<p>Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unknown etiology. The aim of this thesis was to identify susceptibility regions through genetic mapping, using model-based linkage analysis on nuclear and extended SLE multicase families.</p><p>In the first paper we performed a genome scan on 19 genetically homogenous Icelandic and Swedish families. One region at 2q37 was identified with a significant linkage with contribution from both populations (Z=4.24). Five other regions 2q11, 4p13, 9p22, 9p13 and 9q13 showed suggestive linkage (Z>2.0).</p><p>In the second paper, 87 families from 10 different countries were analysed only for chromosome 1. One region at 1q31 showed significant linkage (Z=3.79) with contribution from families from all populations, including Mexicans and Europeans. Four other regions 1p36, 1p21, 1q23, and 1q25, showed levels of suggestive linkage. Linkage for most regions was highly dependent on what population was used, which indicated strong genetic heterogeneity in the genetic susceptibility for SLE.</p><p>In the two last papers, we used the positional candidate gene strategy, in order to investigate candidate genes in two regions linked to SLE. For the Bcl-2 gene (at 18q21) we could not detect any association with SLE using three different markers. However, when we investigated the tightly linked low-affinity family of FcγR genes (at 1q23), we could find association for two risk alleles in the FcγRIIA and FcγRIIIA genes. The risk alleles were transmitted to SLE patients on one specific haplotype and therefore are not independent risk alleles.</p><p>The results show that model-based linkage analysis is a strong approach in the search for susceptibility genes behind complex diseases like SLE.</p>

Systemic lupus erythematosus (SLE) is a complex autoimmune disease with unknown etiology. The aim of this thesis was to identify susceptibility regions through genetic mapping, using model-based linkage analysis on nuclear and extended SLE multicase families. In the first paper we performed a genome scan on 19 genetically homogenous Icelandic and Swedish families. One region at 2q37 was identified with a significant linkage with contribution from both populations (Z=4.24). Five other regions 2q11, 4p13, 9p22, 9p13 and 9q13 showed suggestive linkage (Z&gt;2.0). In the second paper, 87 families from 10 different countries were analysed only for chromosome 1. One region at 1q31 showed significant linkage (Z=3.79) with contribution from families from all populations, including Mexicans and Europeans. Four other regions 1p36, 1p21, 1q23, and 1q25, showed levels of suggestive linkage. Linkage for most regions was highly dependent on what population was used, which indicated strong genetic heterogeneity in the genetic susceptibility for SLE. In the two last papers, we used the positional candidate gene strategy, in order to investigate candidate genes in two regions linked to SLE. For the Bcl-2 gene (at 18q21) we could not detect any association with SLE using three different markers. However, when we investigated the tightly linked low-affinity family of FcγR genes (at 1q23), we could find association for two risk alleles in the FcγRIIA and FcγRIIIA genes. The risk alleles were transmitted to SLE patients on one specific haplotype and therefore are not independent risk alleles. The results show that model-based linkage analysis is a strong approach in the search for susceptibility genes behind complex diseases like SLE.

