Aircraft collision avoidance using spherical visual predictive control and single point features

This paper presents practical vision-based collision avoidance for objects approximating a single point feature. Using a spherical camera model, a visual predictive control scheme guides the aircraft around the object along a conical spiral trajectory. Visibility, state and control constraints are considered explicitly in the controller design by combining image and vehicle dynamics in the process model, and solving the nonlinear optimization problem over the resulting state space. Importantly, range is not required. Instead, the principles of conical spiral motion are used to design an objective function that simultaneously guides the aircraft along the avoidance trajectory, whilst providing an indication of the appropriate point to stop the spiral behaviour. Our approach is aimed at providing a potential solution to the See and Avoid problem for unmanned aircraft and is demonstrated through a series.

Factors associated with common mental disorders during the transition to adulthood : do emerging adults and ‘early starters’ differ? Findings from an Australian birth cohort study

Background: Despite increasing diversity in pathways to adulthood, choices available to young people are influenced by environmental, familial and individual factors, namely access to socioeconomic resources, family support and mental and physical health status. Young people from families with higher socioeconomic position (SEP) are more likely to pursue tertiary education and delay entry to adulthood, whereas those from low socioeconomic backgrounds are less likely to attain higher education or training, and more likely to partner and become parents early. The first group are commonly termed ‘emerging adults’ and the latter group ‘early starters’. Mental health disorders during this transition can seriously disrupt psychological, social and academic development as well as employment prospects. Depression, anxiety and most substance use disorders have early onset during adolescence and early adulthood with approximately three quarters of lifetime psychiatric disorders having emerged by 24 years of age. Aims: This thesis aimed to explore the relationships between mental health, sociodemographic factors and family functioning during the transition to adulthood. Four areas were investigated: 1) The key differences between emerging adults and ‘early starters’, were examined and focused on a series of social, economic, and demographic factors as well as DSM-IV diagnoses; 2) Methodological issues associated with the measurement of depression and anxiety in young adults were explored by comparing a quantitative measure of symptoms of anxiety and depression (Achenbach’s YSR and YASR internalising scales) with DSM-IV diagnosed depression and anxiety. 3) The association between family SEP and DSM-IV depression and anxiety was examined in relation to the different pathways to adulthood. 4) Finally, the association between pregnancy loss, abortion and miscarriage, and DSM-IV diagnoses of common psychiatric disorders was assessed in young women who reported early parenting, experiencing a pregnancy loss, or who had never been pregnant. Methods: Data were taken from the Mater University Study of Pregnancy (MUSP), a large birth cohort started in 1981 in Brisbane, Australia. 7223 mothers and their children were assessed five times, at 6 months, 5, 14 and 21 years after birth. Over 3700 young adults, aged 18 to 23 years, were interviewed at the 21-year phase. Respondents completed an extensive series of self-reported questionnaires and a computerised structured psychiatric interview. Three outcomes were assessed at the 21-year phase. Mental health disorders diagnosed by a computerised structured psychiatric interview (CIDI-Auto), the prevalence of DSM-IV depression, anxiety and substance use disorders within the previous 12-month, during the transition (between ages of 18 and 23 years) or lifetime were examined. The primary outcome “current stage in the transition to adulthood” was developed using a measure conceptually constructed from the literature. The measure was based on important demographic markers, and these defined four independent groups: emerging adults (single with no children and living with parents), and three categories of ‘early starter’, singles (with no children or partner, living independently), those with a partner (married or cohabitating but without children) and parents. Early pregnancy loss was assessed using a measure that also defined four independent groups and was based on pregnancy outcomes in the young women This categorised the young women into those who were never pregnant, women who gave birth to a live child, and women who reported some form of pregnancy loss, either an abortion or a spontaneous miscarriage. A series of analyses were undertaken to test the study aims. Potential confounding and mediating factors were prospectively measured between the child’s birth and the 21-year phase. Binomial and multinomial logistic regression was used to estimate the risk of relevant outcomes, and the associations were reported as odds ratios (OR) and 95% confidence intervals (95%CI). Key findings: The thesis makes a number