STATISTICAL METHODS FOR RARE AND COMMON VARIANT ASSOCIATION STUDIES

Complex human diseases are a major challenge for biological research. The goal of my research is to develop effective methods for biostatistics in order to create more opportunities for the prevention and cure of human diseases. This dissertation proposes statistical technologies that have the ability of being adapted to sequencing data in family-based designs, and that account for joint effects as well as gene-gene and gene-environment interactions in the GWA studies. The framework includes statistical methods for rare and common variant association studies. Although next-generation DNA sequencing technologies have made rare variant association studies feasible, the development of powerful statistical methods for rare variant association studies is still underway. Chapter 2 demonstrates two adaptive weighting methods for rare variant association studies based on family data for quantitative traits. The results show that both proposed methods are robust to population stratification, robust to the direction and magnitude of the effects of causal variants, and more powerful than the methods using weights suggested by Madsen and Browning [2009]. In Chapter 3, I extended the previously proposed test for Testing the effect of an Optimally Weighted combination of variants (TOW) [Sha et al., 2012] for unrelated individuals to TOW &ndash F, TOW for Family &ndash based design. Simulation results show that TOW &ndash F can control for population stratification in wide range of population structures including spatially structured populations, is robust to the directions of effect of causal variants, and is relatively robust to percentage of neutral variants. In GWA studies, this dissertation consists of a two &ndash locus joint effect analysis and a two-stage approach accounting for gene &ndash gene and gene &ndash environment interaction. Chapter 4 proposes a novel two &ndash stage approach, which is promising to identify joint effects, especially for monotonic models. The proposed approach outperforms a single &ndash marker method and a regular two &ndash stage analysis based on the two &ndash locus genotypic test. In Chapter 5, I proposed a gene &ndash based two &ndash stage approach to identify gene &ndash gene and gene &ndash environment interactions in GWA studies which can include rare variants. The two &ndash stage approach is applied to the GAW 17 dataset to identify the interaction between KDR gene and smoking status.

Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies.

A wealth of genetic associations for cardiovascular and metabolic phenotypes in humans has been accumulating over the last decade, in particular a large number of loci derived from recent genome wide association studies (GWAS). True complex disease-associated loci often exert modest effects, so their delineation currently requires integration of diverse phenotypic data from large studies to ensure robust meta-analyses. We have designed a gene-centric 50 K single nucleotide polymorphism (SNP) array to assess potentially relevant loci across a range of cardiovascular, metabolic and inflammatory syndromes. The array utilizes a "cosmopolitan" tagging approach to capture the genetic diversity across approximately 2,000 loci in populations represented in the HapMap and SeattleSNPs projects. The array content is informed by GWAS of vascular and inflammatory disease, expression quantitative trait loci implicated in atherosclerosis, pathway based approaches and comprehensive literature searching. The custom flexibility of the array platform facilitated interrogation of loci at differing stringencies, according to a gene prioritization strategy that allows saturation of high priority loci with a greater density of markers than the existing GWAS tools, particularly in African HapMap samples. We also demonstrate that the IBC array can be used to complement GWAS, increasing coverage in high priority CVD-related loci across all major HapMap populations. DNA from over 200,000 extensively phenotyped individuals will be genotyped with this array with a significant portion of the generated data being released into the academic domain facilitating in silico replication attempts, analyses of rare variants and cross-cohort meta-analyses in diverse populations. These datasets will also facilitate more robust secondary analyses, such as explorations with alternative genetic models, epistasis and gene-environment interactions.

Intentions: a confident-based interaction design for smart spaces

The paradigm of ubiquitous computing has become a reference for the design of Smart Spaces. Current trends in Ambient Intelligence are increasingly related to the scope of Internet of Things. This paradigm has the potential to support cost-effective solutions in the fields of telecare, e-health and Ambient Assisted Living. Nevertheless, ubiquitous computing does not provide end users with a role for proactive interactions with the environment. Thus, the deployment of smart health care services at a private space like the home is still unsolved. This PhD dissertation aims to define a person-environment interaction model to foster acceptability and users confidence in private spaces by applying the concept of user-centred security and the human performance model of seven stages of action.

