouver:
Park C. DNA methylation of NOS genes and carotid intima-media
thickness in children. [Internet] [Masters thesis]. University of Southern California; 2012. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/207627/rec/2073.
Council of Science Editors:
Park C. DNA methylation of NOS genes and carotid intima-media
thickness in children. [Masters Thesis]. University of Southern California; 2012. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/207627/rec/2073

University of Southern California
7.
Sturgeon, Julia D.
Fish consumption and risk of colorectal cancer.
Degree: MS, Applied Biostatistics and Epidemiology, 2015, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/601425/rec/2826
► The association between fish consumption and risk of colorectal cancer was investigated in a population-based, incidence density case control study from northern Israel, the Molecular…
(more)
▼ The association between fish consumption and risk of
colorectal cancer was investigated in a population-based, incidence
density case control study from northern Israel, the Molecular
Epidemiology of Colorectal Cancer study. Food frequency
questionnaire data were used from 1,869 cases and 1,777 controls
ascertained and recruited between March 31, 1998 and February 14,
2005. Questionnaire data included three specific fish categories:
canned tuna, mackerel/salmon/sardines, and cooked/fried fish.
Multivariate unconditional logistic regression was used to assess
the association between each fish consumption variable and risk of
colorectal cancer. After adjusting for age, sex, and ethnicity
consumption of canned tuna was associated with reduced risk of
colorectal cancer. Participants who consumed canned tuna had an 18%
reduced risk of colorectal cancer compared to those who never
consumed canned tuna (odds ratio, 0.82; 95% confidence interval,
[0.71, 0.94]). Comparing the highest tertile of fish consumption
(1+ serving/week) to the lowest tertile of fish consumption (0
servings/month), canned tuna was associated with a 24% reduction of
colorectal cancer risk. Adjusting known risk factors and potential
confounders, consumption of mackerel/salmon/sardines was associated
with a 27% reduced risk of colorectal cancer when comparing the
highest and lowest tertiles of consumption (1+ serving/week vs. 0
servings/month). Consumption of cooked/fried fish was not
associated with risk of colorectal cancer at any level of
consumption. Data from this planned interim analysis suggest that
diets characterized by the consumption of canned tuna as well as
mackerel, salmon, and sardines are associated with reduced risk of
colorectal cancer. Cooked and fried fish consumption was not
associated with risk of colorectal cancer. This finding is
consistent with animal studies that have examined the association
between omega-3 fatty acids and colon tumor growth, indicating that
omega-3 fatty acids inhibit colon carcinogenesis.
Advisors/Committee Members: Gruber, Stephen B. (Committee Chair), Stern, Mariana C. (Committee Member), Gauderman, William James (Committee Member).
Subjects/Keywords: colorectal cancer; fish
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Sturgeon, J. D. (2015). Fish consumption and risk of colorectal cancer. (Masters Thesis). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/601425/rec/2826
Chicago Manual of Style (16th Edition):
Sturgeon, Julia D. “Fish consumption and risk of colorectal cancer.” 2015. Masters Thesis, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/601425/rec/2826.
MLA Handbook (7th Edition):
Sturgeon, Julia D. “Fish consumption and risk of colorectal cancer.” 2015. Web. 02 Mar 2021.
Vancouver:
Sturgeon JD. Fish consumption and risk of colorectal cancer. [Internet] [Masters thesis]. University of Southern California; 2015. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/601425/rec/2826.
Council of Science Editors:
Sturgeon JD. Fish consumption and risk of colorectal cancer. [Masters Thesis]. University of Southern California; 2015. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/601425/rec/2826

University of Southern California
8.
Chang, Chih-Chieh.
Bayesian multilevel quantile regression for longitudinal
data.
Degree: PhD, Biostatistics, 2015, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/532589/rec/1043
► Conventional mixed effects regression focuses only on effects on the conditional mean, which may be inappropriate when the interest is in testing the effects on…
(more)
▼ Conventional mixed effects regression focuses only on
effects on the conditional mean, which may be inappropriate when
the interest is in testing the effects on extremes of the outcome
distribution (e.g. BMI at the 85th percentile). We propose a
multilevel quantile regression model with errors following the
Asymmetric Laplace Distribution with a data-driven skew parameter
under a Bayesian framework. Using our approach, the estimates of
parameters would be unbiased regardless of the structure of random
errors. This approach allows 1)direct modeling of risk effects with
higher accuracy, 2)characterizing inter-subject heterogeneity,
3)accounting for cross-level effects, and 4)modeling non-linear
growth trajectories in longitudinal/multi-level data. Besides
deriving analytic solutions with improved properties, we conducted
simulations to show that our proposed approach consistently
provided appropriate estimates at extreme percentiles even when
dealing with heteroscedastic errors, and multiple random effects
from various levels. We illustrate the new approach through
analysis of longitudinal BMI to model determinants of overweight
status based on data from the Children's Health
Study.
Advisors/Committee Members: Berhane, Kiros T. (Committee Chair), Gauderman, William James (Committee Member), Conti, David V. (Committee Member), McConnell, Rob (Committee Member), Fan, Yingying (Committee Member).
Subjects/Keywords: Bayesian; multilevel modeling; mixed-effect modeling; quantile regression; longitudinal data; childhood obesity
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Chang, C. (2015). Bayesian multilevel quantile regression for longitudinal
data. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/532589/rec/1043
Chicago Manual of Style (16th Edition):
Chang, Chih-Chieh. “Bayesian multilevel quantile regression for longitudinal
data.” 2015. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/532589/rec/1043.
MLA Handbook (7th Edition):
Chang, Chih-Chieh. “Bayesian multilevel quantile regression for longitudinal
data.” 2015. Web. 02 Mar 2021.
Vancouver:
Chang C. Bayesian multilevel quantile regression for longitudinal
data. [Internet] [Doctoral dissertation]. University of Southern California; 2015. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/532589/rec/1043.
Council of Science Editors:
Chang C. Bayesian multilevel quantile regression for longitudinal
data. [Doctoral Dissertation]. University of Southern California; 2015. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/532589/rec/1043

University of Southern California
9.