of important contributions to our understanding of the transition to adulthood, particularly in relation to the mental health consequences associated with different pathways. Firstly, findings from the thesis clearly showed that young people who parented or partnered early fared worse across most of the economic and social factors as well as the common mental disorders when compared to emerging adults. That is, young people who became early parents were also more likely to experience recent anxiety (OR=2.0, 95%CI 1.5-2.8) and depression (OR=1.7, 95%CI 1.1-2.7) than were emerging adults after taking into account a range of confounding factors. Singles and those partnering early also had higher rates of lifetime anxiety and depression than emerging adults. Young people who partnered early, but were without children, had decreased odds of recent depression; this may be due to the protective effect of early marriage against depression. It was also found that young people who form families early had an increased risk of cigarette smoking (parents OR=3.7, 95%CI 2.9-4.8) compared to emerging adults, but not heavy alcohol (parents OR=0.4, 95%CI 0.3-0.6) or recent illicit drug use. The high rates of cigarette smoking and tobacco use disorders in ‘early starters’ were explained by common risk factors related to early adversity and lower SEP. Having a child and early marriage may well function as a ‘turning point’ for some young people, it is not clear whether this is due to a conscious decision to disengage from a previous ‘substance using’ lifestyle or simply that they no longer have the time to devote to such activities because of child caring. In relation to the methodological issues associated with assessing common mental disorders in young adults, it was found that although the Achenbach empirical internalising scales successfully predicted both later DSM-IV depression (YSR OR=2.3, 95%CI 1.7-3.1) and concurrently diagnosed depression (YASR OR=6.9, 95%CI 5.0- 9.5) and anxiety (YASR OR=5.1, 95%CI 3.8- 6.7), the scales discriminated poorly between young people with or without DSM-IV diagnosed mood disorder. Sensitivity values (the proportion of true positives) for the internalising scales were surprisingly low. Only a third of young people with current DSM-IV depression (range for each of the scales was between 34% to 42%) were correctly identified as cases by the YASR internalising scales, and only a quarter with current anxiety disorder (range of 23% to 31%) were correctly identified. Also, use of the DSM-oriented scales increased sensitivity only marginally (for depression between 2-8%, and anxiety between 2-6%) above the standard Achenbach scales. This is despite the fact that the DSM-oriented scales were originally developed to overcome the poor prediction of DSM-IV diagnoses by the Achenbach scales. The internalising scales, both standard and DSM-oriented, were much more effective at identifying young people with comorbid depression and anxiety, with OR’s 10.1 to 21.7 depending on the internalising scale used. SEP is an important predictor of both an early transition to adulthood and the experience of anxiety during that time Family income during adolescence was a strong predictor of early parenting and partnering before age 24 but not early independent living. Compared to families in the upper quintile, young people from families with low income were nearly twice as likely to live with a partner and four times more likely to become parents (OR ranged from 2.6 to 4.0). This association remained after adjusting for current employment and education level. Children raised in low income families were 30% more likely to have an anxiety disorder (OR=1.3, 95%CI 0.9-1.9), but not depression, as young adults when compared to children from wealthier families. Emerging adults and ‘early starters’ from low income families did not differ in their likelihood of having a later anxiety disorder. Young women reporting a pregnancy loss had nearly three times the odds of experiencing a lifetime illicit drug disorder (excluding cannabis) [abortion OR=3.6, 95%CI 2.0-6.7 and miscarriage OR=2.6, 95%CI 1.2-5.4]. Abortion was associated with alcohol use disorder (OR=2.1, 95%CI 1.3- 3.5) and 12-month depression (OR=1.9, 95%CI 1.1- 3.1). These finding suggest that the association identified by Fergusson et al between abortion and later psychiatric disorders in young women may be due to pregnancy loss and not to abortion, per se. Conclusion: Findings from this thesis support the view that young people who parent or partner early have a greater burden of depression and anxiety when compared to emerging adults. As well, young women experiencing pregnancy loss, from either abortion or miscarriage, are more likely to experience depression and anxiety than are those who give birth to a live infant or who have never been pregnant. Depression, anxiety and substance use disorders often go unrecognised and untreated in young people; this is especially true in young people from lower SEP. Early identification of these common mental health disorders is important, as depression and anxiety experienced during the transition to adulthood have been found to seriously disrupt an individual’s social, educational and economic prospects in later life.

