Breast cancer, the most commonly diagnosed cancer in American women, is a heritable disease with nearly one hundred known genetic risk factors. Using next generation sequencing, we explored the contribution of genetics at 12 GWAS-identified loci to breast cancer susceptibility in a multi-ethnic breast cancer case-control study. Methods: The study population consists of 4,611 breast cancer cases and controls (2,316 cases and 2,295 controls) from four mutually exclusive ethnicities: African, Latina, Japanese, or European American.We conducted rare variant association testing between sequenced genotypes and simulated phenotypes to compare the performance of several approaches for assessing rare variant associations across multiple ethnicities and the statistical performance of different ethnic sampling fractions, including single-ethnicity studies and studies that sample up to four ethnicities. Findings from simulation of causal rare variant penetrance models were then applied to a non-synonymous protein-coding rare variant association study of breast cancer. Next, we applied variance partitioning methods to determine what proportion of breast cancer heritability is explained by rare and common, coding and non-coding, and the complete set of sequenced genetic variants. Results: Variance component-based tests were better powered in several scenarios. Multi-ethnic studies were well powered, with inclusion of African Americans providing the largest gains in statistical power. Rare variation in several genes was nominally associated (alpha=0.05) with breast cancer risk. Common variants explained a significant amount of breast cancer heritability (5%; SE=2%). Total breast cancer heritability from all sequenced SNVs from all 12 loci was approximately 11% (S.E.=4%), a substantial portion of breast cancer heritability which ranges from 27% to 32% in European familial studies. Conclusion: Our findings suggest that association studies between rare variants and complex disease should consider including subjects from multiple ethnicities, with preference given to genetically diverse groups. We demonstrate practices with the potential to uncover and localize gene-based associations using gene-based rare variant association testing at 12 GWAS-identified breast cancer susceptibility loci. We also present strong evidence that just this subset of previously-identified loci explains a substantial portion of heritability which suggests that all GWAS-identified loci may explain more breast cancer heritability than the 17% previously reported. / Epidemiology

Nutritional factors have been intensively studied as important determinants of many diseases. Food frequency questionnaires (FFQ), dietary records, 24-hour dietary recalls, nutrient biomarkers are important dietary assessment methods, and are subject to various sources of measurement error. Given the limitations of these methods, much effort has been devoted to refining them and evaluating their ability to measure diet. This dissertation focused on evaluating the performance of a semi-quantitative FFQ (SFFQ), multiple web-based automated-self-administered 24-hour recalls (ASA24), 7-day dietary records (7DDR) and biochemical indicators in assessing nutrient intakes among women. Intraclass correlation coefficient, Spearman correlation coefficient, and validity coefficient calculated by method of triads were used to evaluate the reproducibility and validity of each dietary method. The first paper evaluated the performance of a 152-item SFFQ comparing intakes of nutrients estimated by SFFQ with those measured by the average of two 7DDR, and of four ASA24s kept over a one-year period. The study SFFQ performed consistently well when compared with multiple diet records, and that modifications to the questionnaire over time have adequately taken into account the changes in the food supply and eating patterns that have occurred since 1980. Multiple ASA24s can provide similar estimates of validity as dietary records if day-to-day variation is taken into account. The second paper explored the validity of long-term intakes of energy, protein, sodium and potassium assessed by SFFQ and ASA24s using recovery biomarkers and 7DDR as standards. The study SFFQ and averaged ASA24’s are reasonably valid measurements for energy-adjusted protein, sodium and potassium compared to multiple recovery biomarkers or dietary records. Recovery biomarkers should not be considered to be without error, including systematic within-person error. Finally, the third paper further evaluated the validity of nutrient assessed by SFFQ and ASA24 compared with intakes by the 7DDR and plasma levels of fatty acids, carotenoids, retinol, tocopherols and folate. Again, the study SFFQ provides reasonably valid measurements for specific fatty acid, most carotenoids, alpha-tocopherol and folate compared to concentration biomarkers or dietary records. Compared to SFFQ, almost all nutrients estimated by averaged ASA24s had relatively low correlations with biomarkers, 7DDRs and estimated ‘true’ underlying intakes. / Nutrition

