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The significant social and economic losses as a result of bovine tuberculosis (bTB) present a continuous challenge to cattle industries in the United Kingdom (UK) and worldwide. Furthermore, as a zoonotic disease, bTB may pose a threat to humans. The potential transmission of bTB in cattle, estimated by the basic reproductive ratio (R0) was found to range between 1.0 and 1.9 in previous studies. In the UK, there has been an overall increase in bTB incidence in the last two decades despite national control and eradication programmes spanning over five decades. Such programmes mainly consist of surveillance based on the administration of skin tests and culling of animals reacting positive to these tests. Animal mobility restrictions are implemented in this case. At the same time, several studies have demonstrated that there is significant host genetic variation in individual cattle susceptibility to bTB, making the disease amenable to improvement with genetic or genomic selection. In addition, genomic analyses enhance the understanding of genetic mechanisms underlying the disease and its dynamics. The overall aim of this PhD thesis was to address existing scientific research gaps on the genetics of bTB resistance in dairy cattle. The following specific objectives were set: 1) to identify genomic regions underlying susceptibility to bTB using novel trait definitions, 2) to quantify the impact of long-term genetic selection for increased resistance to bTB on disease prevalence and dynamics and 3) to determine the consequences of genetically selecting for increased resistance to bTB on other economically important traits in dairy cattle. Genome-wide association studies (GWAS), regional heritability mapping (RHM) and chromosomal association analyses were applied in order to identify genomic regions associated with bTB (objective 1). Phenotypes comprised de-regressed estimated breeding values of 804 Holstein-Friesian sires obtain from the UK national genetic evaluation for bTB. Phenotypes pertained to three bTB trait definitions: i) positive reactors to the skin test with positive post-mortem examination results (phenotype 1); ii) positive reactors to the skin test regardless of post-mortem examination results (phenotype 2) and iii) as in (ii) plus non-reactors and inconclusive reactors to the skin test with positive post-mortem examination results (phenotype 3). In all cases, non-reactors without a subsequent positive post-mortem were considered to be healthy animals with regards to bTB. Genotypes based on a 50K SNP DNA array were available and a total of 34,874 SNPs remained after quality control. The estimated polygenic heritability for susceptibility to bTB was 0.26, 0.37 and 0.34 for phenotypes 1, 2 and 3, respectively. GWAS identified a putative SNP on Bos taurus autosomes (BTA) 2 associated with phenotype 1, and another on BTA 23 associated with phenotype 2. Genomic regions encompassing these SNPs were found to harbour potentially relevant annotated genes. RHM confirmed the effect of these genomic regions and identified new regions on BTA 18 for phenotype 1 and BTA 3 for phenotypes 2 and 3. Heritabilities of the genomic regions ranged between 0.05 and 0.08 across the three phenotypes. Chromosome association analysis indicated a major role of BTA 23 on susceptibility to bTB. A stochastic genetic epidemiological model based on four main disease states, namely susceptible (S), exposed (E), infectious (I) and test-sensitive (T), was developed to address objective 2. Effects of selection for increased resistance to bTB were investigated in a closed, genetically heterogeneous simulated population whose structure reflected the UK national dairy herd. Disease dynamics reflected real bTB data from the UK national genetic evaluation. The proposed genetic epidemiological model was implemented to simulate breakdowns under both absence and presence of selection. Genetic selection was simulated over 20 generations in 50 replicates, while exploring various selection intensities reflecting selection of the 10, 25, 50, 70 and 100% (no selection scenario) most resistant sires. Results indicated that selection significantly reduced the average underlying susceptibility across generations. The risk of breakdown was reduced by half after 4 and 6 generations for high selection intensities (10 or 25% of sires selected) and after 9 and 15 generations for low selection intensities (50 or 70% of sires selected). The average percentage of secondary cases was reduced to less than 1% in 4 and 5 generations for high selection intensities, and in 7 and 11 generations for low selection intensities. The reduction in the number of secondary cases across generations could also be indicative of the possible impact of genetic selection on the basic reproductive ratio (R0) which is defined as the number of secondary cases that results from an infectious individual in a naive population. Genetic selection also reduced severity and duration of breakdowns across generations. Finally, with regards to objective 3, a stochastic simulation was used to investigate the long-term effects of selection for resistance to bTB on other economically important traits in the UK dairy selection programme. Selection was simulated in a genetically heterogeneous population across 10 generations in 50 replicates. Animal genetic values for