Meningeome sind Tumore der Hirnhäute und stellen zirka 24-30% aller intrakraniellen Tumore dar. Obwohl sie in den meisten Fällen als solitär, langsam wachsend und benigne (WHO Grad 1) beschrieben werden, ist ihr ausgeprägtes Rezidivverhalten die größte Herausforderung in der Therapie. Bisherige Arbeiten verwendeten zur genetischen Analyse von Meningeomen meist Untersuchungstechniken mit eingeschränkter (molekular-)zytogenetischer Aussagekraft. Mit der Kombination der Methoden Giemsa-Bandendarstellung (GTG-Bänderung), Spektrale Karyotypisierung (SKY-Technik), Fluoreszenz in situ Hybridisierungstechniken (FISH-Analyse) und molekulare Karyotypisierung unter Verwendung von 100K beziehungsweise 6.0 SNP-Arrays (SNP-A Karyotypisierung) sollte es möglich sein, in effizienterer Form bislang unentdeckte chromosomale Aberrationen zu identifizieren und weiterführende tumormechanistische Hinweise zu erhalten. In der vorliegenden Arbeit wurde zunächst ein multipel aufgetretenes Meningeom mit zwei Tumoren unterschiedlicher Malignität (1 WHO Grad 1; 1 WHO Grad 2) analysiert, anschließend erfolgte die Untersuchung einer Gruppe von 10 Meningeomen (5 WHO Grad 1; 5 WHO Grad 2). Bisher nicht beschriebene Aberrationen wie ein dizentrisches Chromosomen 4, die parazentrische Inversion im chromosomalen Bereich 1p36 und die balancierte reziproke Translokation t(4;10)(q12;q26) wurden detektiert. Die genomweite SNP-A Karyotypisierung ermöglichte neben der genaueren Betrachtung der zytogenetischen Ergebnisse die simultane Analyse von Blut und Tumor-DNA der Patienten und lieferte Hinweise auf konstitutionelle Aberrationen. Es zeigte sich eine signifikante Anreicherung von rekurrenten Regionen kopienneutraler Verluste der Heterozygotie als Hinweis auf das Vorliegen potenzieller segmentaler Uniparentaler Disomie (UPD) jeweils in Blut und Tumor der Patienten. Außerdem wurden nur im Tumor befindliche potentielle rekurrente segmentale UPD Regionen detektiert. Die weitere Analyse der konstitutionellen sowie somatischen segmentalen UPD hinsichtlich ihrer Rolle im Rahmen der Tumorgenese ist eine wichtige Aufgabe für die Zukunft.

Reversion-inducing cysteine-rich with Kazal motif (RECK) is a cell surface anchoring protein, which known for the ability to inhibit matrix metalloproteinases (MMPs) and participate in angiogenesis regulation. The inhibition of membrane type-1 matrix metalloproteinase (MT1-MMP), MMP-2, MMP-7 and, MMP-9 by RECK has been demonstrated. Our previous studies show that RECK expression is suppressed by Ras and Her-2/neu oncogene. In addition, oncogenic Ras activates downstream ERK signaling pathway to increase Sp1/HDAC promoter binding affinity which results in reduction of RECK gene transcription and increase of tumor progression and metastasis. From the clinical investigation, RECK expression is down-regulated in a number of cancer types. In breast cancer, RECK expression is associated with the prognosis of the patients. Recently, single nucleotide polymorphisms (SNPs) of RECK promoter have been suggested to be linked with survival rate and prognosis of breast cancer patients. Whether SNP of the RECK promoter has any effect on RECK expression and its clinical significance is still unclear. . In this study, we investigate -402 SNP at RECK promoter and find this SNP directly affects RECK expression through progesterone receptor binding. Additionally, we also address the -402 SNP in the sample collected from patients and analyze its association with clinicopathological parameters to clarify its clinical significance. Our results suggest that RECK SNP may be an valuable prognosis factor for breast cancer.

Kawasaki disease (KD) is characterized by a systemic vasculitis of unknown etiology. More research indicates that KD is related to genetic. In 2003, Sekiya et al. studied the correlation of Th2-related genes and the KD in Japan. They found out that -431T allele would increase the concentration of Thymus and activation-regulated chemokine (TARC)/ CCL17 protein in serum by single nucleotide polymorphism (SNP) -431 C>T of chemokine TARC/ CCL17 operon 5¡¦-flanking region , which suggests that SNP has functionality. Therefore, this study explored the polymorphism and relationship between the regulation of chemokine of TARC/ CCL17 and KD. Firstly, we performed polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP) to detect TARC/CCL17 -431 C>T genotype. Then enzyme immunoassay was used to detect TARC/CCL17 chemokine¡¦s expression. The results showed that the performance of TARC -431 C/T SNP, the alleles from KD patients with -431 T, were significantly less than the non-KD control group. It was observed that the -431 T alleles had a lower chance to occur in KD with aneurysms, but independent with coronary artery lesions (CAL). In addition, the acute stage of KD has a higher TARC protein expression, which gradually decreases during IVIG treatment period. However, the up-regulation of TARC protein may not be the direct consequence caused by the single nucleotide polymorphism of TARC -431 C>T.