Feeding attitudes, practices and traditional dietary beliefs of Chinese mothers with young children in Australia : a mixed methods study

Background and Objectives Obesity and some dietary related diseases are emerging health problems among Chinese immigrants and their children in developed countries. These health problems are closely linked to eating habits, which are established in the early years of life. Young children’s eating habits are likely to persist into later childhood and youth. Family environment and parental feeding practices have a strong effect on young children’s eating habits. Little information is available on the early feeding practices of Chinese mothers in Australia. The aim of this study was to understand the dietary beliefs, feeding attitudes and practices of Chinese mothers with young children who were recent immigrants to Australia. Methods Using a sequential explanatory design, this mixed methods study consisted of two distinct phases. Phase 1 (quantitative): 254 Chinese immigrant mothers of children aged 12 to 59 months completed a cross-sectional survey. The psychometric properties and factor structure of a Chinese version of the Child Feeding Questionnaire (CFQ, by Birch et al. 2001) were assessed and used to measure specific maternal feeding attitudes and controlling feeding practices. Other questions were developed from the literature and used to explore maternal traditional dietary beliefs and feeding practices related to their beliefs, perceptions of picky eating in children and a range of socioeconomic and acculturation factors. Phase 2 (qualitative): 21 mothers took part in a follow-up telephone interview to assist in explaining and interpreting some significant findings obtained in the first phase. Results Chinese mothers held strong traditional dietary beliefs and fed their children according to these beliefs. However, children’s consumption of non-core foods was high. Both traditional Chinese and Australian style foods were consumed by their children. Confirmatory factor analysis revealed that the original 7-factor model of the CFQ provided an acceptable fit to the data with minor modification. However, an alternative model with eight constructs in which two items related to using food rewards were separated from the original restriction construct, not only provided an acceptable fit to the data, but also improved the conceptual clarity of the constructs. The latter model included 24 items loading onto the following eight constructs: restriction, pressure to eat, monitoring, use of food rewards, perceived responsibility, perception of own weight, perception of child’s weight, and concern about child becoming overweight. The internal consistency of the constructs was acceptable or desirable (Cronbach’s α = .60 - .93). Mothers reported low levels of concern about their child overeating or becoming overweight, but high levels of controlling feeding practices: restriction, monitoring, pressure to eat and use of food rewards. More than one quarter of mothers misinterpreted their child’s weight status (based on mothers’ self-reported data). In addition, mothers’ controlling feeding practices independently predicted half of the variance and explained 16% of the variance in child weight status: pressuring the child to eat was negatively associated with child weight status (β = -0.30, p < .01) and using food rewards was positively associated with child weight status (β = 0.20, p < .05) after adjusting for maternal and child covariates. Monitoring and restriction were not associated with child weight status. Mothers’ perceptions of their child’s weight were positively associated with child weight status (β = 0.33, p < .01). Moreover, mothers reported that they mostly decided what (65%) and how much (80%) food their child ate. Mothers who decided what food their child ate were more likely to monitor (β = -0.17, p < .05) and restrict (β = -0.17, p < .05) their child’s food consumption. Mothers who let their child decide how much food their child ate were less likely to pressure their child to eat (β = -0.38, p < .01) and use food rewards (β = -0.24, p < .01). Mothers’ perceptions of picky eating behaviour were positively associated with their use of pressure (β = 0.21, p < .01) and negatively associated with monitoring (β = -0.16, p < .05) and perceptions of their child’s weight status (β = -0.13, p < .05). Qualitative data showed that pressuring to eat, monitoring and restriction of the child’s food consumption were common practices among these mothers. However, mothers stated that their motivation for monitoring and restricting was to ensure the child’s general health. Mothers’ understandings of picky eating behaviour in their children were consistent with the literature and they reported multiple feeding strategies to deal with it. Conclusion Chinese immigrant mothers demonstrated strong traditional dietary beliefs, a low level of concern for child weight, misperceptions of child weight status, and a high overall level of control in child feeding in this study. The Chinese version of the CFQ, which consists of eight constructs and distinguishes between the constructs using food rewards and restriction, is an appropriate instrument to assess feeding attitudes and controlling feeding practices among Chinese immigrant mothers of young children in Australia. Mothers’ feeding attitudes and practices were associated with children’s weight status and mothers’ perceptions of picky eating behaviour in children after adjusting for a range of socio-demographic maternal and child characteristics. Monitoring and restriction of children’s food consumption according to food selection may be positive feeding practices, whereas pressuring to eat and using food rewards appeared to be negative feeding practices in this study. In addition, the results suggest that these young children have high exposure to energy-dense, nutrient-poor food. There is a need to develop and implement nutrition interventions to improve maternal feeding practices and the dietary quality among children of Chinese immigrant mothers in Australia.