He, Jing.
Polygenes and estimated heritability of prostate cancer in
an African American sample using genome-wide association study
data.
Degree: PhD, Biostatistics, 2013, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/319645/rec/5104
► Background: Validated SNPs in genome-wide association studies (GWAS) account for only a small fraction of the variation in human complex traits. Methods: We applied score…
(more)
▼ Background: Validated SNPs in genome-wide association
studies (GWAS) account for only a small fraction of the variation
in human complex traits. Methods: We applied score analysis to 6957
not closely related individuals in African American prostate cancer
(AAPC) GWAS to see whether common variants have an important role
en masse; we estimated the narrow sense heritability of prostate
cancer explained by 316,735 genotyped GWAS SNPs using a linear
mixed model (Yang et al). We simulated genotypes and phenotypes
with low degree of correlation to evaluate how the estimates from
score analysis and linear mixed model are influenced by distant
relatedness among individuals. Results: Score analyses provided
evidences for a substantial polygenic component to the prostate
cancer risk; the narrow sense heritability of prostate cancer in
African Americans was estimated to be 30% by utilizing 316,735 GWAS
SNPs in linear mixed model. In the simulation studies, the narrow
sense heritability estimates were biased up by inclusion of
non-causal SNPs that are associated with distant relatedness.
Conclusion: The narrow sense heritability estimate from linear
mixed model may be an overestimate of the genetic contribution of
the specific set of measured GWAS SNPs and is closer to the overall
narrow sense heritability. Impact: It is important to clarify what
the estimates are telling us because where the phenotypic variation
lays will give hints on the future direction of genetic association
studies.
Advisors/Committee Members: Stram, Daniel O. (Committee Chair), Haiman, Christopher A. (Committee Member), Gauderman, William James (Committee Member), Coetzee, Gerhard (Gerry) A. (Committee Member).
Subjects/Keywords: heritability; GWAS; prostate cancer; population stratification
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
He, J. (2013). Polygenes and estimated heritability of prostate cancer in
an African American sample using genome-wide association study
data. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/319645/rec/5104
Chicago Manual of Style (16th Edition):
He, Jing. “Polygenes and estimated heritability of prostate cancer in
an African American sample using genome-wide association study
data.” 2013. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/319645/rec/5104.
MLA Handbook (7th Edition):
He, Jing. “Polygenes and estimated heritability of prostate cancer in
an African American sample using genome-wide association study
data.” 2013. Web. 02 Mar 2021.
Vancouver:
He J. Polygenes and estimated heritability of prostate cancer in
an African American sample using genome-wide association study
data. [Internet] [Doctoral dissertation]. University of Southern California; 2013. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/319645/rec/5104.
Council of Science Editors:
He J. Polygenes and estimated heritability of prostate cancer in
an African American sample using genome-wide association study
data. [Doctoral Dissertation]. University of Southern California; 2013. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/319645/rec/5104

University of Southern California
10.
Shu, (Allen) Yu-Hsiang.
Pathway-based analysis of multivariate traits using
classical dimensionality reduction methods.
Degree: PhD, Statistical Genetics and Genetic
Epidemiology, 2015, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/528610/rec/4954
► Dimensionality reduction methods (DRMs) can capture important information of the data with fewer components, and testing those components can improve power in association testing. My…
(more)
▼ Dimensionality reduction methods (DRMs) can capture
important information of the data with fewer components, and
testing those components can improve power in association testing.
My work compared three classical DRMs: principal components
analysis (PCA), partial least squares (PLS), and canonical
correlations analysis (CCA), and demonstrated their power advantage
for testing genetic associations between multiple genes and
multiple quantitative traits. I found that the PCA-based approach
is not as powerful as generally recognized. When the covariance of
genetic markers and traits are not (or less) related to the
correlations between them, PCA-based approaches showed relatively
poor power in the simulations. Theoretical insights and the
supportive evidence from the simulation results indicated testing
CCA components has the best performance in joint association tests
among all three DRMs. CCA-based approach and multivariate multiple
regression both showed good power in the scenarios of correlated
genetic markers and correlated traits, and the power performance is
sensitive to the magnitude and direction of the correlations. Based
on the findings, I applied an adaptation method motivated by the
Adaptive Rank Truncated Product (ARTP) for addressing the issue of
selecting CCA components in order to achieve optimal power. The
same settings of simulations were followed, and I concluded that
adaptive CCA-based approach (ACCA) is a powerful association
testing approach for pathway-based analysis.
Advisors/Committee Members: Watanabe, Richard M.Lewinger, Juan Pablo (Committee Chair), Gauderman, William James (Committee Member), Buchanan, Thomas A. (Committee Member).
Subjects/Keywords: pathway-based analysis; dimensionality reduction; permutation test
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Shu, (. Y. (2015). Pathway-based analysis of multivariate traits using
classical dimensionality reduction methods. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/528610/rec/4954
Chicago Manual of Style (16th Edition):
Shu, (Allen) Yu-Hsiang. “Pathway-based analysis of multivariate traits using
classical dimensionality reduction methods.” 2015. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/528610/rec/4954.
MLA Handbook (7th Edition):
Shu, (Allen) Yu-Hsiang. “Pathway-based analysis of multivariate traits using
classical dimensionality reduction methods.” 2015. Web. 02 Mar 2021.
Vancouver:
Shu (Y. Pathway-based analysis of multivariate traits using
classical dimensionality reduction methods. [Internet] [Doctoral dissertation]. University of Southern California; 2015. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/528610/rec/4954.
Council of Science Editors:
Shu (Y. Pathway-based analysis of multivariate traits using
classical dimensionality reduction methods. [Doctoral Dissertation]. University of Southern California; 2015. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/528610/rec/4954

University of Southern California
11.
Choudhury, Farzana.
Age related macular degeneration in Latinos: risk factors
and impact on quality of life.