Med en explorativ ansats syftar denna studie till att kartlägga samband och jämföra grupperingar bland klienter som fått genomföra en ASI-intervju hos Kriminalvården. Studien bygger på 2 317 intervjuer med fokus på missbruksproblematik, gjorda under perioden 2008-2010. Vi illustrerar grafiskt intressanta samband och tittar även på hur klienternas hjälpbehov varierar inom olika livsområden. Ytterligare en aspekt av studien är att utvärdera datamaterialets kvalitet samt att studera eventuellt bortfall för de olika variablerna. Materialet är av relativt god kvalitet och förekomst av respondenters vägran är inte tillräckligt omfattande för att påverka analyser och slutsatser. De felaktigheter som kunde konstateras härhör nästan uteslutande från tillvägagångssätt vid inmatning av data i systemet. Eftersom flertalet av variablerna är kvalitativa visade sig lämpliga analysmetoder vara chi-två-test, korrespondensanalys samt associationsanalys. Den stora majoriteten av våra resultat bekräftar den bild flera tidigare studier ger av gruppen missbrukare och få oväntade samband kunde konstateras. En majoritet av klienterna är män (85%) och den genomsnittliga åldern är 34 år. Intervjuarskattningar av klienternas hjälpbehov visar att narkotika och kriminalitet utgör de absolut största problemen. Dominerande drog är amfetamin (18%), följd av alkohol (15%) och cannabis (10%). Vi kan konstatera att ett flertal signifikanta skillnader föreligger mellan män och kvinnor samt mellan olika åldersgrupper. Unga klienter uppvisar överlag större problem med kriminalitet, narkotika, arbete/försörjning och psykisk hälsa. Med ökande ålder följer istället svårigheter med fysisk hälsa och alkohol. Män uppger vanligen att de har större problem med kriminalitet och narkotika, medan kvinnor ofta redovisar ett större hjälpbehov inom områdena familj/umgänge, fysisk hälsa och psykisk hälsa. / With an explorative approach, this master thesis attempts to map associations and compare groupings of clients who have undergone an ASI Interview by The Swedish Prison and Probation Service, Kriminalvården. The study is based on 2 317 interviews carried out during the period 2008-2010, focusing on abuse of alcohol and narcotic substances. We will graphically illustrate interesting associations and study how the need for help varies throughout different areas of the respondents’ lives. Another aspect of this study is to evaluate the quality of the data material and to investigate non-response in the different variables. The quality of the material is fairly high and non-response is not extensive enough to affect analysis and inference. The errors found are almost exclusively due to how data is fed into the system. Since the majority of variables are qualitative, appropriate methods of analysis proved to be chi-square tests, correspondence analysis and association analysis. Most results confirm the existing image of an abusive personality, which has been presented in several studies before this one. A majority of the clients are men (85%) and the average age is 34 years. Interviewer estimates of the respondents’ need for help show that narcotic substances and criminal behavior are by far the greatest problem areas. The predominant drug is amphetamine (18%), followed by alcohol (15%) and cannabis (10%). We have established several significant differences between men and women, and between clients of different age groups. Young respondents show greater problems concerning criminal behavior, narcotic substances, work/providing and psychological health. With increased age we see enhanced difficulties regarding physical health and alcohol. Men more often exhibit problems concerning criminal behavior and narcotic substances, while women need increased help in areas of family/social life, physical health and psychological health.

Identifying reliable screening tools and characterizing tolerant germplasm sources is essential for developing wheat (Triticum aestivum L.) varieties suited for the hot areas of the world. Our objective was to evaluate heat tolerance of promising wild tetraploid wheat (Triticum turgidum L.) accessions that could be used as sources of heat tolerance in common- and durum-wheat (Triticum durum) breeding programs. We screened 109 wild tetraploid wheat accessions collected by the International Center for Agriculture Research in the Dry Areas (ICARDA) from the hottest wheat growing areas in Africa and Asia, as well as, two common wheat checks for their response to heat stress by measuring damage to the thylakoid membranes, flag leaf temperature depression (FLTD), and spike temperature depression (STD) during exposure to heat stress for 16 beginning at anthesis. Measurements were taken on the day of anthesis then 4, 8, 12, and 16 days post anthesis (DPA) under controlled optimum and heat-stress conditions. Individual kernel weight (IKW) and heat susceptibility index (HSI) measurements were also obtained. Prolonged exposure to heat stress was associated with increased damage to thylakoid membranes, as indicated by the high ratio of constant fluorescence (O) to peak variable fluorescence (P). A positive and significant correlation was found between O/P ratio and both FLTD and STD under heat-stress conditions. A negative and significant correlation was found between FLTD and HSI and between STD and HSI based on the second and third measurements (4 and 8 DPA). Correlations obtained after the third measurement were not significant because heat-stress accelerated maturity and senescence. For a pedigree-based mapping strategy a family approach was then developed by crossing and back-crossing heat-tolerant and heat-susceptible germplasm. A set of 800 lines resulting from the pedigree-based family approach was phenotyped using FLTD, chlorophyll content and yield and its components under heat stress. Genotyping of these lines was accomplished using simple sequence repeat (SSRs) markers. Some QTLs associated with heat stress tolerance were identified. This study identified potential heat-tolerant wild tetraploid wheat germplasm and QTL conditioning heat tolerance that can be incorporated into wheat breeding programs to improve cultivated common and durum wheat.