Mothers' perceptions of introducing solids to their infant at six months of age : identifying critical belief-based targets to promote adherence to current infant feeding guidelines

We investigated critical belief-based targets for promoting the introduction of solid foods to infants at six months. First-time mothers (N = 375) completed a Theory of Planned Behaviour belief-based questionnaire and follow-up questionnaire assessing the age the infant was first introduced to solids. Normative beliefs about partner/spouse (β = 0.16) and doctor (β = 0.22), and control beliefs about commercial baby foods available for infants before six months (β = −0.20), predicted introduction of solids at six months. Intervention programs should target these critical beliefs to promote mothers’ adherence to current infant feeding guidelines to introduce solids at around six months.

Perceived environmental correlates and physical activity: What neighborhood aspects really matter for mothers and fathers of young children?

Limited research has been conducted with at-risk populations in examining perceived environmental correlates of physical activity (PA); thus, we examined this relationship among parents with young children, a group at risk for physical inactivity. Parents (252 mothers, 206 fathers) completed a questionnaire assessing measures of perceived neighborhood environment and a 1-week follow-up of PA behavior. Mothers were more likely than fathers to perceive their neighborhood as unsafe to go for walks at night and less likely to perceive transit stops within 10–15 minutes walking distance, sidewalks on most streets, and facilities to bicycle. Adjusting for demographics, shops within easy walking distance, sidewalks on most streets, and having no more than one motor vehicle were associated with being active for both sexes. Access to transit stops and free/low cost recreational facilities were also associated with mothers’ PA. These findings suggest that environmental factors may support parents being active at recommended levels.

Mothers vs fathers as learner driver supervisors : time commitment, driving activities and perceptions of risk

The learner licence, within a graduated driver licensing system, provides new drivers with the opportunity to learn to drive under the supervision of a more experienced driver. The Queensland graduated driver licensing system requires learner drivers to record a minimum of 100 logbook hours of supervised practice with the support of parents appearing critical to ensure that this is achieved. This paper examines differences between mothers and fathers who supervise learner drivers. Mothers and fathers from Queensland who had recently supervised their child while they learnt to drive completed an internet survey about their experiences. It appears that one strategy that parents use to provide practice hours is for the child to drive themselves or their parents to or from activities that they would have attended anyway in addition to undertaking special trips in the car for the purposes of practising. The results suggest that mothers, when compared with fathers, consider driving at all stages of licensure riskier and that mothers provided more hours of supervision than fathers. However, despite this, there are limited differences between how frequently mothers and fathers provide different driving experiences such as deliberately practising in suburban areas or with passengers in the car. This research fills a gap in the literature by providing important information about the way in which parents supervise their children while they are driving on a learner licence as well as identifying some of the differences and similarities between mothers and fathers.