Some of the major themes that characterize the relationship between the environment and population health in the developing world today include poverty, household access to clean cooking fuel, air pollution, sanitation, and infant/child and maternal health. My dissertation research incorporates some of these themes at the interface of community and household energy in the context of economic development in Ghana. Specifically, my dissertation focuses on features of household energy and poverty in both rural and urban areas, as well as air pollution, and child and maternal health in growing urban areas in what is a data and resource-poor setting of Sub‐Saharan Africa (SSA). Child mortality is declining in most countries. Very few studies have measured child mortality at fine spatial resolutions, which is relevant for assessing community determinants and interventions. The first paper evaluates subnational inequalities in child mortality and its social and environmental determinants in Ghana by applying Bayesian spatial model to Ghana’s 2000 and 2010 National Population and Housing Censuses in 2000 and 2010. The census data were also used to estimate the distributions of households or persons in each of Ghana’s 110 districts for fuel used for cooking, sanitation facility, drinking water source, and maternal and paternal educations. Median district 5q0 declined from 99 deaths per 1,000 live births in 2000 to 70 in 2010. The decline ranged between <5% in some northern districts, where under-five mortality had been higher in 2000, to >40% in southern districts, where it had been lower in 2000, leading to higher inequalities. Primary education increased in men and women and more households had access to improved water and sanitation and cleaner cooking fuels over the same period. Higher use of liquefied petroleum gas for cooking was associated with lower 5q0 in multivariate analysis. Associations for the other social and environmental variables were not consistent or were weak in the different analyses although there were indications of beneficial effects from replacing wood with charcoal or kerosene, from improved sanitation (but not water), and from higher share of mothers and fathers with primary education. The second paper examines personal particulate matter exposures and locations of 56 students from eight schools in four neighborhoods in of varying socioeconomic status in Accra, Ghana, using gravimetric and continuous PM2.5 data, with time-matched global positioning system coordinates. Personal PM2.5 exposures ranged from less than 10 μg/m3 to more than 150 μg/m3 (mean 56 μg/m3). Girls had higher exposure than boys (67 vs. 44 μg/m3; p-value = 0.001). Exposure was inversely associated with distance of home or school to main roads, but the associations were not statistically significant in the multivariate model. Use of biomass fuels in the area where the school was located was also associated with higher exposure, as was household’s own biomass use. Paved schoolyard surface was associated with lower exposure. School locations in relation to major roads, materials of school ground surfaces, and biomass use in the area around schools may be important determinants of air pollution exposure. The third paper assesses the feasibility of using hospital administrative records for understanding air pollution health effects on pregnancy outcomes in Accra. This evaluation addresses whether: (i) the available health administrative data can be used to assess PM pollution-related adverse pregnancy outcomes, in particular birth weight; (ii) the health administrative structure and data can be used in the design of follow-up studies in such settings; (iii) the number of births that occur in the city would provide a large enough sample size; and (iv) birth weight distribution in such complex source-pollution environments varies substantially across neighhorhoods. There are six health districts in the Accra metropolis. In addition to other government and private facilities, each district is served by a Government polyclinic, where maternal and child health records in the district are collated. Neonatal and maternal health records, including anthropometric and demographic information are primarily kept by the individual women in cards provided by the Ghana Health Services. There are an estimated 10,000 births annually in each district. The average birth weight across selected facilities was 3,167±458 g, with individual birth weights ranging from 1,200 g to 6,000 g. Mean birth weight was similar across polyclinics. More than 95% of expectant mothers received at least 4 antenatal care visits at a health facility. Child immunization for the full range of vaccines covers over 80% of children born in the metropolis. A retrospective study of the association of air pollution exposure and birth weight in Accra through the use of hospital administrative records is feasible provided mothers are targeted through the public health units, which is responsible for child immunization. / Environmental Health

