Germline mutations in BRCA2 confer a high risk for the development of breast cancer in the Afrikaner population. A great deal of variability in the development of the disease has been observed among mutation positive family members. Evidence suggested that genes affecting breast cancer risk in the general population could potentially also affect breast cancer risk in BRCA mutation carriers. The cell cycle control pathway was selected as a candidate as the functional loss of the tumour suppressor protein p53 is a common feature in diverse human cancers. The ability of this protein to sense cellular damage and halt the progression of the cell cycle or direct the cells to apoptosis is essential in preventing tumourigenesis. The aim of the study was an attempt to identify potential genetic modifiers of breast cancer risk and penetrance in Afrikaner women carrying the South African founder BRCA2 c.8162delG mutation. It involved environmental factors as well as six polymorphisms detected in critical genes of the Tp53 pathway. The investigated polymorphisms included three variants previously detected in Tp53 (intron 3, exon 4 and intron 6), a polymorphism present in the promoter of MDM2 and two SNPs identified in WAF1 (intron 2 and exon 2). The epidemiological study failed to identify any specific characteristic associated with an increased or protective breast cancer risk and did not explain the observed residual variation. Of the six polymorphisms studied, only one proved to be statistically significant, namely the 5â splice-site variant in intron 2 of WAF1. This polymorphism seemed to explain the variation in penetrance for some of the families, but needs to be confirmed by more extensive studies. A breast cancer recombinant haplotype was compiled using the most informative variants, namely the polymorphism in the MDM2 promoter, the 5â splice-site variant in intron 2 of WAF1 and the SNP in exon 4 of Tp53, but proved to be uninformative. Association studies including gene to gene and gene to environment interactions could assist researchers in their understanding of the mechanistic basis of the polygenic nature of breast cancer.

The incidence of the western diseases, atherosclerosis, CHD and stroke is progressively rising in black populations worldwide and in South Africa. Stroke is an important cause of death in black populations in South Africa and may increases even further if risk factor (coronary and some haemostatic risk factors) prevalence is altered by change in lifestyle and diet, westernisation and migration to an urban environment. Raised fibrinogen levels which are more prevalent in westernised black men than white men, are accepted as an important risk factor for stroke and CHD. It is believed that the possible protective effects of diet against the development of atherosclerosis and thrombosis could be mediated, in part, through haemostasis. A prudent low-fat, high-fibre diet may favourably influence haemostasis. More specifically, oat bran (soluble fibre) has been shown to have beneficial effects on some coronary risk factors and haemostasis. The physiological effects of dietary fibre are strongly related to SCFAs, which are produced by colonic fibre fermentation. According to available literature, SCFAs could possibly have a beneficial effect on lipid profiles and haemostatic risk factors. Little information is, however, available on the effect of a specific combination of SCFAs on fibrinogen levels and other haemostatic factors in human subjects. The main objective of the study was to examine the effect of a combination of SCFAs, resembling oat bran (acetate:propionate:butyrate â 65:19:16) on plasma fibrinogen levels, some haemostatic risk factors and other related risk factors for CHD and stroke in westernised black men. The study was a randomised, placebo-controlled, double-blind clinical trial. 22 subjects falling within a pre-determined set of inclusion criteria, and with higher normal fibrinogen levels were randomly selected into an experimental group (n = 11) and placebo group (n = 10). Supplementation of 12 capsules daily was sustained for five weeks. Total plasma fibrinogen, fibrin monomer concentration, fibrin network properties, factor VII and factor VIII activity, serum lipids, glucose concentrations, some metabolic indicators and fasting acetate concentrations were measured at baseline and at the end of supplementation, in all subjects. The usual dietary intake of the subjects was obtained using a food frequency questionnaire and a 24-hour recall. According to the baseline results, the subject group was homogeneous with an apparently healthy clinical and physical appearance. Although both subject groups had a favourable coronary and haemostatic risk profile, total cholesterol levels as well as factor VII and factor VIII activity were in the higher normal ranges. Furthermore, the 24-hour recall indicated a tendency towards the adoption of an atherogenic Westernised diet. Although SCFA supplementation had no effect on the fibrinogen concentrations, a significant decrease was observed in the fibrin monomer concentrations, network fibrin content, factor VII and factor VIII activity. A significant increase was observed in the compaction of the fibrin networks, as well as a tendency for the mass to length ratio of the fibrin fibres to increase. Furthermore, a statistically significant although not clinically significant increase was indicated in HDL cholesterol concentrations after SCFA supplementation. It was evident from these findings that SCFA supplementation may have a direct effect on haemostasis, especially the fibrin network characteristics, factor VII and factor VIII activities, as well as fibrin monomer concentration. This observation suggests that SCFA supplementation may have a strong protective effect against atherosclerosis and thrombosis. In conclusion, the hypothesis that soluble dietary fibre will influence fibrinogen concentrations and other haemostatic risk factors through production of SCFAs, was proven to be partially true. It was clear that, although fibrinogen concentration was not influenced by SCFA supplementation, beneficial effects on the fibrin network architecture and the positive cascade effect on haemostasis may be a direct effect of SCFAs supplementation. The study further indicated that the known protective effects of dietary fibre on CHD could partially be mediated through effects of SCFAs on fibrin networks. It is recommended that the role of fibrin networks as a risk factor for CHD and the effect of diet on haemostasis should be further investigated.