Investigation of two Wnt signalling pathway single nucleotide polymorphisms in a breast cancer-affected Australian population

In the mammary gland, Wnt signals are strongly implicated in initial development of the mammary rudiments and in the ductal branching and alveolar morphogenesis that occurs during pregnancy. Previously, we identified two Wnt signaling pathway-implicated genes, PPP3CA and MARK4, as having a role in more aggressive and potentially metastatic breast tumors. In this study, we examined two SNPs within PPP3CA and MARK4 in an Australian case-control study population for a potential role in human breast cancers. 182 cases and 180 controls were successfully genotyped for the PPP3CA SNP (rs2850328) and 182 cases and 177 controls were successfully genotyped for the MARK4 SNP (rs2395) using High Resolution Melt (HRM) analysis. Genotypes of randomly selected samples for both SNPs were validated by dye terminator sequencing. Chi-square tests were performed to determine any significant differences in the genotype and allele frequencies between the cases and controls. Chi-square analysis showed no statistically significant difference (p > .05) for genotype frequencies between cases and controls for rs2850328 (χ2 = 1.2, p = .5476) or rs2395 (χ2 = .3, p = .8608). Similarly, no statistical difference was observed for allele frequencies for rs2850328 (χ2 = .68, p = .4108) or rs2395 (χ2 = .02, p = .893). Even though an association of the polymorphisms rs2850328 and rs2395 and breast cancer was not detected in our case-control study population, other variants within the PPP3CA and MARK4 genes may still be associated with breast cancer, as both genes are implicated with processes involved in the disease as well as their mutual partaking in the Wnt signaling pathway.

Single nucleotide polymorphism in hsa-mir-196a-2 and breast cancer risk : a case control study

microRNAs are small, non-coding RNAs that influence gene expression on a post-transcriptional level. They participate in diverse biological pathways and may act as either tumor suppressor genes or oncogenes. As they may have an effect on thousands of target mRNAs, single-nucleotide polymorphisms in microRNA genes might have major functional consequences, because the microRNA's properties and/or maturation may change. miR-196a has been reported to be aberrantly expressed in breast cancer tissue. Additionally, the SNP rs11614913 in hsa-mir-196a-2 has been found to be associated with breast cancer risk in some studies although not in others. This study evaluated the association between rs11614913 and breast cancer risk in a Caucasian case-control cohort in Queensland, Australia. Results do not support an association of the tested hsa-mir-196a-2 polymorphism with breast cancer susceptibility in this cohort. As there is a discrepancy between our results and previous findings, it is important to assess the role of rs11614913 in breast cancer by further larger studies investigating different ethnic groups.

Single-nucleotide polymorphism alleles in the insulin receptor gene are associated with typical migraine

We have identified a migraine locus on chromosome 19p13.3/2 using linkage and association analysis. We isolated 48 single-nucleotide polymorphisms within the locus, of which we genotyped 24 in a Caucasian population comprising 827 unrelated cases and 765 controls. Five single-nucleotide polymorphisms within the insulin receptor gene showed significant association with migraine. This association was independently replicated in a case-control population collected separately. We used experiments with insulin receptor RNA and protein to investigate functionality for the migraine-associated single-nucleotide polymorphisms. We suggest possible functions for the insulin receptor in migraine pathogenesis.

Locked nucleic acid (LNA) single nucleotide polymorphism (SNP) genotype analysis and validation using real-time PCR

With an increased emphasis on genotyping of single nucleotide polymorphisms (SNPs) in disease association studies, the genotyping platform of choice is constantly evolving. In addition, the development of more specific SNP assays and appropriate genotype validation applications is becoming increasingly critical to elucidate ambiguous genotypes. In this study, we have used SNP specific Locked Nucleic Acid (LNA) hybridization probes on a real-time PCR platform to genotype an association cohort and propose three criteria to address ambiguous genotypes. Based on the kinetic properties of PCR amplification, the three criteria address PCR amplification efficiency, the net fluorescent difference between maximal and minimal fluorescent signals and the beginning of the exponential growth phase of the reaction. Initially observed SNP allelic discrimination curves were confirmed by DNA sequencing (n = 50) and application of our three genotype criteria corroborated both sequencing and observed real-time PCR results. In addition, the tested Caucasian association cohort was in Hardy-Weinberg equilibrium and observed allele frequencies were very similar to two independently tested Caucasian association cohorts for the same tested SNP. We present here a novel approach to effectively determine ambiguous genotypes generated from a real-time PCR platform. Application of our three novel criteria provides an easy to use semi-automated genotype confirmation protocol.