Degree: PhD, Epidemiology, 2012, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/105256/rec/580
► Age related macular degeneration (AMD) is a progressive, potentially irreversible disorder of the macular region of retina that can cause severe loss of central vision…
(more)
▼ Age related macular degeneration (AMD) is a
progressive, potentially irreversible disorder of the macular
region of retina that can cause severe loss of central vision in
the late stages. Despite the recent advances in the treatment of
AMD, it remains the leading cause of blindness in people over the
age of 60 in the Western world with significant impact on their
health related quality of life (HRQoL). The global prevalence of
AMD remains largely unknown and the full impact of this
debilitating disease has not been fully characterized. ❧ The
relationship between factors influencing incidence and progression
of AMD in Latinos and the impact of AMD on HRQoL in Latinos remain
largely unexplored. Therefore, to address these issues, I have used
the baseline and 4 years cumulative incidence data from the Los
Angeles Latino Eye Study (LALES), a population based cohort study
of eye disease in Latinos to investigate predictors of AMD
incidence and progression and the impact of AMD on HRQoL. In the
first chapter I gave an overview of AMD and my primary aims. I
discussed briefly about the retina, macula, the definition, brief
pathogenesis, grading scheme and classification of AMD. Then, I
discussed briefly about what is known about the risk factors of AMD
and its impact on HRQoL. Finally I describe the study population
and enumerate the primary aims. ❧ In my first paper (chapter 2) I
evaluated the risk factors associated with 4 year incidence and
progression of AMD. The risk factors were selected based on
literature review and expert clinical opinion. Stepwise logistic
regression was used to develop parsimonious multivariable
predictive models for each AMD end- points. The results from these
analyses revealed that older age and higher pulse pressure were
independently associated with the incidence of any AMD and
different early AMD lesions in this group of Latinos. Additionally,
presence of diabetes mellitus was independently associated with
increased retinal pigment and male gender was associated with
retinal pigment epithelial depigmentation. Older age and current
smoking were independently associated with progression of AMD. Some
of the findings were similar to those reported by studies in
non-Hispanic whites. The interesting and unique finding in this
paper was the association of pulse pressure with incidence of some
early maculopathies that were not previously reported in
Caucasians. Given the equivocal results for risk factors of AMD in
other population based studies and the paucity of data in Latinos,
these finding will aide in our understanding of AMD in this unique
ethnic group. ❧ The short term and long term impact of AMD on
quality of life in Latinos has not been investigated to a great
extent. Given the unique socio-demographic, ethnic and cultural
characteristics of Latinos it is important to estimate the impact
of the patient reported outcomes in this unique group of people.
Therefore, for my second paper I investigated the association of
prevalent AMD and HRQoL, described in the third chapter. Two
validated…
Advisors/Committee Members: Azen, Stanley P.McKean-Cowdin, Roberta (Committee Chair), Varma, Rohiti (Committee Member), Gauderman, William James (Committee Member), Nichol, Michael B. (Committee Member).
Subjects/Keywords: age related macular degeneration; Latinos; risk factors; quality of life
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Choudhury, F. (2012). Age related macular degeneration in Latinos: risk factors
and impact on quality of life. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/105256/rec/580
Chicago Manual of Style (16th Edition):
Choudhury, Farzana. “Age related macular degeneration in Latinos: risk factors
and impact on quality of life.” 2012. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/105256/rec/580.
MLA Handbook (7th Edition):
Choudhury, Farzana. “Age related macular degeneration in Latinos: risk factors
and impact on quality of life.” 2012. Web. 02 Mar 2021.
Vancouver:
Choudhury F. Age related macular degeneration in Latinos: risk factors
and impact on quality of life. [Internet] [Doctoral dissertation]. University of Southern California; 2012. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/105256/rec/580.
Council of Science Editors:
Choudhury F. Age related macular degeneration in Latinos: risk factors
and impact on quality of life. [Doctoral Dissertation]. University of Southern California; 2012. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/105256/rec/580

University of Southern California
12.
Urman, Robert.
Ambient air pollution and lung function in children.
Degree: PhD, Epidemiology, 2015, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/592394/rec/642
► The effect of air pollution on human health has long been a concern. The aim of this dissertation is to explore the negative impact of…
(more)
▼ The effect of air pollution on human health has long
been a concern. The aim of this dissertation is to explore the
negative impact of probable causal pollutants or pollutant mixtures
on respiratory health, with the focus mainly on the impacts of
local or near‐roadway air pollution and that of elemental
composition of particulate matter (PM) on lung function in children
and adolescence. In urbanized locations, such as the
Southern
California communities that constitute the Children’s Health Study
(CHS) and from which the population at focus in this dissertation
is derived, motorized vehicles contribute a significantly large
amount of the air pollution at both the local and regional scales.
Prior studies have reported adverse effects of either regional or
near‐roadway air pollution on lung function, but little has been
done of the joint effects of these exposures. In the first study,
analyses were conducted to assess the joint effects of these
exposures on childhood lung function in the CHS. Results indicate
that near‐roadway and regional air pollution have independent
adverse effects on childhood lung function. However, specific
components of the near‐roadway pollution mixture responsible for
these effects have not been established. A major limitation for
health studies is the lack of exposure models that estimate these
components observed in epidemiological studies over fine spatial
scale of tens to hundreds of meters. In the second study, exposure
models were developed for fine‐scale variation in biologically
relevant elemental carbon (EC). Models that included traffic
measures provided useful estimates for EC₀.₂ and EC₂.₅ on a spatial
scale appropriate for health studies of near-roadway pollution in
selected
Southern California communities. Moreover, numerous
studies have reported adverse effects of PM on lung function in
children, but there has been little investigation of the chronic
effects of PM composition. Transition metals are biologically
plausible agents contributing to these effects. Aerosol size and
water-solubility may be important determinants of metal toxicity.
In the third study, associations between lung development and
concentrations of PM and transition metals (copper [Cu], iron [Fe],
nickel [Ni], vanadium [V], and zinc [Zn]), in three size fractions
[quasi-ultrafine (
Advisors/Committee Members: McConnell, Rob (Committee Chair), Gauderman, William James (Committee Member), Gilliland, Frank D. (Committee Member), Fruin, Scott (Committee Member), Wilson, John P. (Committee Member).
