<p>The aim of this study was to investigate the genetic diversity of the SLC22A1 gene and to deduce its possible pharmacogenetic implications within the Cape Coloured population of South&nbsp / Africa / a uniquely admixed population of immigrant Europeans, Asians and the indigenous populations. Recent studies have reported an abundance of polymorphic variants within this solute&nbsp / carrier transporter gene encoding for the organic cation transporter 1, as well as evidence linking these variants to an effect on metformin uptake. This study included establishing baseline&nbsp / frequency distribution of previously reported alleles for 20 SNP variants within the SLC22A1 gene, as well as the development of SNaPshot&reg / and Multiplex AS-PCR genotyping assays, and&nbsp / also exploring the possibility of using High-resolution melt (HRM) analysis as a costeffective alternative for SNP genotyping. Ethics clearance was obtained from the Ethics Committee of the&nbsp / University of the Western Cape. Biological samples in the form of buccal (oral) swabs were collected from 132 unrelated voluntary donors from the Cape Coloured population residing in the&nbsp / Cape Metropolitan area. Two SNaPshot&reg / Multiplex Systems were specifically designed for the study,successfully optimized and used for genotyping. Hundred genetic profiles were then generated for a total of 20 SNP variants on SLC22A1 gene, using this primer extension-based genotyping method that enables multiplexing up 10 SNPs. Population genetics data obtained for&nbsp / the investigated SNPs were analysed using various statistical analysis software. Important population genetic parameters were calculated, and possible pharmacogenetics implications were then discussed. Among others, allelic and genotypic frequencies, as well as linkage disequilibrium were determined and compared with world populations. Minor deviation from Hardy- Weinberg equilibrium was observed in the Cape Coloured population. No significantLinkage Disequilibrium between the investigated SNPs was observed in this population. A Multiplex allele specific &ndash / PCR (MAS-PCR) genotyping&nbsp / system was successfully designed and optimized for the genotyping of 10 SNPs from the SLC22A1. This system, also developed specifically for this study, was made of 2 multiplexes each covering 5 SNPs. It is an inexpensive genotyping assay that allows for efficient discrimination of SNP polymorphisms in one reaction tube with standard PCR conditions. A pilot study was&nbsp / conducted to explore the possibility of using High-resolution melt (HRM) analysis as a cost-effective alternative for SNP genotyping. In addition to genotyping, HRM analysis can be used to scan&nbsp / large numbers of samples for novel genetic variations.&nbsp / </p>

Bayesian methods are often criticized on the grounds of subjectivity. Furthermore, misspecified priors can have a deleterious effect on Bayesian inference. Noting that model selection is effectively a test of many hypotheses, Dr. Valen E. Johnson sought to eliminate the need of prior specification by computing Bayes' factors from frequentist test statistics. In his pioneering work that was published in the year 2005, Dr. Johnson proposed using so-called local priors for computing Bayes? factors from test statistics. Dr. Johnson and Dr. Jianhua Hu used Bayes' factors for model selection in a linear model setting. In an independent work, Dr. Johnson and another colleage, David Rossell, investigated two families of non-local priors for testing the regression parameter in a linear model setting. These non-local priors enable greater separation between the theories of null and alternative hypotheses. In this dissertation, I extend model selection based on Bayes' factors and use nonlocal priors to define Bayes' factors based on test statistics. With these priors, I have been able to reduce the problem of prior specification to setting to just one scaling parameter. That scaling parameter can be easily set, for example, on the basis of frequentist operating characteristics of the corresponding Bayes' factors. Furthermore, the loss of information by basing a Bayes' factors on a test statistic is minimal. Along with Dr. Johnson and Dr. Hu, I used the Bayes' factors based on the likelihood ratio statistic to develop a method for clustering gene expression data. This method has performed well in both simulated examples and real datasets. An outline of that work is also included in this dissertation. Further, I extend the clustering model to a subclass of the decomposable graphical model class, which is more appropriate for genotype data sets, such as single-nucleotide polymorphism (SNP) data. Efficient FORTRAN programming has enabled me to apply the methodology to hundreds of nodes. For problems that produce computationally harder probability landscapes, I propose a modification of the Markov chain Monte Carlo algorithm to extract information regarding the important network structures in the data. This modified algorithm performs well in inferring complex network structures. I use this method to develop a prediction model for disease based on SNP data. My method performs well in cross-validation studies.