Allelic variation at a single gene increases food value in a drought-tolerant staple cereal

The production of adequate agricultural outputs to support the growing human population places great demands on agriculture, especially in light of ever-greater restrictions on input resources. Sorghum is a drought-adapted cereal capable of reliable production where other cereals fail, and thus represents a good candidate to address food security as agricultural inputs of water and arable land grow scarce. A long-standing issue with sorghum grain is that it has an inherently lower digestibility. Here we show that a low-frequency allele type in the starch metabolic gene, pullulanase, is associated with increased digestibility, regardless of genotypic background. We also provide evidence that the beneficial allele type is not associated with deleterious pleiotropic effects in the modern field environment. We argue that increasing the digestibility of an adapted crop is a viable way forward towards addressing food security while maximizing water and land-use efficiency.

Measurement, modelling and capacity analysis for novel, fixed multi-user single-antenna MIMO-OFDM system, in rural environments

High-speed broadband internet access is widely recognised as a catalyst to social and economic development. However, the provision of broadband Internet services with the existing solutions to rural population, scattered over an extensive geographical area, remains both an economic and technical challenge. As a feasible solution, the Commonwealth Scientific and Industrial Research Organization (CSIRO) proposed a highly spectrally efficient, innovative and cost-effective fixed wireless broadband access technology, which uses analogue TV frequency spectrum and Multi-User MIMO (MUMIMO) technology with Orthogonal-Frequency-Division-Multiplexing (OFDM). MIMO systems have emerged as a promising solution for the increasing demand of higher data rates, better quality of service, and higher network capacity. However, the performance of MIMO systems can be significantly affected by different types of propagation environments e.g., indoor, outdoor urban, or outdoor rural and operating frequencies. For instance, large spectral efficiencies associated with MIMO systems, which assume a rich scattering environment in urban environments, may not be valid for all propagation environments, such as outdoor rural environments, due to the presence of less scatterer densities. Since this is the first time a MU-MIMO-OFDM fixed broadband wireless access solution is deployed in a rural environment, questions from both theoretical and practical standpoints arise; For example, what capacity gains are available for the proposed solution under realistic rural propagation conditions?. Currently, no comprehensive channel measurement and capacity analysis results are available for MU-MIMO-OFDM fixed broadband wireless access systems which employ large scale multiple antennas at the Access Point (AP) and analogue TV frequency spectrum in rural environments. Moreover, according to the literature, no deterministic MU-MIMO channel models exist that define rural wireless channels by accounting for terrain effects. This thesis fills the aforementioned knowledge gaps with channel measurements, channel modeling and comprehensive capacity analysis for MU-MIMO-OFDM fixed wireless broadband access systems in rural environments. For the first time, channel measurements were conducted in a rural farmland near Smithton, Tasmania using CSIRO's broadband wireless access solution. A novel deterministic MU-MIMO-OFDM channel model, which can be used for accurate performance prediction of rural MUMIMO channels with dominant Line-of-Sight (LoS) paths, was developed under this research. Results show that the proposed solution can achieve 43.7 bits/s/Hz at a Signal-to- Noise Ratio (SNR) of 20 dB in rural environments. Based on channel measurement results, this thesis verifies that the deterministic channel model accurately predicts channel capacity in rural environments with a Root Mean Square (RMS) error of 0.18 bits/s/Hz. Moreover, this study presents a comprehensive capacity analysis of rural MU-MIMOOFDM channels using experimental, simulated and theoretical models. Based on the validated deterministic model, further investigations on channel capacity and the eects of capacity variation, with different user distribution angles (θ) around the AP, were analysed. For instance, when SNR = 20dB, the capacity increases from 15.5 bits/s/Hz to 43.7 bits/s/Hz as θ increases from 10° to 360°. Strategies to mitigate these capacity degradation effects are also presented by employing a suitable user grouping method. Outcomes of this thesis have already been used by CSIRO scientists to determine optimum user distribution angles around the AP, and are of great significance for researchers and MU-MUMO-OFDM system developers to understand the advantages and potential capacity gains of MU-MIMO systems in rural environments. Also, results of this study are useful to further improve the performance of MU-MIMO-OFDM systems in rural environments. Ultimately, this knowledge contribution will be useful in delivering efficient, cost-effective high-speed wireless broadband systems that are tailor-made for rural environments, thus, improving the quality of life and economic prosperity of rural populations.