Case-only study of interactions between genetic polymorphisms of GSTM1, P1, T1 and Z1 and smoking in Parkinson's disease

Current opinion contends that complex interactions between genetic and environmental factors play a role in the etiology of Parkinson's disease (PD). Cigarette smoking is thought to reduce risk of PD, and emerging evidence suggests that genetic factors may modulate smoking's effect. We used a case-only design, an approach not previously used to study gene-environment interactions in PD, specifically to study interactions between glutathione-S-transferase (GST) gene polymorphisms and smoking in relation to PD. Four-hundred PD cases (age at onset: 60.0 +/- 10.7 years) were genotyped for common polymorphisms in GSTM1, PI, T1 and Z1 using well-established methods. Smoking exposure data were collected in face-to-face interviews. The independence of the studied GST genotypes and smoking exposure was confirmed by studying 402 healthy, aged individuals. No differences were observed in the distributions of GSTM1, T1 or Z1 polymorphisms between ever-smoked and never-smoked PD cases using logistic regression (all P > 0.43). However, GSTP1 *C haplotypes were over-represented among PD cases who ever smoked (odds ratio for interaction (ORi) = 2.00 (95% Cl: 1.11-3.60, P = 0.03)). Analysis revealed that ORi between smoking and the GSTP1-114Val carrier status increased with increasing smoking dose (P = 0.02 for trend). These data suggest that one or more GSTP1 polymorphisms may interact with cigarette smoking to influence the risk for PD. (C) 2004 Elsevier Ireland Ltd. All rights reserved.

Effect of environment and genotype on bread-making quality of spring-sown spring wheat cultivars in China

Improvement of end-use quality in bread wheat depends on a thorough understanding of current wheat quality and the influences of genotype (G), environment (E), and genotype by environment interaction (G x E) on quality traits. Thirty-nine spring-sown spring wheat (SSSW) cultivars and advanced lines from China were grown in four agro-ecological zones comprising seven locations during the 1998 and 1999 cropping seasons. Data on 12 major bread-making quality traits were used to investigate the effect of G, E, and G x E on these traits. Wide range variability for protein quantity and quality, starch quality parameters and milling quality in Chinese SSSW was observed. Genotype and environment were found to significantly influence all quality parameters as major effects. Kernel hardness, flour yield, Zeleny sedimentation value and mixograph properties were mainly influenced by the genetic variance components, while thousand kernel weight, test weight, and falling number were mostly influenced by the environmental variance components. Genotype, environment, and their interaction had important effects on test weight, mixing development time and RVA parameters. Cultivars originating from Zone VI (northeast) generally expressed high kernel hardness, good starch quality, but poor milling and medium to weak mixograph performance; those from Zone VII (north) medium to good gluten and starch quality, but low milling quality; those from Zone VIII (central northwest) medium milling and starch quality, and medium to strong mixograph performance; those from Zone IX (western/southwestern Qinghai-Tibetan Plateau) medium milling quality, but poor gluten strength and starch parameters; and those from Zone X (northwest) high milling quality, strong mixograph properties, but low protein content. Samples from Harbin are characterized by good gluten and starch quality, but medium to poor milling quality; those from Hongxinglong by strong mixograph properties, medium to high milling quality, but medium to poor starch quality and medium to low protein content; those from Hohhot by good gluten but poor milling quality; those from Linhe by weak gluten quality, medium to poor milling quality; those from Lanzhou by poor bread-making and starch quality; those from Yongning by acceptable bread-making and starch quality and good milling quality; and those from Urumqi by good milling quality, medium gluten quality and good starch pasting parameters. Our findings suggest that Chinese SSSW quality could be greatly enhanced through genetic improvement for targeted well-characterized production environments.