研究指出，在不同人類個體的DNA序列中，只有0.1%的基因組排列是相異的，而其餘的序列則是相同的。這些相異的基因組排列則被稱為單一核苷酸(SNP)。Affymetrix公司發展出一種DNA晶片技術稱之為Affymetrix GeneChip Mapping 100K SNP set，此晶片可用來決定單一核苷酸資料的基因類型(genotype)。Affymetrix公司採用預設「動態模型演算法」(DM)來決定基因型態。本論文的研究目的是探討與示範對於DM方法中預設的S值的四種修正方式。而這四種修正的方法分別是： (1) Standardized L value，(2) Median-polished L value，(3) Median-center L value，和(4) Median-standardized L value。為了比較S值與四種改進方法，本研究藉由SNP的模擬資料來進行比較。資料的模擬是基於利用改寫過的階層式之Bolstad模型（2004），而模擬模型的參數估計是利用華人細胞株及基因資料庫中95位台灣人的100K SNP資料。根據AA模型與AB模型模擬資料的基因型態正確率，Standardized L value是最好的判斷基因型態之方法。在另一方面，因為DM方法並不是設計來決定Null模型的基因型態，因此對於Null模型模擬資料的基因型態判斷會有問題。關於Null模型的基因型態判斷，本論文提供了一些簡短的討論與建議。然而，依然需要進一步的研究探討。 / It is known there is only 0.1% in the DNA sequences that is different among human beings, and the rest of them are the same. These differences in DNA sequences are defined as SNPs (Single Nucleotide Polymorphism). The Affymetrix, Inc. had developed a DNA chip technology called Affymetrix GeneChip Mapping 100K SNP set for SNP data used to determine the genotype call. The default algorithm applied by Affymetrix, Inc. to decide genotype calls is the Dynamic Model-based (DM) algorithm. This study aimed to investigate and demonstrate four different ways to modify the basic component used in DM algorithm, namely, the S value. These four modified methods include: (1) Standardized L value, (2) Median-polished L value, (3) Median-centered L value, and (4) Median-standardized L value. In order to compare the S value with the four modified L values, a simulation study was conducted. A hierarchical version of Bolstad’s model (2004) was adopted to simulate the SNP Data. The parameters for the simulation model were estimated based on 95 Taiwanese 100K SNPs data from Taiwan Han Chinese Cell and Genome bank. The Standardized L value was proven to be the best method based on the accuracy of the genotype calls determined according to the simulated data of AA model and AB model. On the other hand, the genotype call for simulated data under Null model is problematic since the DM approach is not designed to determine the Null model. We have given some brief discussion and remarks of the genotype call for Null model. However, further research is still needed. /