The association of single nucleotide polymorphisms with endometrial cancer risk and prognosis

Endometrial cancer is one of the most common female diseases in developed nations and is the most commonly diagnosed gynaecological cancer in Australia. The disease is commonly classified by histology: endometrioid or non-endometrioid endometrial cancer. While non-endometrioid endometrial cancers are accepted to be high-grade, aggressive cancers, endometrioid cancers (comprising 80% of all endometrial cancers diagnosed) generally carry a favourable patient prognosis. However, endometrioid endometrial cancer patients endure significant morbidity due to surgery and radiotherapy used for disease treatment, and patients with recurrent disease have a 5-year survival rate of less than 50%. Genetic analysis of women with endometrial cancer could uncover novel markers associated with disease risk and/or prognosis, which could then be used to identify women at high risk and for the use of specialised treatments. Proteases are widely accepted to play an important role in the development and progression of cancer. This PhD project hypothesised that SNPs from two protease gene families, the matrix metalloproteases (MMPs, including their tissue inhibitors, TIMPs) and the tissue kallikrein-related peptidases (KLKs) would be associated with endometrial cancer susceptibility and/or prognosis. In the first part of this study, optimisation of the genotyping techniques was performed. Results from previously published endometrial cancer genetic association studies were attempted to be validated in a large, multicentre replication set (maximum cases n = 2,888, controls n = 4,483, 3 studies). The rs11224561 progesterone receptor SNP (PGR, A/G) was observed to be associated with increased endometrial cancer risk (per A allele OR 1.31, 95% CI 1.12-1.53; p-trend = 0.001), a result which was initially reported among a Chinese sample set. Previously reported associations for the remaining 8 SNPs investigated for this section of the PhD study were not confirmed, thereby reinforcing the importance of validation of genetic association studies. To examine the effect of SNPs from the MMP and KLK families on endometrial cancer risk, we selected the most significantly associated MMP and KLK SNPs from genome-wide association study analysis (GWAS) to be genotyped in the GWAS replication set (cases n = 4,725, controls n = 9,803, 13 studies). The significance of the MMP24 rs932562 SNP was unchanged after incorporation of the stage 2 samples (Stage 1 per allele OR 1.18, p = 0.002; Combined Stage 1 and 2 OR 1.09, p = 0.002). The rs10426 SNP, located 3' to KLK10 was predicted by bioinformatic analysis to effect miRNA binding. This SNP was observed in the GWAS stage 1 result to exhibit a recessive effect on endometrial cancer risk, a result which was not validated in the stage 2 sample set (Stage 1 OR 1.44, p = 0.007; Combined Stage 1 and 2 OR 1.14, p = 0.08). Investigation of the regions imputed surrounding the MMP, TIMP and KLK genes did not reveal any significant targets for further analysis. Analysis of the case data from the endometrial cancer GWAS to identify genetic variation associated with cancer grade did not reveal SNPs from the MMP, TIMP or KLK genes to be statistically significant. However, the representation of SNPs from the MMP, TIMP and KLK families by the GWAS genotyping platform used in this PhD project was examined and observed to be very low, with the genetic variation of four genes (MMP23A, MMP23B, MMP28 and TIMP1) not captured at all by this technique. This suggests that comprehensive candidate gene association studies will be required to assess the role of SNPs from these genes with endometrial cancer risk and prognosis. Meta-analysis of gene expression microarray datasets curated as part of this PhD study identified a number of MMP, TIMP and KLK genes to display differential expression by endometrial cancer status (MMP2, MMP10, MMP11, MMP13, MMP19, MMP25 and KLK1) and histology (MMP2, MMP11, MMP12, MMP26, MMP28, TIMP2, TIMP3, KLK6, KLK7, KLK11 and KLK12). In light of these findings these genes should be prioritised for future targeted genetic association studies. Two SNPs located 43.5 Mb apart on chromosome 15 were observed from the GWAS analysis to be associated with increased endometrial cancer grade, results that were validated in silico in two independent datasets. One of these SNPs, rs8035725 is located in the 5' untranslated region of a MYC promoter binding protein DENND4A (Stage 1 OR 1.15, p = 9.85 x 10P -5 P, combined Stage 1 and in silico validation OR 1.13, p = 5.24 x 10P -6 P). This SNP has previously been reported to alter the expression of PTPLAD1, a gene involved in the synthesis of very long fatty acid chains and in the Rac1 signaling pathway. Meta-analysis of gene expression microarray data found PTPLAD1 to display increased expression in the aggressive non-endometrioid histology compared with endometrioid endometrial cancer, suggesting that the causal SNP underlying the observed genetic association may influence expression of this gene. Neither rs8035725 nor significant SNPs identified by imputation were predicted bioinformatically to affect transcription factor binding sites, indicating that further studies are required to assess their potential effect on other regulatory elements. The other grade- associated SNP, rs6606792, is located upstream of an inferred pseudogene, ELMO2P1 (Stage 1 OR 1.12, p = 5 x 10P -5 P; combined Stage 1 and in silico validation OR 1.09, p = 3.56 x 10P -5 P). Imputation of the ±1 Mb region surrounding this SNP revealed a cluster of significantly associated variants which are predicted to abolish various transcription factor binding sites, and would be expected to decrease gene expression. ELMO2P1 was not included on the microarray platforms collected for this PhD, and so its expression could not be investigated. However, the high sequence homology of ELMO2P1 with ELMO2, a gene important to cell motility, indicates that ELMO2 could be the parent gene for ELMO2P1 and as such, ELMO2P1 could function to regulate the expression of ELMO2. Increased expression of ELMO2 was seen to be associated with increasing endometrial cancer grade, as well as with aggressive endometrial cancer histological subtypes by microarray meta-analysis. Thus, it is hypothesised that SNPs in linkage disequilibrium with rs6606792 decrease the transcription of ELMO2P1, reducing the regulatory effect of ELMO2P1 on ELMO2 expression. Consequently, ELMO2 expression is increased, cell motility is enhanced leading to an aggressive endometrial cancer phenotype. In summary, these findings have identified several areas of research for further study. The results presented in this thesis provide evidence that a SNP in PGR is associated with risk of developing endometrial cancer. This PhD study also reports two independent loci on chromosome 15 to be associated with increased endometrial cancer grade, and furthermore, genes associated with these SNPs to be differentially expressed according in aggressive subtypes and/or by grade. The studies reported in this thesis support the need for comprehensive SNP association studies on prioritised MMP, TIMP and KLK genes in large sample sets. Until these studies are performed, the role of MMP, TIMP and KLK genetic variation remains unclear. Overall, this PhD study has contributed to the understanding of genetic variation involvement in endometrial cancer susceptibility and prognosis. Importantly, the genetic regions highlighted in this study could lead to the identification of novel gene targets to better understand the biology of endometrial cancer and also aid in the development of therapeutics directed at treating this disease.

