This thesis studies the problematic of the new polymorphism APOA2 gene and that association with fatty acids contain in a group of Czech Large White pigs. APOA2 gene (ID: 100153243) is a candidate gene for porcine meat quality. The aim of thesis was to analyze the influence of selected polymorphisms on fatty acids and intramuscular fat contain. Among fatty acids was observed a contain of: tetradecenoic acid, palmitic acid, palmitoleic acid, stearic acid, oleic acid, linoleic acid, linolenic acid, arachidonic acid, arachidic acid a eicosapentaenoic acid (EPA). Have been used molecular-genetic methods such as primers design in the OLIGO software, PCR, gel electrophoresis a sequencing by Sanger method. The results were processed by form of genotype frequency and followed by associative analysis with a mixed linear model. The values of the relative alleles frequency of polymorphism APOA2 T>A rs80803879 were as follows: A = 0,086, T = 0,914 and relative alleles frequency of APOA2 G>A rs331415849: A = 0,068 a G = 0,948. Polymorphism associations were found for fatty acids: myristoleic acid, acid palmitoleic acid, oleic acid, arachidonic acid, and arachidic acid.

The genome-wide association study (GWAS) approach has identified novel loci for a variety of complex diseases. However, for most of these disorder much of the heritability is not explained by this approach, which focuses on identifying common variants that are associated with disease risk. The unexplained heritability may be due to genetic or phenotypic heterogeneity or the influence of rare variants. The motivation behind this thesis was to uncover the unexplained heritability by applying joint analyses of sets of variants (gene-based association test) and multiple disease-related phenotypes (called multivariate gene-based association test). First, we evaluated multivariate gene-based methods for detecting association of common genetic variants with correlated phenotypes. An extensive simulation study showed that the method combining the MultiPhen and GATES software performed best for most tested scenarios especially when correlations among phenotypes are relatively low. We developed a new multivariate gene-based test using rare variants called VEMPHAS. A simulation study using VEMPHAS showed that this method correctly controls for type I error in all tested scenarios. We applied VEMPHAS to analysis of various phenotypes related to Alzheimer disease (AD) and found suggestive association (P < 4.15x10-6) with the gene TRIM22, which has been identified in a previous sequencing study of AD onset in PSEN1/2 mutation carriers. We also developed software with a graphical user interface which is designed for integrating information from different types of data sources including genetic data (from GWAS or sequencing), expression data (from RNA-Seq), and protein structures (from protein data banks). This software has several features including 1) testing associations between genetic variants and gene expressions; 2) locating amino acids, encoded by the variants, in a protein structure; and 3) retrieving genetic locations (chromosome and base pair positions) of amino acids of interest in the protein structure. The last feature can be applied for prioritizing coding variants for gene-based association testing. The methods and strategies developed for this dissertation project can effectively uncover a portion of the remaining heritability of complex diseases that is unexplained by traditional GWAS approaches.

Les nouvelles technologies développées ces dernières années dans le domaine de la génétique ont permis de générer des bases de données de très grande dimension, en particulier de Single Nucleotide Polymorphisms (SNPs), ces bases étant souvent caractérisées par un nombre de variables largement supérieur au nombre d'individus. L'objectif de ce travail a été de développer des méthodes statistiques adaptées à ces jeux de données de grande dimension et permettant de sélectionner les variables les plus pertinentes au regard du problème biologique considéré. Dans la première partie de ce travail, un état de l'art présente différentes méthodes de sélection de variables non supervisées et supervisées pour 2 blocs de variables et plus. Dans la deuxième partie, deux nouvelles méthodes de sélection de variables non supervisées de type "sparse" sont proposées : la Group Sparse Principal Component Analysis (GSPCA) et l'Analyse des Correspondances Multiples sparse (ACM sparse). Vues comme des problèmes de régression avec une pénalisation group LASSO elles conduisent à la sélection de blocs de variables quantitatives et qualitatives, respectivement. La troisième partie est consacrée aux interactions entre SNPs et dans ce cadre, une méthode spécifique de détection d'interactions, la régression logique, est présentée. Enfin, la quatrième partie présente une application de ces méthodes sur un jeu de données réelles de SNPs afin d'étudier l'influence possible du polymorphisme génétique sur l'expression du vieillissement cutané au niveau du visage chez des femmes adultes. Les méthodes développées ont donné des résultats prometteurs répondant aux attentes des biologistes, et qui offrent de nouvelles perspectives de recherches intéressantes / New technologies developed recently in the field of genetic have generated high-dimensional databases, especially SNPs databases. These databases are often characterized by a number of variables much larger than the number of individuals. The goal of this dissertation was to develop appropriate statistical methods to analyse high-dimensional data, and to select the most biologically relevant variables. In the first part, I present the state of the art that describes unsupervised and supervised variables selection methods for two or more blocks of variables. In the second part, I present two new unsupervised "sparse" methods: Group Sparse Principal Component Analysis (GSPCA) and Sparse Multiple Correspondence Analysis (Sparse MCA). Considered as regression problems with a group LASSO penalization, these methods lead to select blocks of quantitative and qualitative variables, respectively. The third part is devoted to interactions between SNPs. A method employed to identify these interactions is presented: the logic regression. Finally, the last part presents an application of these methods on a real SNPs dataset to study the possible influence of genetic polymorphism on facial skin aging in adult women. The methods developed gave relevant results that confirmed the biologist's expectations and that offered new research perspectives.