Προβλήματα υπογονιμότητας αντιμετωπίζει το 15% των ζευγαριών, εκ των οποίων το 40%-50% οφείλεται στον ανδρικό παράγοντα. Περιπτώσεις ανδρικής υπογονιμότητας στις οποίες δεν ανευρίσκεται προφανής αιτιολογικός παράγων, αντιπροσωπεύουν το 15% των περιπτώσεων και αναφέρονται ως περιπτώσεις ιδιοπαθούς υπογονιμότητας. Παλαιότερες αλλά και πιο πρόσφατες πληθυσμιακές μελέτες ανέδειξαν γενετικούς παράγοντες ως υπεύθυνους για τον φαινότυπο ορισμένων περιστατικών ιδιοπαθούς υπογονιμότητας και επομένως η μελέτη του γενετικού υπόβαθρου των ανδρών αυτών μπορεί να συμβάλλει στην διερεύνηση του παθογενετικού μηχανισμού της υπογονιμότητας/στειρότητας που παρουσιάζουν. Ειδικότερα, έχει διαπιστωθεί ότι ελλείμματα στις AZF περιοχές του Υ χρωμοσώματος υπάρχουν σε ένα ποσοστό 2% - 11% των υπογόνιμων ανδρών αυτής της κατηγορίας. Επίσης, σε πολύ πρόσφατη μελέτη προσδιορίστηκε η παρουσία ενός απλού νουκλεοτιδικού πολυμορφισμού SNP G197T που εντοπίζεται στο τέλος του πρώτου εξονίου του γονιδίου της πρωταμίνης-1. Ο πολυμορφισμός αυτός οδηγεί σε αντικατάσταση μιας συντηρημένης αργινίνης από σερίνη στην αμινοξική αλληλουχία της πρωταμίνης-1 (R34S), με ενδεχόμενες συνέπειες στο πακετάρισμα και την ακεραιότητα του DNA στην κεφαλή του σπερματοζωαρίου, γεγονότα, που μπορεί να οδηγήσουν σε ιδιοπαθή υπογονιμότητα. Τα αποτελέσματά μας έδειξαν ότι μόνο 3 από τα 100 άτομα (3%) έφεραν ελλείμματα στο Y χρωμόσωμα, ειδικότερα ένα άτομο με ενδιάμεση ολιγοσπερμία έφερε ελλείμματα στις AZFa και AZFb περιοχές και δυο άτομα με αζωοσπερμία έφεραν ελλείμματα στην AZFc περιοχή. Παράλληλα, o πολυμορφισμός SNP G197T δεν ανευρεθεί σε κανένα δείγμα του εξεταζόμενου πληθυσμού. / Infertility affects 10%-20% of all couples attempting pregnancy, with men responsible in 40%-50% of these cases. Male infertility exhibits no obvious clinical or pathophysiological features in 15% of these cases and it is therefore characterized as idiopathic. Genetic studies have revealed deletions in the AZF regions of Y chromosome, which contain genes involved in spermatogenesis, in 2%-11% of men with idiopathic infertility. Recent studies, also correlate male idiopathic infertility with the presence of an heterozygous SNP (G197T ) at the end of the first exon of protamine-1 (PRM1) gene. This SNP converts one of the highly conserved arginine residue to serine residue (R34S) which can substantially alter both DNA binding and protamine to protamine interaction in the sperm nucleus leading to infertility through defective chromatin packaging in the sperm nucleus. The purpose of this study was to evaluate the frequency of deletions in the AZF regions of Υ chromosome and the contribution of the polymorphism SNP G197T in a local sample of 100 men attending the Urology Clinic of the Patras University Hospital for infertility problems of unknown aetiology. Our results revealed that three of our patients (3%) were found to bear deletions in the AZF regions of the Y chromosome, one patient with intermediate oligospermia had deletions in AZFa and AZFb regions and two patients with azoospermia had deletion in AZFc region. On the other hand, the polymorphism SNP G197T has no distribution to the idiopathic infertility of the population studied.