Saliva-derived DNA performs well in large-scale, high-density single-nucleotide polymorphism microarray studies

As of June 2009, 361 genome-wide association studies (GWAS) had been referenced by the HuGE database. GWAS require DNA from many thousands of individuals, relying on suitable DNA collections. We recently performed a multiple sclerosis (MS) GWAS where a substantial component of the cases (24%) had DNA derived from saliva. Genotyping was done on the Illumina genotyping platform using the Infinium Hap370CNV DUO microarray. Additionally, we genotyped 10 individuals in duplicate using both saliva- and blood-derived DNA. The performance of blood- versus saliva-derived DNA was compared using genotyping call rate, which reflects both the quantity and quality of genotyping per sample and the “GCScore,” an Illumina genotyping quality score, which is a measure of DNA quality. We also compared genotype calls and GCScores for the 10 sample pairs. Call rates were assessed for each sample individually. For the GWAS samples, we compared data according to source of DNA and center of origin. We observed high concordance in genotyping quality and quantity between the paired samples and minimal loss of quality and quantity of DNA in the saliva samples in the large GWAS sample, with the blood samples showing greater variation between centers of origin. This large data set highlights the usefulness of saliva DNA for genotyping, especially in high-density single-nucleotide polymorphism microarray studies such as GWAS.