bTB and other traits were simulated based on variance and genetic correlation estimates obtained from literature. Independent culling levels selection of sires was applied in every generation whereby selection was first based on increasing resistance to bTB, then improving either an overall index, milk fat yield (FY) or milk protein yield (PY). This mimics real life practices regarding the newly released national genetic evaluations for bTB resistance. The overall index comprised several traits of interest such as milk yield (MY), FY, PY, feet and legs (FL), mammary (MAM), milk somatic cell count (SCC), calving interval (CI), non-return to service at 56 days (NR56) and lifespan (LS). A fertility index (FI) consisting of CI and NR56 was also considered in the analyses. Regarding bTB, different levels of selection intensities were explored corresponding to selection of the 10, 25, 50, 70 and 100% (no selection) most resistant sires. Two levels of selection intensity on the overall index, FY or PY were considered corresponding to selecting the best 5 and 10% of sires that were left after first selecting for bTB resistance. Results indicated that selection for increased bTB resistance would generally not have far-reaching consequences on other important traits. As expected, susceptibility to bTB declined with time and increasing selection intensity. Trends for all production traits (MY, FY and PY) in the present study were affected by selection for increased bTB resistance because of their significant genetic correlations with bTB. However, body conformation traits (FL and MAM) were not affected by selection for increased bTB resistance due to zero correlation assumed between these traits and bTB in the present study. Selection on bTB hampered improvement of SCC but enhanced LS because it was correlated unfavourably with SCC but favourably with LS. In all selection scenarios, the overall index improved and was generally not affected by selection for bTB resistance. Similarly, the FI was not affected by selection on bTB in all cases. However, secondary selection on production traits only (FY or PY) led to a decline in FI. Results presented in this thesis add insight into the genetic architecture of bTB and offer a prediction of potential effects of genetic selection for increased resistance to bTB in dairy cattle. The genomic regions and candidate genes identified to be associated with susceptibility to bTB will assist to further elucidate pathways critical to cattle susceptibility to bTB. / Consistent with previous studies of other populations and trait definitions, results from genomic association analyses suggest that susceptibility of cattle to bTB is heritable and likely a polygenic trait, amenable to improvement by genetic and/or genomic selection. Embarking on routine selection for resistance to bTB will reduce future bTB prevalence and severity of breakdowns across selection generations, as manifested by results of this thesis. The results also highlight the importance of considering selection as a complementary strategy to existing interventions. This has the potential to accelerate control and ultimate eradication of bTB. This strategy could assist the UK to achieve the national goal of being officially bTB free by 2038. Furthermore, as indicated by results of this thesis, selection against bTB in the national breeding programme will not adversely affect other economically important traits. Assimilation of bTB into the overall index will better manage possible antagonistic correlations between bTB susceptibility and some of the other traits.

Paratuberculosis represents a major problem in farmed ruminants and at the present is considered a potential zoonosis. The disease is caused by Mycobacterium avium subsp. paratuberculosis, and susceptibility to infection is suspected to have a genetic component. Caspase recruitment domain 15 (CARD15) gene encodes for a cytosolic protein implicated in bacterial recognition during innate immunity. Crohn's disease (CD) is an idiopathic inflammatory bowel disease in humans comparable in many features to bovine paratuberculosis involving an abnormal mucosal immune response. The association between mutations in the CARD15 gene and increased risk of Crohn's disease has been described. The objective of this candidate gene case-control study was to characterize the distribution of three polymorphisms in the bovine CARD15 gene and test their association with paratuberculosis infection in cattle. Three previously reported single nucleotide polymorphisms (E2[-32] intron 1; 2197/C733R and 3020/Q1007L) were screened for the study population (431 adult cows). The statistical analysis resulted in significant differences in allelic frequencies between cases and controls for SNP2197/C733R (P < 0.001), indicating a significant association between infection and variant allele. In the analysis of genotypes, a significant association was also found between SNP2197/C733R and infection status (P < 0.0001); cows with the heterozygous genotype were 3.35 times more likely to be infected than cows with the reference genotype (P = 0.01). Results suggest a role for CARD15 gene in the susceptibility of cattle to paratuberculosis infection. These data contribute to the understanding of paratuberculosis, suggest new similarities with Crohn's disease and provide new information for the control of bovine paratuberculosis.