Subjects/Keywords: air pollution; traffic; lung function; children
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Urman, R. (2015). Ambient air pollution and lung function in children. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/592394/rec/642
Chicago Manual of Style (16th Edition):
Urman, Robert. “Ambient air pollution and lung function in children.” 2015. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/592394/rec/642.
MLA Handbook (7th Edition):
Urman, Robert. “Ambient air pollution and lung function in children.” 2015. Web. 02 Mar 2021.
Vancouver:
Urman R. Ambient air pollution and lung function in children. [Internet] [Doctoral dissertation]. University of Southern California; 2015. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/592394/rec/642.
Council of Science Editors:
Urman R. Ambient air pollution and lung function in children. [Doctoral Dissertation]. University of Southern California; 2015. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/592394/rec/642

University of Southern California
13.
Dueker, Donna Carmel.
Evaluation of new methods for estimating exposure to
traffic-related pollution and early health effects for large
population epidemiological studies.
Degree: PhD, Epidemiology, 2012, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/17036/rec/2536
► Objective: There is emerging evidence that local traffic-related pollution (TRP) has adverse health effects that are independent of regional pollution effects. Current methods to assess…
(more)
▼ Objective: There is emerging evidence that local
traffic-related pollution (TRP) has adverse health effects that are
independent of regional pollution effects. Current methods to
assess TRP exposure have limitations that may account for
uncertainty and inconsistency in the observed traffic-related
health effects. New methods are needed to assess TRP exposure in
different microenvironments and to assess early biological effects
of these exposures in population based studies of air pollution. I
evaluated new tools that can be used to assess time and activity
and also evaluated the impact on novel biological markers of
exposure to TRP and biomarkers of early biological effects. ❧
Specifically the objectives of my research were: 1) to evaluate the
accuracy of a time-resolved step counter in children and the
duration of consecutive zero step count minutes that indicated
non-wear time periods 2) evaluate the ability of a GPS data logger
to assess location of children during usual activity and 3) to
assess feasibility of collecting urine samples at school and to
evaluate urinary biomarkers of exposure and early effect of
traffic-related air pollution. The overall goal of my research was
to identify methods that could greatly improve exposure assessments
of TRP by providing an integrated metric of dose that could be used
to strengthen studies investigating the relationship between TRP
exposure and health affects. ❧ Methods: To evaluate these tools, I
conducted two studies. In the first study, a new time-resolved step
counter, the SportBrain, was evaluated for accuracy. Seventeen
children walked or ran on a treadmill at 2, 3, 4 and 5 miles/hour
and walked around a track while wearing the SportBrain and
Digiwalker SW-701 pedometers. We compared percent error in step
counts for the two pedometers relative to observer counts. A
sub-sample wore an accelerometer and SportBrain pedometer during up
to 5 days of usual activity. In the second study, up to five urine
samples per child were collected before and after a school field
trip with bus travel on a busy highway from fifteen 9-10 year olds
recruited from two classrooms in a low pollution region of Los
Angeles. Samples were analyzed for biomarkers of exposure (ten
polycyclic aromatic hydrocarbon metabolites and 1-aminopyrene) and
of effect (Clara cell protein 16 and 8-iso-PGF2, a major
F2-isoprostane). Four days of data from 17 children wearing GPS
loggers recording every 15 seconds were evaluated for completeness
by time of day during weekend and weekdays and for accuracy during
nighttime at home. Percentage of possible GPS recorded points and
of 5-minute intervals with at least one recorded location were
examined. ❧ Results: The SportBrain pedometer performed with
acceptable accuracy at all evaluated treadmill speeds and during
self-paced walking, recording steps within an average of 4% of
observed step counts. During normal wear only 1% of zero count
periods were less than 60 minutes. 60% of participants collected
all five urine samples. There was no statistically…
Advisors/Committee Members: McConnell, Rob (Committee Chair), Gauderman, William James (Committee Member), Fruin, Scott (Committee Member), Cockburn, Myles (Committee Member), Wilson, John P. (Committee Member).
Subjects/Keywords: air pollution; time-activity; urinary biomarker; physical activity; GPS; pedometer; exposure assessment
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Dueker, D. C. (2012). Evaluation of new methods for estimating exposure to
traffic-related pollution and early health effects for large
population epidemiological studies. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/17036/rec/2536
Chicago Manual of Style (16th Edition):
Dueker, Donna Carmel. “Evaluation of new methods for estimating exposure to
traffic-related pollution and early health effects for large
population epidemiological studies.” 2012. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/17036/rec/2536.
MLA Handbook (7th Edition):
Dueker, Donna Carmel. “Evaluation of new methods for estimating exposure to
traffic-related pollution and early health effects for large
population epidemiological studies.” 2012. Web. 02 Mar 2021.
Vancouver:
Dueker DC. Evaluation of new methods for estimating exposure to
traffic-related pollution and early health effects for large
population epidemiological studies. [Internet] [Doctoral dissertation]. University of Southern California; 2012. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/17036/rec/2536.
Council of Science Editors:
Dueker DC. Evaluation of new methods for estimating exposure to
traffic-related pollution and early health effects for large
population epidemiological studies. [Doctoral Dissertation]. University of Southern California; 2012. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/17036/rec/2536

University of Southern California
14.
Wang, Shengzhi.
A genome wide association study of multiple sclerosis (MS)
in Hispanics.