<p>The aim of this study was to investigate the genetic diversity of the SLC22A1 gene and to deduce its possible pharmacogenetic implications within the Cape Coloured population of South&nbsp / Africa / a uniquely admixed population of immigrant Europeans, Asians and the indigenous populations. Recent studies have reported an abundance of polymorphic variants within this solute&nbsp / carrier transporter gene encoding for the organic cation transporter 1, as well as evidence linking these variants to an effect on metformin uptake. This study included establishing baseline&nbsp / frequency distribution of previously reported alleles for 20 SNP variants within the SLC22A1 gene, as well as the development of SNaPshot&reg / and Multiplex AS-PCR genotyping assays, and&nbsp / also exploring the possibility of using High-resolution melt (HRM) analysis as a costeffective alternative for SNP genotyping. Ethics clearance was obtained from the Ethics Committee of the&nbsp / University of the Western Cape. Biological samples in the form of buccal (oral) swabs were collected from 132 unrelated voluntary donors from the Cape Coloured population residing in the&nbsp / Cape Metropolitan area. Two SNaPshot&reg / Multiplex Systems were specifically designed for the study,successfully optimized and used for genotyping. Hundred genetic profiles were then generated for a total of 20 SNP variants on SLC22A1 gene, using this primer extension-based genotyping method that enables multiplexing up 10 SNPs. Population genetics data obtained for&nbsp / the investigated SNPs were analysed using various statistical analysis software. Important population genetic parameters were calculated, and possible pharmacogenetics implications were then discussed. Among others, allelic and genotypic frequencies, as well as linkage disequilibrium were determined and compared with world populations. Minor deviation from Hardy- Weinberg equilibrium was observed in the Cape Coloured population. No significantLinkage Disequilibrium between the investigated SNPs was observed in this population. A Multiplex allele specific &ndash / PCR (MAS-PCR) genotyping&nbsp / system was successfully designed and optimized for the genotyping of 10 SNPs from the SLC22A1. This system, also developed specifically for this study, was made of 2 multiplexes each covering 5 SNPs. It is an inexpensive genotyping assay that allows for efficient discrimination of SNP polymorphisms in one reaction tube with standard PCR conditions. A pilot study was&nbsp / conducted to explore the possibility of using High-resolution melt (HRM) analysis as a cost-effective alternative for SNP genotyping. In addition to genotyping, HRM analysis can be used to scan&nbsp / large numbers of samples for novel genetic variations.&nbsp / </p>

Hypothyroidism is a common endocrine disorder affecting women of reproductive age. On a global level, iodine deficiency is still the most common cause of hypothyroidism. Also genetic variations, in particular SNP rs4704397 in the PDE8B gene, are responsible for a significant proportion of TSH variations.  Untreated hypothyroidism has significant adverse effects on pregnancy and fetal outcome. Most international guidelines suggest targeted thyroid testing in pregnant women with risk factors for thyroid disturbances. In a case-control study, an association between homozygous A/A as well as homozygous G/G carriers of SNP rs 4704397 in PDE8B and recurrent miscarriage was found. The explanation for this association is unknown. In a nationwide survey, all guidelines for thyroid testing and management of hypothyroidism during pregnancy in Sweden were collected and compared with international guidelines. The local guidelines were variable and poorly compliant with the international guidelines. In a follow-up in one district, 5,254 pregnant women were included for subsequent review of their medical reports. We found a targeted thyroid testing rate of 20.1% in clinical practice, with an overall frequency of women with trimester-specific elevated TSH of 18.5%. More disturbingly, half of the women who were on levothyroxine treatment at the time of conception had an elevated TSH level at thyroid testing. In a subsequent cohort study of the 5,254 women, we found the prevalence of trimester-specific elevated TSH and overt hypothyroidism to be equal in targeted thyroid tested and untested women. In a cross-sectional study, a median urinary iodine concentration (UIC) of 98 μg/l was found in the study population. According to WHO/UNICEF/IGN criteria, the population-based median UIC during pregnancy should be 150-249 μg/l. In conclusion, genetic variations may contribute to adverse pregnancy outcomes. In clinical practice, thyroid testing and the management of hypothyroidism during pregnancy is unsatisfactory, regarding the whole chain from development of local guidelines to their implementation and to targeted thyroid testing. Moreover, our results indicate insufficient iodine status in the pregnant population of Sweden.