Background: Imputation of partially missing or unobserved genotypes is an indispensable tool for SNP data analyses. However, research and understanding of the impact of initial SNP-data quality control on imputation results is still limited. In this paper, we aim to evaluate the effect of different strategies of pre-imputation quality filtering on the performance of the widely used imputation algorithms MaCH and IMPUTE. Results: We considered three scenarios: imputation of partially missing genotypes with usage of an external reference panel, without usage of an external reference panel, as well as imputation of ompletely un-typed SNPs using an external reference panel. We first created various datasets applying different SNP quality filters and masking certain percentages of randomly selected high-quality SNPs. We imputed these SNPs and compared the results between the different filtering scenarios by using established and newly proposed measures of imputation quality. While the established measures assess certainty of imputation results, our newly proposed measures focus on the agreement with true genotypes. These measures showed that pre-imputation SNP-filtering might be detrimental regarding imputation quality. Moreover, the strongest drivers of imputation quality were in general the burden of missingness and the number of SNPs used for imputation. We also found that using a reference panel always improves imputation quality of partially missing genotypes. MaCH performed slightly better than IMPUTE2 in most of our scenarios. Again, these results were more pronounced when using our newly defined measures of imputation quality. Conclusion: Even a moderate filtering has a detrimental effect on the imputation quality. Therefore little or no SNP filtering prior to imputation appears to be the best strategy for imputing small to moderately sized datasets. Our results also showed that for these datasets, MaCH performs slightly better than IMPUTE2 in most scenarios at the cost of increased computing time.

Submitted by Ana Maria Fiscina Sampaio (fiscina@bahia.fiocruz.br) on 2013-10-18T17:18:19Z No. of bitstreams: 1 Tamiris Tatiane Dias Analise de quasespecies...2013.pdf: 8521760 bytes, checksum: 4e4fc2d3b2f4ee514d97744b378b3fe0 (MD5) / Made available in DSpace on 2013-10-18T17:18:19Z (GMT). No. of bitstreams: 1 Tamiris Tatiane Dias Analise de quasespecies...2013.pdf: 8521760 bytes, checksum: 4e4fc2d3b2f4ee514d97744b378b3fe0 (MD5) Previous issue date: 2013 / Fundação Oswaldo Cruz. Centro de Pesquisas Gonçalo Moniz. Salvador, BA, Brasil / A transmissão materno-infantil (TMI) é a causa mais comum de infecção pelo vírus da hepatite C (HCV) entre as crianças. Objetivo: Esse estudo teve como objetivo avaliar fatores virais implicados na TMI do HCV. Materiais e métodos: Quatro gestantes e um par mãe-recém-nascido (RN), todos infectados pelo HCV, foram incluídos neste estudo. Sequências das regiões 5’UTR, E1, HVR1, E2 e NS5B foram obtidas através de sequenciamento direto do produto do PCR e clonagem. A diversidade quasiespécie foi analisada utilizando-se diferentes parâmetros (taxa de clonotipos, frequência de mutações, Pn e entropia de Shannon normalizada), comparando (1) grupos TMI+ e TMI-, e (2) par mãe-RN. Um framework foi usado para avaliar a associação entre a frequência dos nucleotídeos e a TMI. Resultados: Dois casos de TMI foram identificados, mas apenas a amostra de um RN estava disponível. As cargas virais de todos os sujeitos estavam acima do limite de quantificação. Ambos os casos de TMI pertenciam ao genótipo 1a apenas este subtipo foi analisado subsequentemente. O sequenciamento direto dos produtos de PCR não representou, de maneira confiável, a complexidade quasiespécie e não foi utilizado. Não houve clonotipos coincidentes entre os grupos TMI+ e TMI-, exceto pela região 5’UTR. Em nível de aminoácido, mãe e RN compartilharam apenas do clonotipo predominante. Todos os clonotipos minoritários foram exclusivos. Foi observada maior diversidade quasiespécie nas regiões E2 e NS5B. A HVR1 apresentou a menor diversidade dentro da região codificante. A diversidade quasiespécie do grupo TMI+ foi sempre maior do que aquela vista no grupo TMI-; no entanto, não houve significância estatística. Trinta e cinco mutações na região codificante foram associadas significativamente com a TMI. Dados do par mãe-RN sugerem que a transmissão intrauterina ocorreu em um momento inicial da gestação e que o vírus provavelmente atravessou o tecido placentário, levando a um gargalo de garrafa. Conclusões: A diversidade quasiespécie não foi associada à TMI, mas a presença de mutações ao longo da região codificante sugere que o genoma completo contribui para a capacidade de transmissão intrauterina. São necessários estudos adicionais para determinar se essas variantes podem ser úteis para predizer a TMI. / Introduction: Mother-to-child-transmission (MTCT) is the most common cause of hepatitis C virus (HCV) infection in children. Objective: This study aimed to evaluate viral factors implicated in HCV MTCT. Methods: Four HCV-infected pregnant women and one HCV-infected mother-newborn pair were included in this study. Sequences were obtained from the regions 5’UTR, E1, HVR1, E2 and NS5B by direct PCR product sequencing and cloning. Quasispecies diversity was analyzed by different parameters (clonotype ratio, mutation frequency, Pn and normalized Shannon entropy), comparing (1) MTCT+ vs. MTCT- groups, and (2) mother-newborn pair. A framework was used to establish association between nucleotide frequency and MTCT. Results: Two cases of MTCT were identified, but a sample from only one newborn was available. Viral loads from all subjects were above the quantification limit. Both cases of MTCT belonged to genotype 1a and only this subtype was further analyzed. Direct sequencing from PCR products did not reliably represent the quasispecies complexity and was not used. There were no coincident clonotypes between MTCT+ and MTCT- groups, except for 5’UTR. At the amino acid level, mother and newborn shared only the master clonotype. All minor clonotypes were exclusive. Higher quasispecies diversity was observed within E2 and NS5B regions. HVR1 presented the lowest diversity within the coding region. Quasispecies diversity from the MTCT+ group was always greater than seen in the MTCT- group; however, no statistically significance was observed. Thirty-five mutations in the coding regions were significantly associated with MTCT. Data from the mother-newborn pair suggest that the intrauterine transmission occurred in an earlier time point of the pregnancy and that the virus probably crossed the placental tissue leading to a bottleneck. Conclusions: Quasispecies diversity was not associated with MTCT but the presence of mutations along the coding region suggests that the whole genome contributes to the ability of intrauterine transmission. Further studies are required to establish if these variants could be useful to predict MTCT.