Mixed model formulations for multi-environment trials

When studying genotype X environment interaction in multi-environment trials, plant breeders and geneticists often consider one of the effects, environments or genotypes, to be fixed and the other to be random. However, there are two main formulations for variance component estimation for the mixed model situation, referred to as the unconstrained-parameters (UP) and constrained-parameters (CP) formulations. These formulations give different estimates of genetic correlation and heritability as well as different tests of significance for the random effects factor. The definition of main effects and interactions and the consequences of such definitions should be clearly understood, and the selected formulation should be consistent for both fixed and random effects. A discussion of the practical outcomes of using the two formulations in the analysis of balanced data from multi-environment trials is presented. It is recommended that the CP formulation be used because of the meaning of its parameters and the corresponding variance components. When managed (fixed) environments are considered, users will have more confidence in prediction for them but will not be overconfident in prediction in the target (random) environments. Genetic gain (predicted response to selection in the target environments from the managed environments) is independent of formulation.

Trait physiology and crop modelling as a framework to link phenotypic complexity to underlying genetic systems

New tools derived from advances in molecular biology have not been widely adopted in plant breeding for complex traits because of the inability to connect information at gene level to the phenotype in a manner that is useful for selection. In this study, we explored whether physiological dissection and integrative modelling of complex traits could link phenotype complexity to underlying genetic systems in a way that enhanced the power of molecular breeding strategies. A crop and breeding system simulation study on sorghum, which involved variation in 4 key adaptive traits-phenology, osmotic adjustment, transpiration efficiency, stay-green-and a broad range of production environments in north-eastern Australia, was used. The full matrix of simulated phenotypes, which consisted of 547 location-season combinations and 4235 genotypic expression states, was analysed for genetic and environmental effects. The analysis was conducted in stages assuming gradually increased understanding of gene-to-phenotype relationships, which would arise from physiological dissection and modelling. It was found that environmental characterisation and physiological knowledge helped to explain and unravel gene and environment context dependencies in the data. Based on the analyses of gene effects, a range of marker-assisted selection breeding strategies was simulated. It was shown that the inclusion of knowledge resulting from trait physiology and modelling generated an enhanced rate of yield advance over cycles of selection. This occurred because the knowledge associated with component trait physiology and extrapolation to the target population of environments by modelling removed confounding effects associated with environment and gene context dependencies for the markers used. Developing and implementing this gene-to-phenotype capability in crop improvement requires enhanced attention to phenotyping, ecophysiological modelling, and validation studies to test the stability of candidate genetic regions.

Analysis of line x environment interactions for yield in navy beans. 2. Pattern analysis of lines and environment within years

Seven years of multi-environment yield trials of navy bean (Phaseolus vulgaris L.) grown in Queensland were examined. As is common with plant breeding evaluation trials, test entries and locations varied between years. Grain yield data were analysed for each year using cluster and ordination analyses (pattern analyses). These methods facilitate descriptions of genotype performance across environments and the discrimination among genotypes provided by the environments. The observed trends for genotypic yield performance across environments were partly consistent with agronomic and disease reactions at specific environments and also partly explainable by breeding and selection history. In some cases, similarities in discrimination among environments were related to geographic proximity, in others management practices, and in others similarities occurred between geographically widely separated environments which differed in management practices. One location was identified as having atypical line discrimination. The analysis indicated that the number of test locations was below requirements for adequate representation of line x environment interaction. The pattern analyses methods used were an effective aid in describing the patterns in data for each year and illustrated the variations in adaptive patterns from year to year. The study has implications for assessing the number and location of test sites for plant breeding multi-environment trials, and for the understanding of genetic traits contributing to line x environment interactions.