Degree: MS, Biostatistics, 2013, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/290074/rec/209
► Genetic factors are postulated to contribute to the difference of susceptibility as well as clinical outcomes of multiple sclerosis (MS) in different populations. The Hispanic…
(more)
▼ Genetic factors are postulated to contribute to the
difference of susceptibility as well as clinical outcomes of
multiple sclerosis (MS) in different populations. The Hispanic
population offers a unique potential to identify novel genetic
variants involved in differential disease presentation of MS (e.g.
the site of lesions in the central nervous system, opticospinal
(OSMS) vs classical MS) due to the genetic diversities in this
admixed population. While MS overall is more common in Whites of
European ancestry, if and how the heterogeneity of genetic
admixture in Hispanics contributes to characteristics of the
disease is unknown. ❧ Methods: 127 Hispanics with MS were genotyped
and their global ancestries were estimated. They were then
classified into either classical MS or OSMS based on clinical and
radiological assessment. For statistical testing of the association
of genetic ancestry to OSMS vs. classical MS and to clinical
characteristics, linear regression or t-tests were used for
continuous outcomes and logistic regression or chi-square tests
were used for binary outcomes. For the genome-wide investigation of
SNP associations, logistic regression was used with adjustment by
age, gender and global ancestry to control for potential
confounding due to population admixture. The Wald test is used to
determine the statistical significance. ❧ Results: For the 142 MS
patients participated in the study, Asian characteristic of the
disease, such as OSMS was noted in 25 patients (17.6% of total
patients) while classical MS was observed in 102 patients (71.8% of
the total patients). There was no significant difference of age,
gender, ethnicity, migration history, age at diagnosis or disease
duration between OSMS and classical MS patients. However, increased
disability was significantly noted in OSMS patients (Mean score of
disability measurement ±SD, 4.64±2.05) as compared to classical MS
patients (2.47±1.92) (p=3.0e-05). In addition, age at the first
symptom onset is significantly younger in OSMS (26.36±11.6)
compared with classical MS (31.47±11.9) (p=0.057). Interestingly,
the migration history of the patients (early migration vs late
migration) as well as their neurological disability severity (EDSS
score) are statistically significant associated with the risk of
OSMS as compared to classical MS (odds ratio=3.63, p value=0.055
for migration history and odds ratio=1.99, p value
Advisors/Committee Members: Conti, David V. (Committee Chair), Gauderman, William James (Committee Member), Cozen, Wendy (Committee Member), Amezcua, Lilyana (Committee Member).
Subjects/Keywords: multiple sclerosis; genome wide association study; Hispanics; logistic regression
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Wang, S. (2013). A genome wide association study of multiple sclerosis (MS)
in Hispanics. (Masters Thesis). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/290074/rec/209
Chicago Manual of Style (16th Edition):
Wang, Shengzhi. “A genome wide association study of multiple sclerosis (MS)
in Hispanics.” 2013. Masters Thesis, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/290074/rec/209.
MLA Handbook (7th Edition):
Wang, Shengzhi. “A genome wide association study of multiple sclerosis (MS)
in Hispanics.” 2013. Web. 02 Mar 2021.
Vancouver:
Wang S. A genome wide association study of multiple sclerosis (MS)
in Hispanics. [Internet] [Masters thesis]. University of Southern California; 2013. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/290074/rec/209.
Council of Science Editors:
Wang S. A genome wide association study of multiple sclerosis (MS)
in Hispanics. [Masters Thesis]. University of Southern California; 2013. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/290074/rec/209

University of Southern California
15.
Kuroki, Yusuke.
Identifying diverse pathways to cognitive decline in later
life using genetic and environmental factors.
Degree: PhD, Psychology, 2014, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/438231/rec/3333
► The ε4 allele of the apolipoprotein E is associated with dementia. However, ε4 is neither necessary nor sufficient to cause dementia and leaves much of…
(more)
▼ The ε4 allele of the apolipoprotein E is associated
with dementia. However, ε4 is neither necessary nor sufficient to
cause dementia and leaves much of variability in dementia
unexplained. One possible reason for unexplained variability is
gene‐environment (G × E) interactions. Are there lifestyle factors
that can moderate the effect of APOE ε4 on memory? To address this
question, two analytical approaches were proposed. First, the
gene‐environment interaction on episodic memory was examined using
the structural equation modeling (SEM). Specifically, the present
study asked, “Does the effect of the ε4 on memory vary by
education, job authority, or physical activity?” Second, an
innovative exploratory technique called structural equation model
tree (SEM Trees; Brandmaier, von Oertzen, McArdle, &
Lindenberger, 2013) was used. Data from the Wisconsin Longitudinal
Study were used. Memory was assessed with immediate recall, delayed
recall and digit ordering. Results of SEM (n = 10,317) showed that
APOE ε4, education, job authority and physical activity affected
memory; however, education, job authority or physical activity did
not moderate the effect of APOE ε4 on memory. Results of SEM Trees
(n = 4569) showed that gender, IQ, literacy use at work,
personality, smoking, and four genetic polymorphisms in APOC3,
DRD2, CH25H, and SSADH produced complex interactions and influenced
memory decline in late life. However, the influences of genetic
variants on memory were subtle. This study also demonstrates the
utility of SEM Trees as a powerful technique for exploring the data
within a theoretical context.
Advisors/Committee Members: McArdle, John J. (Committee Chair), John, Richard S. (Committee Member), Zelinski, Elizabeth M. (Committee Member), Gauderman, William James (Committee Member).
Subjects/Keywords: structural equation models; gene‐environment interaction; data‐mining; aging; episodic memory
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APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Kuroki, Y. (2014). Identifying diverse pathways to cognitive decline in later
life using genetic and environmental factors. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/438231/rec/3333
Chicago Manual of Style (16th Edition):
Kuroki, Yusuke. “Identifying diverse pathways to cognitive decline in later
life using genetic and environmental factors.” 2014. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/438231/rec/3333.
MLA Handbook (7th Edition):
Kuroki, Yusuke. “Identifying diverse pathways to cognitive decline in later
life using genetic and environmental factors.” 2014. Web. 02 Mar 2021.
Vancouver:
Kuroki Y. Identifying diverse pathways to cognitive decline in later
life using genetic and environmental factors. [Internet] [Doctoral dissertation]. University of Southern California; 2014. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/438231/rec/3333.
Council of Science Editors:
Kuroki Y. Identifying diverse pathways to cognitive decline in later
life using genetic and environmental factors. [Doctoral Dissertation]. University of Southern California; 2014. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/438231/rec/3333

University of Southern California
16.
Hwang, Amie Eunah.
Early childhood health experience & adult phenotype in
twins.
Degree: PhD, Epidemiology, 2012, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/5262/rec/2144
► Childhood health experience may have a long term effects lasting into adulthood. Childhood infections have an etiologic role in the development of cancers and chronic…
(more)
▼ Childhood health experience may have a long term
effects lasting into adulthood. Childhood infections have an
etiologic role in the development of cancers and chronic diseases.