Positive energy imbalance occurs when energy intake exceeds energy expenditure. In modern society, increased consumption of caloric-dense food and reduced energy expenditure due to low physical activity and sedentary lifestyle drive positive energy imbalance. Manifested as weight gain, positive energy imbalance is implicated in the development and progression of several cancers. This dissertation focuses on reduced energy expenditure, sedentary behavior and weight gain in relation to cancer risk. In chapter 1, we prospectively evaluated the relationship between physical activity and incident cancers of the digestive system encompassing the digestive tract (mouth, throat, esophagus, stomach, small intestine, and colorectum) and digestive accessory organs (pancreas, gallbladder, and liver) among men in the Health Professionals Follow-Up Study. In men, a higher level of physical activity, regardless of its intensity, was associated with a decreased risk of digestive system cancers, particularly digestive tract cancers. The association was independent of obesity and diabetes. In chapter 2, we examined whether sedentary lifestyle, as indicated by time spent sitting watching TV, has an effect on colorectal cancer risk independent of physical activity. The relationship was prospectively investigated among women in the Nurses’ Health Study and men in the Health Professionals Follow-Up Study. In the combined population of women and men, prolonged sitting watching TV was an independent risk factor for colorectal cancer. The elevated risk associated with prolonged sitting was not completely offset by participation in physical activity. In chapter 3, we assessed the strength and shape of the dose-response relationships between adult weight gain and risk of adiposity-related cancers (e.g., cancers of the breast, endometrium, ovary, prostate, colon, pancreas) using dose-response meta-analysis. Adult weight gain was linearly associated with risk of breast, endometrial, and ovarian cancers among postmenopausal women not using hormone therapy; with risk of colon cancer, particularly among men. Results of this dissertation suggest that increasing the overall amount of physical activity, reducing sedentary time, particularly sitting watching TV, and avoiding adult weight gain should be widely encouraged for the prevention of several major cancers. / Nutrition

Starting with the publication of the first genome-wide association study (GWAS) in 2005, the last decade has seen the identification of thousands of novel genetic susceptibility loci. These common, low-penetrance single nucleotide polymorphisms (SNPs) have been associated with myriad phenotypes, ranging from benign (e.g., skin and hair pigmentation) to medically informative (e.g., risk of Alzheimer’s disease), and, in a few cases, clinically actionable (e.g., genotype-guided dosing of the anti-coagulant warfarin). While the clinical applications of GWAS findings remain limited, the commercial industry that has grown up around this research – providing testing for ancestry-, trait-, and disease-associated SNPs directly to consumers – continues to expand. In Sections 1 and 2 of this dissertation, I evaluate the impact of direct-to-consumer personal genomic testing (DTC-PGT) on its customers. First, I quantify the effect of providing genetic risk information on consumers’ perceived risk of four common cancers, and consider the implications of my findings in the context of clinical cancer risk counseling. Second, I describe post-PGT prescription medication behaviors, evaluate the relationship between these behaviors and the pharmacogenomic information provided to consumers, and finally interpret my findings against the backdrop of recent efforts by the Food and Drug Administration (FDA) to regulate the DTC-PGT industry. In Section 3, I take a step back and evaluate the evidence underlying a hypothesized concurrence between the genetic susceptibility loci for late-onset Alzheimer’s disease (LOAD) and those for early subjective memory complaints (SMCs) in cognitively intact adults. I conclude by discussing how my findings contribute to our understanding of the biological relationship between these phenotypes and to efforts to target risk SNPs and/or SMCs in screening tools for LOAD. / Epidemiology