The aim of the study was to elucidate the variation in phenotypic expression observed within BRCA2 c.8162delG mutation positive families. The study attempted to identify possible genetic factors that contribute to the residual risk conferred by the BRCA2 founder mutation. As BC is a polygenetic disorder, polymorphisms within various low penetrance genes may contribute to the expression of the disease. The selection of the SNPs were based on the results of the CIMBA consortium and have been proven to be associated with an increased BC risk in the general population (Easton et al., 2007) and in BRCA2 mutation carriers specifically (Antoniou et al., 2008). Two SNPs (rs2234693 [PvuII] and rs9340799 [XbaI]) present within ESR1 as well as SNPs present in TNRC9 (rs3803662), LSP1 (rs3817198), MAP3K1 (rs889312) and FGFR2 (rs2981582) identified by GWAS have been implicated in BC risk. These six polymorphisms have been selected to evaluate the risk within the Afrikaner BRCA2 8162delG (c.7934del, p.Arg2645AsnfsX3) mutation carriers specifically. Genotyping of rs2234693 (PvuII) and rs9340799 (XbaI) was done by PCR-RFLP analysis whereas Taqman® assays were used for genotyping rs3803662 (TNRC9), rs3817198 (LSP1), rs889312 (MAP3K1) and rs2981582 (FGFR2). Automated allelic discrimination using the BioRad CFX Manager v1.1.308.1111 software were compared to manual discrimination methods to ensure robust genotyping. Cohenâs kappa analysis suggested a combination of automated (Method 1) and manual (Method 3) genotyping was best suited for accurate allelic discrimination except for LSP1. Due to an putative SNP detected within LSP1, the validity of the LSP1 results should be treated cautiously as no information on the frequency of the second putative SNP in white European individuals is available. Of the six polymorphisms analyzed, only rs2234693 (PvuII), indicated a possible association with BC (P-value = 0.0896), which should be explored within a larger study group. For FGFR2, the HWE results indicated that the deviation observed in the BRCA2 mutation carrier group could possibly be associated with BC. Haplotypes compiled for rs2234693 (PvuII) and rs9340799 (XbaI) as well as the remaining four SNPs were uninformative as it revealed no differences between the BC patients and the Cases. These results may have been due to the high allelic heterogeneity observed within the Afrikaner population, as well as the small test group used.. Although the results of this study did not deliver significant results, it did provide insight into allelic distributions of the SNPs in the Afrikaner BRCA2 8162delG (c.7934del, p.Arg2645AsnfsX3) mutation carriers specifically. Larger scale genotyping could lead to more significant findings to help elucidate the polygenetic nature of BC with the Afrikaner.

Many recent studies have identified rare variants that contribute to common, complex disease. It is believed that rare variants likely have a larger effect size (compared to GWAS findings) and can act alone, in concert with other rare variants, or together with common variants. Multiple rare variants can potentially account for a portion of missing heritability in a given trait; therefore, binning or burden testing, may better account for genetic heterogeneity. BioBin, an innovative collapsing method developed in the Ritchie lab, utilizes a flexible repository of data assembled from multiple public databases. The novelty of BioBin lies in access to comprehensive knowledge-guided multi-level binning. BioBin can apply multiple levels of burden testing, including: functional regions, evolutionary conserved regions, genes, and/or pathways. BioBin does not include a specific statistical association test, since the application of statistical testing is dependent on data type and analysis in question. Therefore, the user has the flexibility to apply tests appropriately without constraint. BioBin has been tested in the context of extensive simulation studies, compared with multiple published statistical methods, and applied to the NHLBI GO Exome Sequencing Project for Cystic Fibrosis. BioBin is a very useful and flexible tool to analyze sequence data and can uncover novel associations with complex disease.