<p>  </p> <p>Emerging pathogenic fungi have become a topic of conservation concern due to declines seen in several host taxa. One newly emerging fungal pathogen, <em>Ophidiomyces ophiodiicola</em>, has been well documented as the causative agent of Snake Fungal Disease (SFD). SFD has been found in a variety of snake species across the United States, including the Eastern Massasauga (<em>Sistrurus catenatus</em>), a federally threatened rattlesnake species. Most work to date has involved detecting SFD for diagnosis of infection through direct sampling from snakes. Attempts to detect <em>O. ophiodiicola</em> in the environment to better understand its distribution, seasonality, and habitat associations are lacking. I collected topsoil and ground water samples from four macrohabitat types in northern Michigan at a site where SFD infection has been seen in Eastern Massasauga. I used a quantitative PCR (qPCR) assay targeting the internal transcribed spacer region (ITS) developed for diagnosis of SFD after extracting DNA from samples. <em>Ophidiomyces</em> DNA was successfully detected in topsoil, with minimal to no detection in groundwater samples. The frequency in which <em>Ophidiomyces</em> was detected in a sample did not differ between habitats, but samples grouped seasonally showed higher detection occurring during mid-summer. Investigation of the correlation of environmental parameters on <em>Ophidiomyces</em> occurrence recovered no relationships. Our data suggests that season has some effect on the presence of <em>Ophidiomyces</em>. Differences between habitats may exist but are likely more dependent on the time of sampling and currently uninvestigated soil parameters. These findings build on our understanding of <em>Ophidiomyces</em> ecology and epidemiology and inform where snakes like the Eastern Massasauga may be encountering the fungal pathogen. Furthermore, they assist with developing conservation practices aimed at reducing <em>O. ophiodiicola </em>exposure in imperiled snake species. </p>

Steroid hormones act as important regulators of physiological processes including gene expression. They provide possible mechanistic explanations of observed sex-dimorphisms in obesity and coronary artery disease (CAD). Here, we aim to unravel causal relationships between steroid hormones, obesity, and CAD in a sex-specific manner. In genome-wide meta-analyses of four steroid hormone levels and one hormone ratio, we identified 17 genome-wide significant loci of which 11 were novel. Among loci, seven were female-specific, four male-specific, and one was sex-related (stronger effects in females). As one of the loci was the human leukocyte antigen (HLA) region, we analyzed HLA allele counts and found four HLA subtypes linked to 17-OH-progesterone (17-OHP), including HLA-B*14*02. Using Mendelian randomization approaches with four additional hormones as exposure, we detected causal effects of dehydroepiandrosterone sulfate (DHEA-S) and 17-OHP on body mass index (BMI) and waist-to-hip ratio (WHR). The DHEA-S effect was stronger in males. Additionally, we observed the causal effects of testosterone, estradiol, and their ratio on WHR. By mediation analysis, we found a direct sex-unspecific effect of 17-OHP on CAD while the other four hormone effects on CAD were mediated by BMI or WHR. In conclusion, we identified the sex-specific causal networks of steroid hormones, obesity-related traits, and CAD.