For example, Epstein Barr virus (EBV) and Helicobactor pylori are
well established causes of EBV-positive Hodgkin’s lymphoma and
stomach cancer, respectively. Height has also been commonly
associated with many cancers and other chronic conditions. It is
usually interpreted as a proxy for childhood socioeconomic status
or nutrition. However the effect of height on diseases has been
consistently reported independent of the effects of childhood
socioeconomic status and diet, suggesting height may represent
other underlying biological mechanisms. Studies examining childhood
experiences are challenging due to unreliable recall by study
participants and the unavailability and incomplete of medical
records. ❧ Twins offer unique advantages for studying childhood
health experience because they can provide relative differences in
exposure, they can validate each other’s answers, and they are
either partially or entirely matched on genome. This dissertation
consists of several projects examining childhood health in which
twins identified from the
California Twin Program were the
participants. For two of the studies, both young adult twins and
their mothers were interviewed, providing consistent and reliable
information pertaining to the twins’ childhood illness history. In
a descriptive study, comparing responses from mothers and twins
about childhood exposures, I found all subjects were able to
provide the most information on differences between the twins when
questions were framed in a comparative fashion with ordinal
answers. Although the number of pairs reporting differences in
exposures was small, their answers were generally consistent with
their mothers. ❧ Infectious mononucleosis, a disease caused by a
delayed infection of EBV, is associated with EBV positive Hodgkin’s
lymphoma and multiple sclerosis. I conducted a heritability study
in monozygotic and dizygotic twins and found evidence suggesting a
genetic component in the development of infectious mononucleosis. ❧
The effect of childhood illnesses on adult height was assessed in
healthy identical twins differing in height as adults, to control
for genetic factors, childhood socioeconomic status and parental
exposures. The twin who reported more frequent episodes of febrile
illnesses was twice as likely to become the shorter twin as an
adult. This effect was consistent after adjusting for birth weight
and birth height and was strongest and most significant during
toddler years (1-5 years of age). ❧ In conclusion, these studies
suggest that childhood illnesses are a determinant of adult height.
In the future, these findings can be applied to elucidate the
relationship between childhood infections and adult
diseases.
Advisors/Committee Members: Cozen, Wendy (Committee Chair), Mack, Thomas M. (Committee Member), Bernstein, Leslie (Committee Member), Gauderman, William James (Committee Member), Crimmins, Eileen M. (Committee Member).
Subjects/Keywords: childhood; infectious disease; infectious mononucleosis; concordance; height; growth; twin; long term recall; parental report; pediatric
Record Details
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Hwang, A. E. (2012). Early childhood health experience & adult phenotype in
twins. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/5262/rec/2144
Chicago Manual of Style (16th Edition):
Hwang, Amie Eunah. “Early childhood health experience & adult phenotype in
twins.” 2012. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/5262/rec/2144.
MLA Handbook (7th Edition):
Hwang, Amie Eunah. “Early childhood health experience & adult phenotype in
twins.” 2012. Web. 02 Mar 2021.
Vancouver:
Hwang AE. Early childhood health experience & adult phenotype in
twins. [Internet] [Doctoral dissertation]. University of Southern California; 2012. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/5262/rec/2144.
Council of Science Editors:
Hwang AE. Early childhood health experience & adult phenotype in
twins. [Doctoral Dissertation]. University of Southern California; 2012. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/5262/rec/2144

University of Southern California
17.
Chen, Fang.
Polygenic analyses of complex traits in complex
populations.
Degree: PhD, Biostatistics, 2013, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/124501/rec/5105
► Genome-wide association scans (GWAS) have identified numerous common variants associated with hundreds of complex diseases. In this dissertation, I investigated the properties of the GWAS-identified…
(more)
▼ Genome-wide association scans (GWAS) have identified
numerous common variants associated with hundreds of complex
diseases. In this dissertation, I investigated the properties of
the GWAS-identified common SNPs in multiple populations, and
estimated their aggregate effects on complex diseases. In the first
Chapter, I assessed the generalizability of a risk score derived
from 12 SNPs known to be associated with breast cancer risk in
European or Asian populations in the Multiethnic Cohort (MEC). I
performed a case-control study with 2,224 cases and 2,827 controls
nested in the MEC and found that when viewed as a summary risk
score, the total number of risk alleles carried by women was
significantly associated with breast cancer risk overall (OR per
allele: 1.09; 95% CI: 1.06-1.12; p=2.0×10-10) and in all
populations except African Americans, in which no significant
association was observed (OR, 1.03; 95% CI, 0.98-1.08). These
results emphasized the need for large-scale association studies in
multiple racial/ethnic groups, especially in populations of African
ancestry. ❧ Since body mass index and type 2 diabetes (T2D) are
established risk factors for (post-menopausal) breast cancer, I
tested for the pleiotropic effects of 31 common variants for T2D
and obesity in a case-control study of 1,915 breast cancer cases
and 2,884 controls nested within the MEC. However, following
adjustment for multiple tests, we found no significant association
between any variant and breast cancer risk, as in shown in Chapter
Two. ❧ In Chapter Three I analyzed a large study of breast cancer
in African American women (3,016 cases and 2,745 controls), where I
tested 19 known risk variants identified by GWAS and replicated
associations (P=0.3, n=1,415 and Pr (IBD=1)>=0.4, n=575), the
additive heritability estimate increased to 76.5% (se: 11.7%) and
75.1% (13.3%), respectively which is consistent with the view (Zuk
et al PNAS 2011) that the additive component of genetic variation
for height may have been overestimated in earlier studies (80%) and
the proportion could also include variation due to epistatic
effects. ❧ This dissertation contributes to the polygenic analyses
of complex traits in two aspects: first, it emphasizes the
necessity of using genetic markers that are specific to the
populations of interest for disease prediction in different
populations. Second, analyses performed in this dissertation add to
the investigation of the “missing heritability” problem. I
concluded from this dissertation that the hypothesis that common
variants explain a large proportion of heritability remains
unproven, and that studies of additional genetic markers such as
rare variants, and investigations of non-linear effects of genetic
markers including epistatic effects are needed in order to gain a
better understanding of the genetic characteristics of complex
traits.