Since Parsons et al. (2008) found the frequent mutations of IDH1 (12%) in GBMs, various reports have studied the prevalence and characteristic of IDH1 and IDH2 mutations.The mutations in the isocitrate dehydrogenase 1 (IDH1) gene occur in nearly 40% of gliomas. The frequency of IDH1 mutations are inversely connected with grade II (~80%), III (~50%), and IV (~ 10%) gliomas. Importantly, the status of IDH1 mutations is associated with a better outcome and demonstrated a diagnostic value. We analyzed also these mutations in distribution, association with tumor-derived other genetic alterations and the diagnostic and prognostic value in a cohort of 1332 glioma patients.A synonymous single nucleotide polymorphism [SNP rs 11554137; C (cytosine) substituted by T (thymin)] has been studied in gliomas patients. The SNP rs 11554137 (in codon 105) are located in the same exon with the IDH1 R132 mutations (in codon 132). And gliomas patients with SNP rs 11554137: C>T had a poorer outcome than patients without SNP rs 11554137. This was observed a similarly adverse effect in survival in patients with AML. Mutations in codon 132 can cause a decrease of IDH1/2 activity and also gain a new enzyme function for the NADPH dependent reduction of alpha-ketoglutarate to 2-hydroxyglutarate. High 2HG and low NADPH levels might sensitize tumors to oxidative stress, potentiating response to radiotherapy, and may account for the prolonged survival of patients harboring the mutations. So we studied further the alterations of function in IDH1R132H mutant cells in vitro. Based on the decrease of defence and the increase of impairing factors in tumor cells, we found that the tumors harbouring IDH1 mutations may have an elevated radiosensitivity. In the present study, we described the impact of IDH1 mutations in gliomas and search for new perspectives for the treatment strategy.

Mapping quantitative trait loci (QTL) for traits under consideration for genetic improvement is becoming more common for many aquatic species, including Atlantic salmon. The objective of the study was to map QTL associated with length, weight, shape, parr mark number and contrast in three F2 hybrid families of European and North American strains of Atlantic salmon using single nucleotide polymorphisms. GridQTL software was used to perform separate analyses for male and female linkage maps. Numerous highly significant QTL were detected for every trait. Locations of QTL differed based on age and map used. Some QTL locations for the analyzed traits were similar to those of other studies on purebred and backcross Atlantic salmon populations; however, many more QTL were detected in the hybrid F2’s. The amount of genetic variation in skin colour and pattern displayed within the transAtlantic F2 families greatly exceeded the ranges seen in nature. / NSERC Strategic Grant

Infertility affects 15 % of couples, which corresponds to 60 - 80 million worldwide. The microenvironments in which the oocyte, embryo and fetus mature are vital to the establishment and development of a healthy pregnancy. Different biological systems, such as angiogenesis, the immune system and apoptosis need to be adequately regulated for pregnancy to occur and progress normally. The overall aim of this thesis was to investigate the impact of Histidine-rich glycoprotein (HRG) and Src homology 2 domain-containing adapter protein B (SHB) on human female fertility. HRG is a plasma protein that regulates angiogenesis, the immune system, coagulation/fibrinolysis and apoptosis, by building complexes with various ligands. The impact of HRG on fertility is studied here for the first time. HRG is present in follicular fluid, the Fallopian tube, endometrium, myometrium and placenta. HRG distribution within embryo nuclei depends on developmental stage. Blastocysts express and secrete HRG. The HRG C633T single nucleotide polymorphism (SNP) appears to affect the chance of pregnancy and, correspondingly, parameters associated with pregnancy in IVF. Additionally, this HRG genotype may increase the risk in IVF of only developing embryos unfit for transfer. SHB is an adaptor protein involved in intracellular signaling complexes that regulate angiogenesis, the immune system and cell proliferation/apoptosis. Shb knockout mice have altered oocyte/follicle maturation and impaired embryogenesis. The impact of three SHB polymorphisms (rs2025439, rs13298451 and rs7873102) on human fertility is studied for the first time. The SNP prevalences did not differ between infertile and fertile women. BMI, gonadotropin dosages, the percentage of immature oocytes, the number of fertilized oocytes, the percentage of good-quality embryos and the day of embryo transfer seems to be affected by SHB genotype. In conclusion, HRG and SHB appear to influence female fertility. They are potential biomarkers that might be used for predicting pregnancy chance in infertile women. Knowledge of these genotypes may improve patient counseling and individualization of treatment.

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.