The clinical course of multiple sclerosis (MS) is highly variable, and research data collection is costly and time-consuming. Much is known about the genetic risk of acquiring MS, but little is understood about the effect of genetics on the clinical course. This work uses natural language processing techniques applied to electronic medical records (EMR) to identify MS patients and key clinical traits of disease course. 5,789 individuals with MS were identified by algorithm. Algorithms were also developed with high precision and specificity to extract detailed features of the clinical course of MS, including clinical subtype, presence of oligoclonal bands, year of diagnosis, year and origin of first symptom, Expanded Disability Status Scale scores, timed 25-foot walk scores, and MS medications. DNA was available for 1,221 individuals through BioVU. These samples and 2,587 control samples were genotyped on the ImmunoChip. After extensive sample and SNP quality control, replication of known MS risk loci confirmed that the genetic architecture of this EMR-derived population is similar to that of other published MS datasets. Genetic analyses of seven clinical traits were performed using the data extracted from the medical records: age at diagnosis, age and CNS origin of first neurological symptom, presence of oligoclonal bands, Multiple Sclerosis Severity Score, timed 25-foot walk, and time to secondary progressive MS. No outstanding results were observed, but many interesting results require further investigation. This work shows the potential of using EMR-derived data in research studies of disease course.

Fashion magazines are the most accessible source for women to learn the latest about fashion and trends. Publishing company Condé Nast owns many consumer fashion magazines including the American editions of Lucky and Vogue. Even though both magazines are classified under the genre of fashion, these magazines are branded differently. Vogue features editorial styling, which is garments arranged lavishly and creatively for the glossy fashion spreads. However, Lucky magazine contains both editorial and lifestyle styling. To reinforce the styled image, fashion magazines place captions in these editorials. Captions transform these garments into written language. Since each magazine uses different types of styling, editors are writing captions in different formats. The purpose of the study is to investigate the stylistic similarities and differences of fashion captions in Lucky and Vogue. Additionally, semantic-syntax tree diagrams were used to determine how the fashion captions communicate meaning. This study followed a mixed methods approach using a purposive sample (n=14). The March and September issues were examined from 2010-2013. Data results show magazines are written primarily in grammatical modifiers. Different from prior research, nouns were the largest category, and adjectives composed the second largest category. Some captions did not have verbs resulting in mainly a descriptive narrative. Each magazine differed in the types of verbs used, frequency of proper nouns, and types of prepositions. Furthermore, when editors are not telling a fashion story, then captions are written as imperative commands. When telling a fashion story, the garment is often personified to take on human characteristics or described as possessing certain characteristics. Both magazines use these writing styles to convey different ideas and content to the reader. The results of this study strengthened the belief that a distinct stylistic form of writing exists in fashion captions. From this study, fashion editors and scholars may become more aware of the current stylistic formations featured in fashion captions, and further enhance their knowledge of how to communicate editorial trends and themes to their intended audience.

Common age, related eye diseases are a major driving force behind vision disability and blindness. The three most common diseases afflicting Americans today are age-related macular degeneration (AMD), primary open-angle glaucoma (POAG), and diabetic retinopathy (DR). Much is known about the environmental factors contributing to disease risk and progression in these conditions, but the genetic architecture remains elusive. We performed a meta-analysis of known AMD-related variants and variants in cholesterol pathways in the three major race-ethnicities in the United States, and Chinese and Malay individuals from Singapore. Additionally, we identified potential novel associations between mitochondrial variants and risk of AMD in NHANES Mexican Americans. African American case and control samples for POAG and DR were extracted from the Vanderbilt de-identified electronic medical records system called the Synthetic Derivative. A large subset of these individuals were genotyped on the Illumina Metabochip array. Genetic association analyses were performed to replicate previously identified and novel associations in patients with POAG and separately for patients with DR. Nominally significant associations ( p < 10-4) in POAG analyses suggest that vascular and angiogenic pathways may play a role in POAG risk in African Americans. In the study of DR, variants located in genes known to play a role in epithelial and endothelial tight cellular junctions, wound healing were nominally associated in the Synthetic Derivative African American DR population.