Ovarian cancer is the deadliest gynecological malignancy affecting women. Diagnosis often occurs late due to non-specific symptoms, but if detected early, there is excellent chance for survival. One of the most important risk factors is family history. Up to 24% of cases are due to inherited loss-of-function mutations in genes involved in the DNA damage response. The theory underlying hereditary cancers is Knudson's two-hit theory of cancer causation, where two hits are necessary for cancer to occur in an individual: one in the germline and one in the tissue. The genes, CHEK1 and CHEK2, are modulators of the DNA damage response, and could be susceptible to a first hit. There is little to no evidence about whether loss-of-function mutations in either of these two genes can lead to ovarian cancer. Using a cohort of 587 ovarian cancer cases and 557 controls, this study sought to determine if CHEK1 and CHEK2 are associated with ovarian cancer. Applying Fisher's exact test to compare mutation rates and the t test to compare age at time of diagnosis, the alternative hypothesis about an association between disease and mutations in CHEK1 and CHEK2 was rejected, but an association between younger age at diagnosis in cases and mutations in either gene was confirmed. The association between age and mutations in either of these genes suggests that there is some influence of age on disease, but a clear association between development of disease and mutations cannot yet be established. This research has implications for social change: By recognizing the need to test earlier in women with mutations in CHEK1 and/or CHEK2, they will have a higher chance of survival and better health outcomes, not only for ovarian cancer but for related cancers as well.

Genetic susceptibility test results have been found to cause differences in coping behavior following testing for the APOE-ε4 gene, associated with Alzheimer's disease. Coping behaviors differ within the first 12 months of testing. Currently, no studies have been conducted beyond the first 12 months comparing positive (P) and negative (N) groups or how sex relates to coping behavior based on positive test results. Based on the theory of primary and secondary control, and theory of stress, appraisal, and coping this study compared differences in coping strategies based on genetic test results and between sexes with positive test results beyond the first 12 months. Participants (n = 280) were selected who had undergone testing for the APOE-ε4 gene 12 or more months prior to the study and had a relative diagnosed with AD. Coping strategies were measured using the Brief COPE scale. Independent measures t test results were significant, indicating differences in coping between P and N groups. The P group reported significantly higher levels of cognitive and emotional coping strategies than did the N group 12 or more months after receiving test results. These findings were consistent with previous studies that produced significances in cognitive and emotional coping strategies between groups in the first 12 months. The findings were non significant for cognitive and emotional coping strategies for sex in the positive group. This study contributes to social change by informing impact decision making by individuals with positive test results for the APOE-ε4 gene in making financial changes, life styles changes, and family and work adjustments affecting their community and society.

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2014-05-20T18:01:40Z No. of bitstreams: 1 Polyanna Carôzo de Oliveira. Ancrestalidade... 2014.pdf: 1254857 bytes, checksum: e5708eec3bc58766116c313a7e16ea18 (MD5) / Made available in DSpace on 2014-05-20T18:01:40Z (GMT). No. of bitstreams: 1 Polyanna Carôzo de Oliveira. Ancrestalidade... 2014.pdf: 1254857 bytes, checksum: e5708eec3bc58766116c313a7e16ea18 (MD5) Previous issue date: 2014 / Fundação Oswaldo Cruz. Centro de Pesquisa Gonçalo Moniz. Salvador, BA, Brasil / O Cancêr de Próstata (CaP) é um dos tipos de neoplasias mais frequentes nos homens em todo o mundo e também na população masculina brasileira. A incidência, mortalidade e agressividade do CaP são maiores em homens negros. De acordo com o IBGE a Bahia é o estado que apresenta a maior porcentagem de população afrodescendente e os indivíduos que moram em Salvador apresentam maior ancestralidade africana que os nascidos no interior do estado. O presente estudo verificou a associação entre maior ancestralidade genética africana e genes de suscetibilidade ao CaP em pacientes do estado da Bahia oriundos do setor particular e público de serviço à saúde. Participaram do estudo 189 homens com CaP, sendo 82 atendidos no serviço privado e 107 no serviço público e 112 homens saudáveis atendidos no serviço público. Foram utilizados 9 marcadores informativos de ancestralidade (AIM) para estimar a ancestralidade genética e quatro genes de suscetibilidade: CYP3A4, CYP17, GSTM1 e GSTT1.No grupo caso houve maior contribuição europeia (47%) e no grupo controle maior contribuição africana (43%). Entre os genes de suscetibilidade, observou-se que o genótipo GG, bem como a associação dos genótipos GG+AG na variante CYP3A4-392 A>G estiveram relacionados ao aumento do risco de CaP tanto de modo global, bem como em indivíduos com maior ancestralidade africana, além de estarem associado positivamente com o aumento da agressividade do tumor para esta população. A variante CYP17-34 T>C não apresentou relação com aumento do risco para o CaP entre casos e controles, mas ao estratificar a população observou-se maior risco associado ao genótipo heterozigoto (TC) em indivíduos com maior contribuição