Prevalence of childhood asthma in Taiwan has increased 9 times from 1.3% to 10-14% in the past 4 decades. Many studies worldwide have demonstrated that many genes in different chromosomes are implicated in childhood asthma in different ethnic populations. A growing body of evidence suggests that allergic sensitization could occur in perinatal stage and correlate to the development of childhood asthma. Epidemiological studies, however, indicate that prevalence of childhood asthma is much higher in developed countries than that in developing countries; and prevalence of childhood asthma in metropolitan area is higher than that in country sites. This suggests that certain genes can interact with the environmental factors in developed countries to promote the development of childhood atopic disorders. Interests are now increasing on what is (are) the real pathogenic gene-gene interaction(s) for childhood atopic disorders under influence of age, gender and environmental factors? In a large perinatal cohort study with 1,211 pregnant women and their offspring from the obstetrics and pediatrics of Kaohsiung Chang Gung Memorial Hospital, we analyzed 159 allergy candidate genes with 384 single nucleotide polymorphisms and showed that 14 genes over 22 somatic and X chromosomes risk to or protective from cord blood immunoglobulin E (CBIgE) elevation are different from those genes associated with IgE elevation in children under 1.5, 3 and 6 years of age (12, 15 and 12 genes, respectively). CX3CL1, IL13, PDGFRA and FGF1 polymorphisms were associated with elevated IgE at earlier ages (newborn, 1.5 and 3 years); HLA-DPA1, HLA-DQA1, CCR5 and IL5RA polymorphisms were associated with IgE production at 6 years of age. Further analysis by multifactor dimensionality reduction (MDR) developed from data reduction strategy, we found that there are interactions among innate immunity, adaptive immunity, and response and remodeling genes on IgE production begin in prenatal stage. For example, The gene-gene interaction among IL13, rs1800925, CYFIP2, rs767007 and PDE2A, rs755933 was significantly associated with IgE production at 3 years of age. This suggests that different genotypes of genes interact one another on the IgE production contributing to the development of allergic diseases. Since the concentration of IgE is an important indicator of atopic disorders and allergic sensitization, we believe after clarifying the natural course of the genomic profiles on IgE elevation, certain early predictor(s) and preventive regimens for allergic sensitization or atopic disorders may be made possible.