Indiana University-Purdue University Indianapolis (IUPUI) / Forensic DNA phenotyping is an up and coming area in forensic DNA analyses that enables the prediction of physical appearance of an individual from DNA left at a crime scene. At present, there has been substantial work performed in understanding what genes/markers are required to produce a reliable prediction of categorical eye and hair color from the DNA of an individual of interest. These pigmentation markers (variants from HERC2, OCA2, TYR, SLC24A4, SLC45A2, IRF4 to name a few) are at the core of several prediction systems for eye and hair color such as IrisPlex, HIrisPlex, and the Snipper 2.5 suite. The contribution of these markers towards prediction in most cases however, only factors in an independent effect and do not take into account potential interactions or epistasis in the production of the final phenotypic color. Epistasis is a phenomenon that occurs when a gene’s effect relies on the presence of ‘modifier genes’, and can display different effects (enhance/repress a particular color) in genotype combinations rather than individually. In an effort to detect such epistatic interactions and their influence on hair color prediction models, for this current study, 872 individuals were genotyped at 61 associative and predictive pigmentation markers from several diverse population subsets. Individuals were phenotypically evaluated for eye and hair color by three separate independent assessments. Several analyses were performed using statistical approaches such as multifactor dimensionality reduction (MDR) for example, in an effort to detect if there are any SNP- SNP epistatic interactions present that could potentially enhance eye and hair color prediction model performances. The ultimate goal of this study was to assess what SNP-SNP combinations amongst these known pigmentation genes should be included as an additional variable in future prediction models and how much they can potentially enhance overall pigmentation prediction model performance. The second part of the project involved the analyses of several differentially expressed candidate genes between different hair color follicles of the same individual using quantitative Real Time PCR. We looked at 26 different genes identified through a concurrent non-human primate study being performed in the laboratory. The purpose of this study was to gain more insight on the level of differentially expressed mRNA between different hair color follicles within the same human individual. Data generated from this part of the project will act as a pilot study or ‘proof of principle’ on the mRNA expression of several pigmentation associated genes on individual beard hair of varying phenotypic colors. This analysis gives a first glimpse at expression levels that remain constant or differentiate between hairs of the same individual, therefore limiting the contribution of individual variation.