The following dissertation addresses of two themes: the role of vitamin D and neurodegenerative diseases and methodologic concepts related to correlated missing outcome data. In the first chapter, the relation between vitamin D (characterized by circulating levels of 25Zhydroxyvitamin D 25[OH]D) and multiple sclerosis (MS) activity and progression is assessed in a secondary analysis of a population of over 1400 relapsing remitting MS patients with multiple asynchronous assessments of 25(OH)D. Overall, using a combination of clinical and magnetic resonance imaging endpoints, higher levels of vitamin D were associated with lesser MS activity. Results were more equivocal for clinical and brain volume measures. In the second chapter, the relation between dietary vitamin D and risk of amyotrophic lateral sclerosis (ALS) is assessed in pooled analysis of five prospective cohort studies. The study included nearly 1500 cases of ALS that occurred in a population of over 1 million individuals. Using dietary intake derived from food-frequency questionnaires, no association between dietary intake of vitamin D and risk of ALS was observed in any model. Similarly null results were observed for vitamin D intake from food and supplemental vitamin D. The third chapter addresses a methodologic concern when disease outcomes can be classified into multiple subtypes. It was not well understood of how to properly address marker-specific effects of a particular risk when markers are correlated and some are missing. This was addressed using an analysis of breast cancer in the Nurses’ Health Study (NHS) considering 5 markers with varying levels of correlation and missingness. Correlation among outcome measures was addressed through the calculation of an adjusted hazard ratio and four approaches for missing data were evaluated: the complete case, inverse probability weighting, missing indicator and multiple imputation. In the NHS, 4380 cases (with pathology reports) of breast cancer occurred; however, only 1551 cases had information on all five markers. We considered a list of established breast cancer risk factors and calculate adjusted marker-specific effects addressing missing using each of the 4 approaches. Effect estimates were generally similar for each method but corresponding standard errors were smaller using the multiple imputations and missing indicator approaches. Subsequent simulation studies suggest the missing indicator approach to produce the least bias and increases in standard error compared with datasets with complete information on all markers.

Identifying the key determinants of poor developmental outcomes is critical in improving the lives of millions of children who suffer from poor physical growth and cognitive deficits. Much research suggests that early life conditions, particularly those experienced within the household, critically influence children’s development across the life course. In this dissertation exercise, I explore how three dimensions of early experiences – prenatal conditions, parental education, and household socioeconomic conditions – influence children’s physical and cognitive development. Chapter 1 finds that the influences of low birth weight, often touted as a key determinant of later health, wane over time with increasing importance of postnatal factors. Chapter 2 also counters accepted evidence that maternal education matters more for children’s physical development by finding that both parents’ education matters equally in both infancy and childhood with no mechanisms distinguishing maternal and paternal education. Chapter 3 supports the evidence that household socioeconomic status matters for children’s cognitive development and finds that household assets are the critical determinant of cognitive status. Findings from each of these chapters will not only contribute new scientific evidence but will also help inform policies and programs to improve children’s health and well-being.

Due to their cholesterol content, limiting egg intake has been widely recommended for prevention of cardiovascular disease (CVD). However, recent reports by the 2015 Dietary Guidelines Committee and AHA/ACC suggest that there is insufficient evidence that dietary cholesterol is appreciably associated with blood cholesterol. In addition, the literature on the association with type 2 diabetes (T2D) is inconsistent. These analyses aim to determine the association between egg intake and the risk of CVD and T2D in the Nurses’ Health Study (NHS), the Nurses’ Health II Study (NHSII), Health Professionals Follow-up Study (HPFS) and the NIH-AARP Diet and Health Study (AARP), and conduct a meta-analyses. Egg intake was assessed via validated semi-quantitative food frequency questionnaires. Cox proportional hazard models, adjusted for age, lifestyle and dietary factors, were used to estimate relative risks (HR) and 95% Confidence Intervals (CI). We observed 12,832 and 16,570 cases of incident CVD and T2D in NHS, NHSII and HPFS, and 11,268 CVD mortality cases in AARP. An increase of one egg per day was not associated with risk of CVD in NHS, NHSII and HPFS (HR: 1.04, 95% CI: (0.96, 1.13)). In the AARP study an increase of one egg per day was associated with an increased risk of CVD mortality (HR: 1.13, 95% CI: (1.05, 1.20)) and, an increased risk of CVD mortality among diabetics (HR: 1.25, 95%CI: (1.11, 1.41)). One egg per day was associated with an increased risk of CVD (HR: 1.05, 95% CI: (1.01, 1.09)) in a meta-analysis of the current results and previously published studies. We also saw an increased risk of CVD among diabetics (HR: 1.24, 95% CI: (1.12, 1.37)). We observed an increased risk of T2D with an increase of one egg per day (HR: 1.09, 95% CI: (1.01, 1.18)) in NHS, NHSII and HPFS, and in the meta-analysis (HR: 1.13, 95% CI: (1.07, 1.19)). Although there does not seem to be a significant association between egg intake and risk of CVD or T2D in healthy individuals, people at risk for CVD or T2D and those who currently have T2D may want to limit egg intake.