africana, mas não houve relação entre a variante e o aumento da agressividade do tumor. Por fim, o genótipo GSTM1-0 esteve associado ao aumento do risco para o CaP de modo geral, mas não esteve relacionado com o aumento da agressividade do tumor. Estes resultados podem auxiliar estudos de associação entre CaP e maior suscetibilidade de populações afrodescendentes e assim, ajudar na melhoria das estratégias em torno de programas de saúde que visem ampliar a triagem e o diagnóstico precoce para esta populações mais vulneráveis. / Prostate cancer (PCa) is one of the most common types of cancer in men worldwide and also in Brazilian male population. The incidence, mortality and PCa aggressiveness are higher in black men. According to the IBGE, Bahia is the state with the highest percentage of people of African descent and people who live in Salvador has the largest African ancestry born in the state. The present study sought to determine the association between African ancestry and greater susceptibility genes in PCa patients of Bahia state from public and private sector health service. The study included 189 men with PCa, 82 served in the private and 107 public service and 112 healthy men served in the public service. We used ancestry informative markers 9 (AIM) to estimate genetic ancestry and 4 susceptibility genes, among them: CYP3A4, CYP17, GSTM1 e GSTT1. The case group was greater European contribution (47%) in the control group and largest African contribution (43%). Between susceptibility genes, it was found that the GG genotype, and the association of the genotypes GG + GA in CYP3A4-392A>G varinatwere associated with an increased risk of PCa so both overall as well as for individuals with higher African ancestry, and are positively associated with increased tumor agressivadade for this population. The variant CYP17-34T>C gene was not associated with increased risk for PCa between cases and controls, but to stratify the population was more strongly associated with the risk genotype (TC) in subjects with higher African contribution, but there was no relationship between the variant and increased tumor aggressiveness. Finally, GSTM1-0 genotype was associated with increased risk for CaP generally, but not correlate with increasing tumor aggressiveness. These results may help studies of association between PCa and greater susceptibility of African descent populations and thus help improve strategies around health programs aimed at increasing screening and early diagnosis for this most vulnerable populations.

Background: Psoriasis is a complex disease with a genetic component contributing to disease pathogenesis. Chronic plaque psoriasis can be dichotomised into two subtypes according to age of onset; type 1 (early-onset; <40 years) and type 2 (late-onset; ≥40 years). Despite clinical and biological differences between the two subtypes, the genetics underpinning late-onset psoriasis remains poorly characterised compared to early-onset psoriasis. Aims: The aim of this project was to identify genetic loci associated with late-onset psoriasis, to assess the overlap of loci with early-onset psoriasis and to elucidate the functional role of the identified variants. Methods: The study had three parts; the first was a candidate-gene association study of the IL1B gene. A total of 16 SNPs from the region were genotyped in 595 late-onset and 1,137 early-onset psoriasis samples and compared to 4,770 controls from the European population. The second was a large-scale study conducted in 543 late-onset psoriasis and 4,373 controls using the Immunochip array. The third was a functional study using bioinformatics data mining, chromatin immunoprecipitation and electrophoretic mobility shift assay techniques to analyse the role of a disease-associated variant at the biological level. Results: The candidate-gene study replicated a previously reported association at a promoter polymorphism, rs16944 (P<0.05), within the IL1B gene and discovered a novel association at a second variant, rs11687624 (P<3.12x10-3), in late-onset psoriasis. None of the variants analysed were significantly associated with early-onset psoriasis. Bioinformatic eQTL data suggests the two variants and their proxies are associated with the expression of IL1A, IL1B, IL38 and PAX8. The Immunochip study identified 6 non-HLA loci (P<2.3x10-5) previously associated with early-onset psoriasis to also be associated with late-onset psoriasis (IFIH1, IL12B, IL23A, IL23R, TRAF3IP2 and ZNF313). Conditional analysis of the MHC region also identified two loci (HLA-C and HLA-A). A novel locus, IL1R1, was associated with late-onset psoriasis, but not early-onset psoriasis. Bioinformatic data mining found no role for the IL1R1 variants as eQTLs and prioritised the IL1B variant rs2708914 for functional analysis. The transcription factor STAT3 was found to be enriched at rs2708914 in keratinocyte and CD8+ T-lymphocyte cell lines. Allele-specific binding could not be established. Conclusions: This project is the largest genetic study of late-onset psoriasis to date and provides evidence that it shares susceptibility loci with early-onset psoriasis as well as having specific susceptibility loci. These findings provide further evidence for the dichotomisation of chronic plaque psoriasis, firstly to facilitate better understanding of the pathogenesis of the two subtypes and secondly to enable tailored therapy to be developed. Both have potential benefits for patients in the future. The genetic and functional studies conducted have provided a platform from which further studies can be carried out.

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