Indiana University-Purdue University Indianapolis (IUPUI) / Recent genome-wide association studies (GWAS) have identified many common genetic variants that are associated with women’s reproductive timing characteristics including ages at menarche and at natural menopause. However, the associations of these variants with other human health related phenotypes such as blood pressure, cancer, diabetes, obesity, and body height growth have not been well studied. No published studies to our knowledge have directly assessed the genetic influence of reproductive timing related variants on the aforementioned common traits. A better understanding of pleiotropic effects of these variants is important because it will help elucidate the precise mechanisms of common traits/diseases such as hypertension which have not been fully understood so far, and give clues for developing better solutions for disease prevention and treatment. We, therefore, conducted three studies to explore genetic variant effects on blood pressure and body height growth. In the first study, we analyzed data from a local cohort of 601 healthy adolescents from Indianapolis schools. Mixed effect model analysis revealed that 11 reproductive related single nucleotide polymorphisms (SNPs) were significantly associated with blood pressure in the study subjects. In order to assess if these genetic effects extended to the adult blood pressure, we performed the second study to investigate the genetic effect on blood pressure in adults. We used the summary statistics obtained from the two large international GWAS consortia, the Blood Pressure Consortium and the ReproGen Consortium. Bivariate analyses showed that more than 100 SNPs were associated with both blood pressure and reproductive timing. As the blood pressure development is closely related to somatic growth, we conducted the third study to exam the genetic effect of reproductive-timing related variants on the linear growth from the aforementioned local cohort. We identified 8 genetic variants significantly associated with the catch-up of linear growth in the study subjects. In conclusion, these three studies collectively provided evidence in support of the pleiotropic effects of the reproductive timing variants, suggesting the common genetic basis underlying the correlated traits. Future research is needed to validate the findings. / 2 years