Alzheimer disease (AD) is the most common cause of dementia. As with many complex diseases, the identified variants do not explain the total expected genetic risk that is based on heritability estimates for AD. Isolated founder populations, such as the Amish, are advantageous for genetic studies as they overcome limitations associated with complex population studies. Amish AD cases harbored a significantly higher burden of the known risk alleles compared to Amish cognitively normal controls, but a significantly lower burden when compared to cases from a cohort of unrelated individuals. These results suggest that known loci explain some of the genetic effects and that there may be different underlying genetic architectures between the two populations. Whole-exome sequencing of a selected subset of the overall study population was used as a screening tool to identify variants located in the regions of the genome that are most likely to contribute risk. By then genotyping the top candidate variants from the known AD genes and implicated linkage regions from previous studies in the full data set, new associations could be confirmed. The most significant result (p = 0.0012) was for rs73938538, a synonymous variant in LAMA1 within the previously identified linkage peak on chromosome 18, but this association did not generalize when tested in a dataset of unrelated individuals. These results indicate that exonic variation in a majority of previously associated LOAD genes, and regions implicated by previous linkage studies, does not contribute to risk for LOAD in the Amish.

One third of the worlds population has been infected with Mycobacterium tuberculosis (MTB). Most of those exposed develop an asymptomatic latent infection. In the absence of co-morbidities, only 5-10% of people progress to active tuberculosis disease (TB) post-exposure, defined as primary TB. However, immunosuppression resulting from malnutrition or human immunodeficiency virus (HIV) co-infection increases the likelihood of both primary TB and activation of a latent infection. As a result, tuberculosis remains a major global health problem. Worldwide, TB is the second-leading cause of mortality from a single infectious agent, after HIV. In 2013, 9 million new cases of clinical tuberculosis were diagnosed and 1.5 million deaths were attributed to the disease. An estimated 360,000 deaths occurred in people co-infected with HIV, and 75% of these cases occurred in sub-Saharan Africa. MTB infection and tuberculosis disease have a substantial heritable component. In this project, we studied a genetic resistance phenotype to TB disease and MTB infection, as opposed to more standard approaches tailored towards finding loci associated with susceptibility. We recruited HIV-positive patients from three recently concluded prospective cohorts of TB from Uganda and Tanzania. We hypothesized that HIV-positive individuals living in MTB hyperendemic areas who do not develop TB disease represent an extreme resistance phenotype. A study of 175,906 variants in 267 cases and 314 controls revealed a genome-wide significant association of a common TB resistance single nucleotide polymorphism, rs4921437, in the regulatory region of IL12, a gene previously associated with susceptibility. We also hypothesized that HIV-positive individuals who do not establish MTB infection despite living in hyperendemic regions are genetically resistant. In a study of 162,228 variants in 244 cases and 235 controls, we discovered a genome-wide significant association of a resistance variant rs877356 near IL9, a gene previously associated with bronchial hyperresponsiveness and asthma. Furthermore, we evaluated the effects of multi-locus interactions in a candidate gene approach and found that epistasis also plays a significant role in risk of MTB infection and TB disease. We present a novel approach to genome-wide association studies, also applicable to whole genome sequencing studies, where the use of an extreme resistance phenotype allowed us to identify large effect sizes and attain genome-wide significance in cohorts of a relatively small sample size. The use of HIV status as a central feature of our hypothesis as opposed to a confounder or exclusion criterion is also unique.

Cardiovascular disease (CVD) is an inclusive term encompassing several disorders of the circulatory system that together account for the majority of global non-communicable disease (NCD) mortality. Major thrombotic events, due in part to impaired fibrinolysis, are a unifying characteristic of several CVDs. Plasminogen activator inhibitor-1 (PAI-1) is a major regulator of fibrinolysis, and PAI-1 levels associate with CVD susceptibility and severity in several populations. The main objectives of this dissertation were to evaluate the genetic impact of common single nucleotide polymorphisms (SNPs) on inter-individual variation in PAI-1 levels in a Ghanaian population, and present a novel method to identify candidate genes for prioritization in future studies. We discovered novel associations between single variants in the arylsulfatase b (ARSB), carboxypeptidase A2 (CPA2), and leukocyte receptor cluster member 9 (LENG9) and median PAI-1 levels. Quantile regression analyses directed at the upper quartile of the PAI-1 distribution was performed to uncover novel variants with significant impact on this clinically relevant portion of the PAI-1 distribution. Upper quartile regression analyses revealed significant associations between single variants in period circadian clock 3 (PER3), a discovery that supports previous evidence of the involvement of the circadian pathway in regulation of PAI-1 levels in Caucasian populations as well as model organisms. This finding suggests that the significance of the circadian pathway as a whole may be generalizable across populations, even though gene effects may be population specific. We present a novel approach; Multi-lOcus based selection of Candidate genes (MOCA), which incorporates multi-variant association signals into the prioritization of genes for further evaluation. MOCA identified four significantly associated loci; these loci included 28 novel candidate genes for PAI-1 levels. Each MOCA identified locus was located within previously identified CVD and/or PAI-1 related quantitative trait loci (QTL).