The neural correlates of reading impairment in adults with developmental dyslexia:evidence from fMRI between group analyses and an fMRI multiple-case study

The goal of this project was to investigate the neural correlates of reading impairment in dyslexia as hypothesised by the main theories – the phonological deficit, visual magnocellular deficit and cerebellar deficit theories, with emphasis on individual differences. This research took a novel approach by: 1) contrasting the predictions in one sample of participants with dyslexia (DPs); 2) using a multiple-case study (and between-group comparisons) to investigate differences in BOLD between each DP and the controls (CPs); 3) demonstrating a possible relationship between reading impairment and its hypothesised neural correlates by using fMRI and a reading task. The multiple-case study revealed that the neural correlates of reading in dyslexia in all cases are not in agreement with the predictions of a single theory. The results show striking individual differences - even, where the neural correlates of reading in two DPs are consistent with the same theory, the areas can differ. A DP can exhibit under-engagement in an area in word, but not in pseudoword reading and vice versa, demonstrating that underactivation in that area cannot be interpreted as a ‘developmental lesion’. Additional analyses revealed complex results. Within-group analyses between behavioural measures and BOLD showed correlations in the predicted regions, areas outside ROI, and lack of correlations in some predicted areas. Comparisons of subgroups which differed on Orthography Composite supported the MDT, but only for Words. The results suggest that phonological scores are not a sufficient predictor of the under-engagement of phonological areas during reading. DPs and CPs exhibited correlations between Purdue Pegboard Composite and BOLD in cerebellar areas only for Pseudowords. Future research into reading in dyslexia should use a more holistic approach, involving genetic and environmental factors, gene by environment interaction, and comorbidity with other disorders. It is argued that multidisciplinary research, within the multiple-deficit model holds significant promise here.

Avaliação de polimorfismos funcionais nos genes de reparo XRCC1, APEX1, XPD e XPF em carcinomas de células escamosas orais

Base excision repair (BER) and nucleotide excision repair (NER) pathways play critical role in maintaining genome integrity. Polymorphisms in BER and NER genes which modulate the DNA repair capacity may affect the susceptibility and prognosis of oral cancer. This study was conducted with genomic DNA from 92 patients with oral squamous cell carcinomas (OSCC) and 130 controls. The cases were followed up to explore the associations between BER and NER genes polymorphisms and the risk and prognosis of OSCC. Four single-nucleotide polymorphisms (SNPs) in XRCC1 (rs25487), APEX1 (rs1130409), XPD (rs13181) and XPF (rs1799797) genes were tested by polymerase chain reaction – quantitative real time method. The GraphPad Prism version 6.0.1 statistical software was applied for statistical analysis of association. Odds ratio (OR), hazard ratio (HR), and their 95 % confidence intervals (CIs) were calculated by logistic regression. Kaplan-Meier curve and Cox proportional hazard model were used for prognostic analysis. The presence of polymorphic variants in XRCC1, APEX1, XPD and XPF genes were not associated with an increased risk of OSCC. Gene-environment interactions with smoking were not significant for any polymorphism. The presence of polymorphic variants of the XPD gene in association with alcohol consumption conferred an increased risk of 1.86 (95% CI: 0.86 – 4.01, p=0.03) for OSCC. Only APEX1 was associated with decreased specific survival (HR 3.94, 95% CI: 1.31 – 11.88, p=0.01). These results suggest an interaction between polymorphic variants of the XPF gene and alcohol consumption. Additionally APEX1 may represent a prognostic marker for OSCC.

A Biocultural Examination of Student Learning Behaviors in Large Undergraduate Lectures

Thesis (Ph.D.)--University of Washington, 2016-08

GGE biplot analysis of multi-environment yield trials of rice produced in a temperate climate

Low temperature is one of the main environmental constraints for rice ( Oryza sativa L.) grain production yield. It is known that multi-environment studies play a critical role in the sustainability of rice production across diverse environments. However, there are few studies based on multi-environment studies of rice in temperate climates. The aim was to study the performance of rice plants in cold environments. Four experimental lines and six cultivars were evaluated at three locations during three seasons. The grain yield data were analyzed with ANOVA, mixed models based on the best linear unbiased predictors (BLUPs), and genotype plus Genotype × Environment interaction (GGE) biplot. High genotype contribution (> 25%) was observed in grain yield and the interaction between genotype and locations was not very important. Results also showed that ‘Quila 241319’ was the best experimental line with the highest grain yield (11.3 t ha-1) and grain yield stability across the environments; commercial cultivars were classified as medium grain yield genotypes.