Die vorliegende Dissertation hat sich mit der Fragestellung beschäftigt, inwiefern die Einzelnukleotid-Polymorphismen (kurz SNP) rs10754558 und rs35829419 des NLRP3-Gens mit einer Suszeptibilität für eine NAFL und/oder NASH assoziiert sind. Die Studienkohorte bestand aus 202 Teilnehmern der Würzburger NAFLD-Kohorte der Universitätsklinik Würzburg, 159 NAFLD-Patienten, die im Rahmen der Fettlebersprechstunde der Universitätsklinik Würzburg behandelt wurden und 43 gesunde Kontrollen. Voraussetzung für die Aufnahme in das Patientenkollektiv der durch die Ethikkomission genehmigten Studie war zuallererst die Aufklärung und Zustimmung des Patienten, außerdem eine klinisch oder histologisch diagnostizierte Fettlebererkrankung. Sekundäre Ursachen einer Fettleber oder andere Lebererkrankungen waren Ausschlusskriterien. Alle Teilnehmer erhielten eine Blutentnahme, 97 NAFLD-Patienten eine Leberbiopsie, davon 10 perkutan und 87 subkapsulär im Zuge einer bariatrischen OP. Die Genotypisierung übernahm das Labor der Universitätsklinik Homburg, die weiteren Analysen der Blutwerte, der peripheren und intrahepatischen Immunzellen und die Begutachtung der Leber-Histologie fanden an der Universitätsklinik Würzburg im Rahmen eines vorherigen Forschungsvorhabens statt (Rau et al., 2016). Für beide SNPs war das Hardy-Weinberg-Equilibrium im Studien- sowie Patientenkollektiv erfüllt. Zwischen den einzelnen Genotypen und dem Vorliegen einer NAFL und/oder NASH fanden sich für beide SNPs keine signifikanten Zusammenhänge. Für den Wildtyp CC des SNP rs10754558 ergaben sich in der Studienkohorte signifikant höhere AST-Mediane (p=0,018) und häufiger hochnormale (in den oberen 20 % des Normbereichs) ALT-Werte (p=0,02) im Vergleich zu den Genotypen CG und GG. Hier lässt sich über eine protektive Rolle des Minor Allels in Bezug auf Leberwerterhöhungen spekulieren. Da bisher die Funktion von rs10754558 im NLRP3-Gen noch nicht ausreichend erforscht ist, sollten Untersuchungen auf transkriptioneller Ebene folgen und Studien mit anderen Polymorphismen des NLRP3-Gens und mit NAFLD-assoziierter Gene durchgeführt werden, um eine mögliche Assoziation mit anderen für die Entwicklung der NAFLD relevanten SNPs nicht zu übersehen. In der Analyse mit den Entzündungswerten zeigten sich für die Genotypen CG und GG signifikant erhöhte Frequenzen von Th1-Zellen im peripheren Blut (p=0,003). Zusätzlich lässt sich das vermehrte Vorkommen von Th1-Zellen auch im Rahmen der bestehenden Adipositas bzw. des metabolischen Syndroms im Sinne einer low grade inflammation interpretieren (s. Diskussion). Immerhin sind 95 % der NAFLD-Patienten der Studienkohorte von Adipositas betroffen. Die Ergebnisse zu SNP rs35829419, einer gain-of-function Variante im NLRP3-Gen, waren nur eingeschränkt beurteilbar, da keine homozygoten Allel-A-Träger vorlagen und die Stichprobenzahl für die Analyse der intrahepatischen Immunzellen viel zu gering war, um aussagekräftig sein zu können. In der gesamten Kohorte stellte sich ein signifikanter Zusammenhang zwischen dem heterozygoten Genotyp von rs35829419 und einer erhöhten Frequenz an Th2-Zellen (p=0,024) im peripheren Blut heraus. Innerhalb der NAFLD gingen frühere Studien bisher eher von einer Th1-dominierten Immunantwort aus (Bertola et al., 2010), wenn nicht gar einer Th2-Defizienz (Guebre-Xabier et al., 2000). Das hier vorliegende Ergebnis könnte immerhin auf eine höhere entzündliche Aktivität bei Minor-Allelträgern hindeuten. Die weitere Untersuchung mit größeren Stichproben und weiteren Polymorphismen, die in der NAFLD-Pathogenese bekanntermaßen eine Rolle spielen, erscheint auch für den SNP rs35829419 sinnvoll. Im Hinblick auf die zunehmende Prävalenz der NAFLD als Volkskrankheit der westlichen Welt wird die personalisierte Medizin, inklusive Prävention, Diagnostik und Therapie immer mehr an Bedeutung zunehmen. Die Identifizierung von genetischen Risikovarianten, die an der Pathogenese der NAFLD beteiligt sind, ist ein erster Schritt auf dem Weg hin zu besseren Therapiemöglichkeiten. / This dissertation has dealt with the question of the extent to which the single nucleotide polymorphisms (SNP) rs10754558 and rs35829419 of the NLRP3 gene are associated with susceptibility to NAFL and/or NASH. The study cohort consisted of 202 participants of the Würzburg NAFLD cohort of the University Hospital Würzburg, 159 NAFLD patients who were treated during the fatty liver consultation hours of the University Hospital Würzburg and 43 healthy controls. The prerequisite for inclusion in the patient population of the study approved by the ethics committee was first and foremost the information and consent of the patient, as well as a clinically or histologically diagnosed fatty liver disease. Secondary causes of fatty liver or other liver diseases were exclusion criteria. All participants received a blood sample, 97 NAFLD patients a liver biopsy, of which 10 percutaneously and 87 subcapsular in the course of bariatric surgery. The genotyping was carried out by the laboratory of the University Hospital Homburg, the further analyses of the blood values, the peripheral and intrahepatic immune cells and the assessment of the liver histology took place at the University Hospital Würzburg as part of a previous research project (Rau et al., 2016). For both SNPs, the Hardy Weinberg equilibrium was fulfilled in the study and patient collective. There were no significant associations between the individual genotypes and the presence of NAFL and/or NASH for either SNP. For the wild type CC of SNP rs10754558, significantly higher AST medians (p=0.018) and more frequently highly normal (in the upper 20% of the normal range) ALT values (p=0.02) were found in the study cohort compared to the genotypes CG and GG. Here one can now speculate about a protective role of the minor allele with regard to liver value increases. Since the function of rs10754558 in the NLRP3 gene has not yet been sufficiently researched, studies at the transcriptional level should follow and studies with other polymorphisms of the NLRP3 gene and with NAFLD-associated genes should be carried out in order not to overlook a possible association with other SNPs relevant for the development of NAFLD. The analysis with the inflammation values showed significantly increased frequencies of Th1 cells in peripheral blood for the genotypes CG and GG (p=0.003). In addition, the increased occurrence of Th1 cells can also be interpreted in the context of existing obesity or metabolic syndrome in the sense of low-grade inflammation (see discussion). After all, 95% of NAFLD patients in the study cohort are affected by obesity. The results for SNP rs35829419, a gain-of-function variant in the NLRP3 gene, could only be assessed to a limited extent because there were no homozygous allele A carriers and the sample number for the analysis of intrahepatic immune cells was far too small to be meaningful. Throughout the cohort, there was a significant association between the heterozygous genotype of rs35829419 and an increased frequency of Th2 cells (p=0.024) in peripheral blood. Within NAFLD, previous studies have tended to assume a Th1-dominated immune response (Bertola et al., 2010 ), if not Th2 deficiency (Guebre-Xabier et al., 2000). The present result could at least indicate a higher inflammatory activity in minor allele carriers. Further investigation with larger samples and other polymorphisms, which are known to play a role in NAFLD pathogenesis, would also be useful for SNP rs35829419. In view of the increasing prevalence of NAFLD as a widespread disease in the Western world, personalized medicine, including prevention, diagnostics, and therapy, will become increasingly important. The identification of genetic risk variants involved in the pathogenesis of NAFLD is a first step towards better treatment options.