Amyotrophic lateral sclerosis (ALS) is a progressive debilitating disease of the upper and lower motor neurons. Median survival of ALS patients is consistently estimated at between 2-3 years from symptom onset, with some evidence that survival is increasing due to improved care. There are few well-established risk factors for ALS, and there is conflicting evidence regarding the trends in ALS incidence and mortality over the past several decades. In Chapter I we investigate the trends in ALS incidence and mortality in Denmark between 1970 and 2009. We employed age-period-cohort models to model both the incidence and mortality rates of ALS over time for the first time. We found a significant rise in ALS incidence and mortality over several decades, and we observed evidence for a birth cohort component to the rise in ALS, which is consistent with an environmental cause of ALS. In Chapter II we investigate the role of physical trauma – both head and other – in the development of ALS. We employed the Danish registries and linked health data from the hospital system to prior diagnoses for physical trauma. We found a borderline significant association between physical trauma and ALS, which grew stronger upon restricting to physical traumas before the age of 55. Chapter III concerns the risk of ALS in those employed by the military in Denmark. We linked occupational records from the Danish Pension Fund to health records of the hospital system. We found a significantly elevated rate of ALS among those who had been previously employed by the military, with the highest rates in the decade immediately following cessation of employment. These analyses strengthen the knowledge base for the epidemiology of ALS, and suggest future avenues of research to further understand the etiology of the disease.

In Chapters 1 and 2, we examined two key components of heathy dietary patterns, specific types of dietary fat and consumption of fruit and vegetables, in relation to total and cause-specific mortality in two prospective cohort studies, the Nurses’ Health Study and the Health Professionals Follow-up Study. Dietary intake was assessed using semi-quantitative food frequency questionnaires at baseline and updated every 2 to 4 years. In Chapter 1, we found that higher saturated and trans fat intakes were associated with higher mortality, whereas polyunsaturated and monounsaturated fat intakes were inversely associated with mortality. Replacing 5% of energy from saturated fats with equivalent energy from polyunsaturated fats and monounsaturated fats was associated with 27% and 13% estimated reductions in total mortality, respectively. Intake of n-6 polyunsaturated fat, especially linoleic acid, was inversely associated with mortality, while marine n-3 polyunsaturated fat intake was associated with a modestly lower total mortality. In Chapter 2, we observed an inverse and nonlinear association between fruit and vegetable consumption and mortality. Consumption of five servings of fruit and vegetables daily, two servings for total fruit and three servings for total vegetables, were associated with the lowest total mortality, but above that level, higher consumptions were not associated with additional risk reductions. Higher consumptions of most fruit and vegetable subgroups were associated with lower risks of total mortality, whereas higher intakes of starchy vegetables such as peas and corn were associated with slightly higher risk of total mortality. In Chapter 3, we investigated the interrelationships between plasma ceramide concentrations, Mediterranean dietary pattern and cardiovascular disease (CVD) in the PREDIMED trial, a randomized controlled trial on the Mediterranean diet for primary prevention of CVD, using a case-cohort design. We observed strong positive associations between plasma ceramide concentrations and CVD risk. The association between ceramide concentration and incident CVD significantly varied by intervention groups. A Mediterranean diet may mitigate the deleterious effects of elevated plasma ceramide concentration. In summary, our findings from the three studies support current dietary recommendations to replace saturated and trans fat with unsaturated fats, increase fruit and vegetable consumption and adopt healthy Mediterranean-style dietary patterns.