Advisors/Committee Members: Stram, Daniel O. (Committee Chair), Haiman, Christopher A. (Committee Member), Gauderman, William James (Committee Member), Lewinger, Juan Pablo (Committee Member), Coetzee, Gerhard (Gerry) A. (Committee Member).
Subjects/Keywords: common variants; GWAS; heritability; polygenes
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Chen, F. (2013). Polygenic analyses of complex traits in complex
populations. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/124501/rec/5105
Chicago Manual of Style (16th Edition):
Chen, Fang. “Polygenic analyses of complex traits in complex
populations.” 2013. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/124501/rec/5105.
MLA Handbook (7th Edition):
Chen, Fang. “Polygenic analyses of complex traits in complex
populations.” 2013. Web. 02 Mar 2021.
Vancouver:
Chen F. Polygenic analyses of complex traits in complex
populations. [Internet] [Doctoral dissertation]. University of Southern California; 2013. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/124501/rec/5105.
Council of Science Editors:
Chen F. Polygenic analyses of complex traits in complex
populations. [Doctoral Dissertation]. University of Southern California; 2013. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/124501/rec/5105

University of Southern California
18.
Lee, Won H.
Observed and underlying associations in nicotine
dependence.
Degree: PhD, Statistical Genetics and Genetic
Epidemiology, 2014, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/85457/rec/4506
► Tobacco-related morbidity and mortality remain among the costliest worldwide public health issues and the most preventable. Nicotine dependence is the primary factor in the persistence…
(more)
▼ Tobacco-related morbidity and mortality remain among
the costliest worldwide public health issues and the most
preventable. Nicotine dependence is the primary factor in the
persistence of this problem, leading to ongoing efforts to
characterize nicotine dependence. Ongoing efforts have also led to
the development of treatments to deal with this addictive drug.
Nicotine replacement therapies, such as transdermal and nasal spray
treatments, and other drugs, such as bupropion, targeted at
neurotransmitters effected by nicotine, have had varying degrees of
effectiveness for smoking cessation. Studies investigating genetic
variants involved in the dopamine reward pathway, nicotine
metabolism, and related mechanisms and pathways have shown that
specific genetic profiles have different levels of nicotine
dependence and respond differentially to treatments for nicotine
dependence. For example, differential treatment effects for
bupropion have been observed for variants within genes involved in
the dopamine reward pathway on smoking cessation, with bupropion
inhibiting the reuptake of dopamine. Bupropion has also been shown
to be an antagonist for the nicotinic acetylcholine receptors,
which bind nicotine. These two actions in concert highlight the
interplay between treatments and genes. The metabolism of nicotine
has also been of particular interest. Specifically, CYP2A6 has been
shown to be a primary mechanism in the metabolism of nicotine to
cotinine and then 3-hydroxycotinine (3HC). The nicotine metabolite
ratio (NMR), the ratio of 3HC to cotinine, has subsequently been
shown to be a reliable proxy for nicotine metabolism. Moreover,
those carrying the CYP2A6 variant have been shown to have lower NMR
levels, and be slow metabolizers, and those wildtype for CYP2A6
have been shown to be normal or fast metabolizers. ❧ This intricate
web of dependence, genetic variation, cessation treatments, and
nicotine metabolism has led us to develop a latent variable
framework that attempts to capture an underlying process that
characterizes a nicotine profile. Latent variable models have been
used in the social sciences as a means of estimating constructs
that synthesize indices of behavior. Indices for smoking may not
capture the extent or degree of dependence on their own, but a
latent variable, in describing relationships between measured
variables, may ascertain otherwise unobservable effects. The
potential problem then may be the interpretation of a latent
variable. A hypothetical construct of “nicotine dependence” or
“biological pathway X” may or may not be reliable in capturing
desired effects. ❧ We present a framework that incorporates a
Dirichlet process that does not constrain this underlying process
to a single distribution, but can flexibly cluster individuals into
profiles based on observed biomarker levels, genetic variation and
other biological and psychological characteristics. This non- or
semiparametric model made up of a mixture of parametric
distributions is able to allocate observed measurements into k
clusters. It…
Advisors/Committee Members: Conti, David V. (Committee Chair), Gauderman, William James (Committee Member), Knowles, James (Committee Member), Leventhal, Adam M. (Committee Member), Thomas, Duncan C. (Committee Member).
Subjects/Keywords: genetic association; nicotine dependence; dopamine reward pathway; nicotine metabolism; Dirichlet process; nonparametric latent variable framework
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Lee, W. H. (2014). Observed and underlying associations in nicotine
dependence. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/85457/rec/4506
Chicago Manual of Style (16th Edition):
Lee, Won H. “Observed and underlying associations in nicotine
dependence.” 2014. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/85457/rec/4506.
MLA Handbook (7th Edition):
Lee, Won H. “Observed and underlying associations in nicotine
dependence.” 2014. Web. 02 Mar 2021.
Vancouver:
Lee WH. Observed and underlying associations in nicotine
dependence. [Internet] [Doctoral dissertation]. University of Southern California; 2014. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/85457/rec/4506.
Council of Science Editors:
Lee WH. Observed and underlying associations in nicotine
dependence. [Doctoral Dissertation]. University of Southern California; 2014. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/85457/rec/4506

University of Southern California
19.
Su, (Ray) Yu-Chen.
Adaptive set-based tests for pathway analysis.