A phenomenological study of contemplative experiences : implications for interior design

This research reports on a project concerned with the relationship between the person and the environment in the context of achieving a contemplative or existential state – a state which can be experienced either consciously or subconsciously. The need for such a study originated with the desire to contribute to the design of multicultural spaces which could be used for a range of activities within the public and the personal arena, activities including contemplation, meditation and prayer. The concept of ‘sacred’ is explored in the literature review and in primary interviews with the participants of this study. Given that the word ‘sacred’ is highly value-laden and potentially alienating for some people, it was decided to use the more accessible term ‘contemplative’. The outcomes of the study inform the practice of interior design and architecture which tends currently to neglect the potential for all spaces to be existentially meaningful. Informed by phenomenological methodology, data were collected from a diverse group of people, using photo-elicitation and interviews. The technique of photo-elicitation proved to be highly effective in helping people reveal their everyday lived experience of contemplative spaces. Reflective analysis (Van Manen 2000) was used to explore the data collected. The initial stage of analysis produced three categories of data: varying conceptions of contemplation, aspects of the person involved in the contemplation, and aspects of environment involved in contemplation. From this, it was found that achieving a state of contemplation involves both the person and the environment in a dialectic process of unfolding. The unfolding has various physical, psycho-social, and existential dimensions or qualities which operate sequentially and simultaneously. Two concepts emerged as being central to unfolding: ‘Cleansing’ and ‘Nothingness’. Unfolding is found to comprise the Core; Distinction; Manifestation; Cleansing; Creation; and Sharing. This has a parallel with Mircea Eliade’s (1959) definition of sacred as something that manifests itself as different from the profane. The power of design, re-contextualization through utility and purpose, and the existential engagements between the person and environment are used as a basis for establishing the potential contribution of the study to interior design. In this way, the study makes a contribution to our understanding of how space and its elements inspire, support and sustain person environment interaction – particularly at the existential level – as well as to our understanding of the multi-dimensional and holistic nature of this interaction. In addition, it points to the need for a phenomenological re-conceptualisation of the design/client relationship. In summary, the contributions of this research are: the exploration of contemplative experience as sacred experience; an understanding of the design of space as creating engagement between person and environment; a rationale for the introduction of a phenomenological approach to the relationship between designer and clients; and raising awareness of the spiritual in a holistic approach to design.

Manipulating task constraints to improve tactical knowledge and collective decision-making in rugby union

In team sports such as rugby union, a myriad of decisions and actions occur within the boundaries that compose the performance perceptual- motor workspace. The way that these performance boundaries constrain decision making and action has recently interested researchers and has involved developing an understanding of the concept of constraints. Considering team sports as complex dynamical systems, signifies that they are composed of multiple, independent agents (i.e. individual players) whose interactions are highly integrated. This level of complexity is characterized by the multiple ways that players in a rugby field can interact. It affords the emergence of rich patterns of behaviour, such as rucks, mauls, and collective tactical actions that emerge due to players’ adjustments to dynamically varying competition environments. During performance, the decisions and actions of each player are constrained by multiple causes (e.g. technical and tactical skills, emotional states, plans, thoughts, etc.) that generate multiple effects (e.g. to run or pass, to move forward to tackle or maintain position and drive the opponent to the line), a prime feature in a complex systems approach to team games performance (Bar- Yam, 2004). To establish a bridge between the complexity sciences and learning design in team sports like rugby union, the aim of practice sessions is to prepare players to pick up and explore the information available in the multiple constraints (i.e. the causes) that influence performance. Therefore, learning design in training sessions should be soundly based on the interactions amongst players (i.e.teammates and opponents) that will occur in rugby matches. To improve individual and collective decision making in rugby union, Passos and colleagues proposed in previous work a performer- environment interaction- based approach rather than a traditional performer- based approach (Passos, Araújo, Davids & Shuttleworth, 2008).