全球面臨人口老化與人口不斷成長的壓力下，對於醫療服務的需求不斷提升。醫療服務領域中常以資料探勘「關聯規則」分析，挖掘隱藏在龐大的醫學資料庫中的知識(knowledge)，以支援臨床決策或創新醫療服務。隨著醫療服務與應用推陳出新(如，電子健康紀錄或行動醫療等)，與醫療機構因應政府政策需長期保存大量病患資料，讓醫療領域面臨如何有效的處理巨量資料。 然而傳統的關聯規則演算法，其效能上受到相當大的限制。因此，許多研究提出將關聯規則演算法，在分散式環境中，以Hadoop MapReduce框架實現平行化處理巨量資料運算。其相較於單節點 (single-node) 的運算速度確實有大幅提升。但實際上，MapReduce並不適用於需要密集迭帶運算的關聯規則演算法。 本研究藉由Spark記憶體內運算框架，在分散式叢集上實現平行化挖掘多維度多顆粒度挖掘關聯規則，實驗結果可以歸納出下列三點。第一點，當資料規模小時，由於平行化將資料流程分為Map與Reduce處理，因此在小規模資料處理上沒有太大的效益。第二點，當資料規模大時，平行化策略模式與單機版有明顯大幅度差異，整體運行時間相差100倍之多；然而當項目個數大於1萬個時，單機版因記憶體不足而無法運行，但平行化策略依舊可以運行。第三點，整體而言Spark雖然在小規模處理上略慢於單機版的速度，但其運行時間仍小於Hadoop的4倍。大規模處理速度上Spark依舊優於Hadoop版本。因此，在處理大規模資料時，就運算效能與擴充彈性而言，Spark都為最佳化解決方案。 / Under the population aging and population growth and rising demand for Healthcare. Healthcare is facing a big issue how to effectively deal with huge amounts of data. Cased by new healthcare services or applications (such as electronic health records or health care, etc), and also medical institutions in accordance with government policy for long-term preservation of a large number of patient data. But the traditional algorithms for mining association rules, subject to considerable restrictions on their effectiveness. Therefore, many studies suggest that the association rules algorithm in a distributed computing, such as Hadoop MapReduce framework implements parallel to process huge amounts of data operations. But in fact, MapReduce does not apply to require intensive iterative computation algorithm of association rules. Studied in this Spark in-memory computing framework, implemented on a distributed cluster parallel mining association rules mining multidimensional granularity, the experimental results can be summed up in the following three points. 1th, when data is small, due to the parallel data flow consists of Map and Reduce, so not much in the small-scale processing of benefits. 2nd, when the data size is large, parallel strategy models and stand-alone obviously significant differences overall running time is 100 times as much when the item number is greater than 10,000, however, stand-alone version cannot run due to insufficient memory, but parallel strategies can still run. 3rd, overall Spark though somewhat slower than the single version in small scale processing speed, but the running time is less than 4 times times the Hadoop. Massive processing speed Spark is still superior to the Hadoop version. Therefore, when working with large data, operational efficiency and expansion elasticity, Spark for optimum solutions.

La plupart des maladies humaines ont une étiologie complexe avec des facteurs génétiques et environnementaux qui interagissent. Utiliser des phénotypes corrélés peut augmenter la puissance de détection de locus de trait quantitatif. Ce travail propose d’évaluer différentes approches d’analyse bivariée pour des traits corrélés en utilisantl’information apportée par les marqueurs au niveau de la liaison et de l’association. Legain relatif de ces approches est comparé aux analyses univariées. Ce travail a étéappliqué à la variation de la densité osseuse à deux sites squelettiques dans une cohorted’hommes sélectionnés pour des valeurs phénotypiques extrêmes. Nos résultats montrentl’intérêt d’utiliser des approches bivariées en particulier pour l’analyse d’association. Parailleurs, dans le cadre du groupe de travail GAW16, nous avons comparé lesperformances relatives de trois méthodes d’association dans des données familiales. / The majority of complex diseases in humans are likely determined by both genetic andenvironmental factors. Using correlated phenotypes may increase the power to map theunderlying Quantitative Trait Loci (QTLs). This work aims to evaluate and compare theperformance of bivariate methods for detecting QTLs in correlated phenotypes by linkageand association analyses. We applied these methods to data on Bone Mineral Density(BMD) variation, measured at the two skeletal sites, in a sample of males selected forextreme trait values. Our results demonstrate the relative gain, in particular for associationanalysis, of bivariate approaches when compared to univariate analyses. Finally, we studythe performances of association methods to detect QTLs in the GAW16 simulated familydata.