Degree: PhD, Statistical Genetics and Genetic
Epidemiology, 2015, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/535696/rec/517
► With a typical sample size of a few thousand subjects, a single genomewide association study (GWAS) using traditional one‐SNP‐at‐a‐time methods can only detect genetic variants…
(more)
▼ With a typical sample size of a few thousand subjects,
a single genomewide association study (GWAS) using traditional
one‐SNP‐at‐a‐time methods can only detect genetic variants
conferring a modest effect on disease risk. Set‐based methods,
which analyze sets of SNPs jointly, can detect variants with
smaller effects acting within a gene, a pathway, or other
biologically relevant sets. While self‐contained set‐based methods
(those that test sets of variants without regard to variants not in
the set) are generally more powerful than competitive set‐based
approaches (those that rely on comparison of variants in the set of
interest with variants not in the set), there is no consensus as to
which self‐contained methods are best. In particular, several
competitive set tests have been proposed to directly or indirectly
‘adapt’ to the a priori unknown proportion and distribution of
effects of the truly associated SNPs in the set, which is a major
determinant of their power. ❧ A popular adaptive set‐based test is
the adaptive rank truncated product (ARTP), which seeks the set of
SNPs that yields the best‐combined evidence of association. We
compared the standard ARTP, several ARTP variations we introduced,
and other adaptive methods in a comprehensive simulation study to
evaluate their performance. We used permutations to assess
significance for all the methods and thus provide a level playing
field for comparison. We found the standard ARTP test to have the
highest power across our simulations followed closely by the global
model of random effects (GMRE) and a LASSO based test. ❧ However,
ARTP requires permuted data and p-values that may be
computationally intensive. This motivates a fast alternative
approach to replace permutations. We proposed a Fast Adaptive
Set‐based Test (FAST), which samples permutation equivalents from
the asymptotic distribution of all marginal parameter estimates of
interest. An R package “fastARTP” was written to apply the FAST
framework to draw permutation equivalents then applied on to the
ARTP method. We consequently applied “fastARTP” package on a
genomewide pathway analysis using the Children Health Study
(CHS).
Advisors/Committee Members: Lewinger, Juan Pablo (Committee Chair), Gauderman, William James (Committee Member), Conti, David V. (Committee Member), Schumacher, Fredrick (Committee Member), Sun, Fengzhu Z. (Committee Member).
Subjects/Keywords: set‐based test; genetic pathway analysis; adaptive pathway analysis; genomewide pathway analysis; self‐contained pathway analysis
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Su, (. Y. (2015). Adaptive set-based tests for pathway analysis. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/535696/rec/517
Chicago Manual of Style (16th Edition):
Su, (Ray) Yu-Chen. “Adaptive set-based tests for pathway analysis.” 2015. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/535696/rec/517.
MLA Handbook (7th Edition):
Su, (Ray) Yu-Chen. “Adaptive set-based tests for pathway analysis.” 2015. Web. 02 Mar 2021.
Vancouver:
Su (Y. Adaptive set-based tests for pathway analysis. [Internet] [Doctoral dissertation]. University of Southern California; 2015. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/535696/rec/517.
Council of Science Editors:
Su (Y. Adaptive set-based tests for pathway analysis. [Doctoral Dissertation]. University of Southern California; 2015. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/535696/rec/517

University of Southern California
20.
Liu, Jinghua.
Population substructure and its impact on genome-wide
association studies with admixed populations.
Degree: PhD, Statistical Genetics and Genetic
Epidemiology, 2012, University of Southern California
URL: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/78608/rec/5120
► Association studies among admixed populations pose many challenges. The purpose of this study is to compare the methods for ancestry estimation and to investigate the…
(more)
▼ Association studies among admixed populations pose
many challenges. The purpose of this study is to compare the
methods for ancestry estimation and to investigate the control for
confounding and the capture of heterogeneity in SNP effect by the
use of individual ancestries. In addition, a general regression
framework is proposed to perform admixture mapping for both
case-only and case-control study designs among admixed populations.
For confounding and heterogeneity, simulation results indicate that
1) adjustment for global ancestry can control for confounding; 2)
additional adjustment for local ancestry may increase power when
the induced admixture LD is in the opposite direction as the LD in
the ancestral populations; 3) the inclusion of a SNP by local
ancestry interaction term can increase power when there is
substantial differential LD between ancestry populations. Real data
analysis in a genome-wide data using the
University of
Southern
California's Children's Health Study of childhood asthma highlights
rs10519951 (p=8.5E-7) from the model with the interaction term, a
SNP lacking any evidence of association from the SNP association
analysis (p=0.5). For the admixture mapping, simulation and real
data analysis results among African Americans from the Multiethnic
Cohort Study of prostate cancer indicate that 1) case-only analysis
suffers from spurious results among the regions with biased local
ancestry estimation; 2) our proposed regression model yield similar
performance as the existing methods; 3) it is more powerful to
incorporate genotype information for admixture mapping; 4) and it
is more powerful to incorporate SNP by local ancestry interaction
to capture the admixture signal and heterogeneity by local ancestry
simultaneously.
Advisors/Committee Members: Conti, David V. (Committee Chair), Gilliland, Frank D. (Committee Member), Gauderman, William James (Committee Member), Thomas, Duncan C. (Committee Member), Knowles, James (Committee Member).
Subjects/Keywords: genetic association study; GWAS; admixture mapping; population stratification; confounding; heterogeneity; admixed population
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❌
APA ·
Chicago ·
MLA ·
Vancouver ·
CSE |
Export
to Zotero / EndNote / Reference
Manager
APA (6th Edition):
Liu, J. (2012). Population substructure and its impact on genome-wide
association studies with admixed populations. (Doctoral Dissertation). University of Southern California. Retrieved from http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/78608/rec/5120
Chicago Manual of Style (16th Edition):
Liu, Jinghua. “Population substructure and its impact on genome-wide
association studies with admixed populations.” 2012. Doctoral Dissertation, University of Southern California. Accessed March 02, 2021.
http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/78608/rec/5120.
MLA Handbook (7th Edition):
Liu, Jinghua. “Population substructure and its impact on genome-wide
association studies with admixed populations.” 2012. Web. 02 Mar 2021.
Vancouver:
Liu J. Population substructure and its impact on genome-wide
association studies with admixed populations. [Internet] [Doctoral dissertation]. University of Southern California; 2012. [cited 2021 Mar 02].
Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/78608/rec/5120.
Council of Science Editors:
Liu J. Population substructure and its impact on genome-wide
association studies with admixed populations. [Doctoral Dissertation]. University of Southern California; 2012. Available from: http://digitallibrary.usc.edu/cdm/compoundobject/collection/p15799coll3/id/78608/rec/5120
.