Quinoa (Chenopodium quinoa Willd.) is a staple grain for the indigenous people of the Andean region of South America with excellent nutritional qualities, including protein content. The objective of this study is to report on the development of fluorescence-tagged simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) to (1) genetically characterize the inherent diversity of 152 accessions of C. quinoa; (2) determine to what degree the CIP-FAO collection represents the range of genetic diversity in quinoa; and (3) test four hypotheses regarding quinoa?s center of diversity, Highland and Lowland clustering patterns, origin of Lowland varieties, and the origin of domestication. Thirty-five SSR loci comprising 432 alleles ranging from 5 (QAAT10) to 28 (QAAT50) alleles per locus (mean=13) were used to survey the 152 accessions of quinoa from the USDA and CIP-FAO collections. Heterozygosity was detected in 14.25% of the accessions for SNP loci and in at least one locus for 51% of the accessions. Both UPGMA and PCA analyses partitioned the quinoa accessions into two main clusters. The first major cluster consisted of accessions from the Andean highlands of Peru, Bolivia, Ecuador, Argentina, and extreme northeastern Chile. The other main cluster contained accessions from both the Lowlands of Chile and those collected by Emigdio Ballón The CIP-FAO collection appears to give a good representation of quinoa's genetic diversity within these two main clusters. The significance of patterns of genetic diversity within C. quinoa is discussed.

Discovering, screening, and associating changes in DNA sequence are important to a broad range of disciplines and play a central role in Forensic Science. The typical types of changes include sequence variations [single nucleotide polymorphisms (SNP)] and length variations [short tandem repeats (STR)]. The steps for forensic DNA sample processing are similar for both types of changes but diverge at the point of detection. A number of approaches are being explored for SNP genotyping while STR analysis primarily consists of size-based analysis by capillary electrophoresis. Limitations exist for all current detection methods that pose significant impacts to forensic analysis. Bi-allelic SNPs result in three possible genotypes with a minimal amount of information generated per marker. Limitations for SNP analysis are due to the inability to amplify a suitable number of SNP markers from low DNA content samples to provide an appropriate level of discrimination. Multi-allelic STR markers are currently the marker of choice for forensic typing but a variety of experimental artifacts are possible that consist of either biology or technology related causes. Molecular genotyping methods developed across other disciplines have potential to alleviate some of these shortcomings but no current approach is capable of genotyping both SNP and STR loci with a single chemistry. The need for a more effective, efficient, and generalized approach led to development of a unique method called Dye Probe Fluorescence Resonance Energy Transfer (dpFRET) and determination of its suitability for forensic analysis. The development phase of the research consisted of synthetic testing to establish proof of concept for the chemistry followed by polymerase chain reaction (PCR) based assays to demonstrate real world applications. Following successful development, the boundaries and limitations for the technology were established (sensitivity, allelic dropout, mixed samples) and efforts were made to improve the approach. In the process, parallel testing for other fields including molecular pathology and conservation biology were incorporated to explore potential widespread application of this new approach. The overall goal of this project was to develop and explore the limitations for a unique approach to genotyping both SNPs and STRs. A majority of the work involved development of the method itself with the ultimate objective of application for forensic science. The focus of this project was to address and alleviate some of the shortcomings of current approaches that result in potential limitations for forensic analysis. It is expected that future applications of this technology might impact a wide range of disciplines to aid in discovery, screening and association of changes in DNA sequence.

No description available.

No description available.