Stroke is characterized with loss of one or more functions of the body resulted by inadequate blood supply to the brain. Most of the cases result from a blood clot forms on an atherosclerotic plaque in the brain which is called as ischemic stroke. Structure of the arteries and vascular tone are listed in major determinants in the development of the disorder. Soluble epoxide hydrolase (sEH, EPHX2) catalyzes conversion of epoxyeicosatrienoic acids to inactive diol metabolites. EETs are potent vasodilators that participate in the regulation of vascular tone and cerebral blood flow. Microsomal epoxide hydrolase (mEH, EPHX1) is a critical phase I enzyme that catalyzes the conversion of various xenobiotic epoxide substrates and polycyclic aromatic hydrocarbons (PAHs). Animal studies show that tobacco smoke mutagens such as PAHs and heterocyclic amines directly increase the development of atherosclerotic lesions. The main purpose of this study is evaluation of effect of Arg287Gln single nucleotide polymorphism of EPHX2 gene and Tyr113His and His139Arg single nucleotide polymorphisms of EPHX1 gene as a risk factor for ischemic stroke in Turkish population. Blood samples of 237 ischemic stroke patients and 120 controls were collected and all polymorphisms were determined by PCR-RFLP method. Mutant allele frequencies in terms of Arg287Gln polymorphism of EPHX2 gene (A) were found as 0.08 for patient group and 0.09 for controls. Tyr113His polymorphism of EPHX1 gene (C) were found as 0.27 for patient group and 0.31 for controls when, His139Arg polymorphism of EPHX1 gene (G) were 0.820 and 0.814 for patient and control groups, respectively. The differences between mutant allele frequencies of patients and controls were not found to be statistically significant. Subgroup analysis was used to investigate the effects of conventional vascular factors according to the genotypes in the stroke susceptibility. Smoking, diabetes, obesity and hypertension were found to significantly increase the risk of having stroke. More detailed analysis on these factors with respect to genotypes showed that the risk of hypertensive individuals having ischemic stroke was higher in wild type homozygous genotype groups of Tyr113His (TT) and His139Arg (AA) polymorphisms and heterozygous and mutant homozygous genotypes of Arg287Gln (GA+AA) polymorphism than their counterparts (OR= 3.21, 3.15 and 4.69, respectively). Smoker people within the heterozygous and mutant homozygous genotypes group of Arg287His (GA+AA) polymorphism and wild type homozygous group of His139Arg (AA) polymorphism were found to be more susceptible to have stroke (OR= 11.81 and 4.78 respectively). Finally, diabetes mellitus was found to double the risk of having stroke regardless of the genetic background. Logistic regression analyses were used to ascertain the effects of vascular factors, lipid parameters and genotypes in the stroke susceptibility. LDL-cholesterol (OR=1.46 / 95%CI, 1.12-1.89, P=0.00), smoking (OR=3.46 / 95%CI, 1.66-7.21, P=0.00) and hypertension (OR=3.19 / 95%CI, 1.92-5.30, P=0.00) were found to be significant risk factors for ischemic stroke, whereas HDL (OR=0.27 / 95%CI, 0.12-0.65, P=0.02) was found to be a protective factor in general population. In this study, the relation of Tyr113His and His139Arg polymorphisms of EPHX1 gene and risk of ischemic stroke is investigated for the first time in literature while, Arg287Gln polymorphism and ischemic stroke risk in Turkish population was studied for the first time.

This study presents a CMOS integrated sensor chip suitable for sensing biological samples like DNA. The sensing part of the chip consists of a 32 X 32 pixel array with a 15 &micro / m pixel pitch. Pixels have 5 &micro / m X 5 &micro / m detector electrodes implemented with the top metal of the CMOS process, and they are capable of detecting charge transferred or induced on those electrodes with a very high sensitivity. This study also includes development of an external electronics containing ADC for analog to digital data conversion. This external circuitry is implemented on a PCB compatible with the Opal Kelly XM3010 FPGA that provides data storage and transfer to PC. The measured noise of the overall system is 6.7 e- (electrons), which can be shrunk down to even 5.1 e- with an over sampling rate. This kind of sensitivity performance is very suitable for DNA detection, as a single nucleotide of a DNA contains 1 or 2 e- and as 10 to 20 base pair long DNA&rsquo / s are usually used in microarray applications. The measured dynamic range of the system is 71 dB, in other words, at most 24603 e- per frame (20 ms) can be detected. The measured leakage is 31 e-/frame, but this does not have a dramatic effect on the sensitivity of the system, noting that the leakage is a predictable quantity. DNA detection tests are performed with the chip in addition to electronic performance measurements. The surface of the chip is covered with a nitride passivation layer to prevent the pixel crosstalk and is modified with an APTES polymer for suitable DNA immobilization. DNA immobilization and hybridization tests are performed with 5&rsquo / -TCTCACCTTC-3&rsquo / probe and its complementary 3&rsquo / -AGAGTGGAAG-5&rsquo / target sequences. Hybridization performed in 1 pM solution is shown to have a larger steady state leakage than the immobilization in a 13 &micro / M solution, implying the ability to differentiate between the full match and full mismatch sequences. To best of our knowledge, the measured pM sensitivity has not yet been reported with any label free CMOS DNA microarrays in literature, and it is comparable with the sensitivity of techniques like QCM or the fluorescence imaging. The 1 pM sensitivity is not a theoretical limit of the sensor, since theoretically the sensitivity level of 6.7 e- can offer much better results, down to the aM level, as far as the noise of electronics is considered, nevertheless the sensitivity is expected to be limited by DNA immobilization and hybridization probabilities which are determined by the surface modification technique and applied protocol. Improving those can lead to much smaller detection limits, such as aM level as stated above.

Graves¡¦ disease (GD), an organ specific autoimmune disease, requires two signals to activate the T cells. In addition to the specific binding of T cell receptor to the antigenic peptide-MHC complex, an antigen-independent costimulatory pathway reportedly require generate subsequent cytokines and cell surface molecules. This regulation of T-cell response is a highly-organized multiple step program. T cell costimulatory signals is found to regulate the magnitude and duration of various type of autoimmune diseases. This study is to test whether genetic polymorphism of these costimulatory genes is related with the disease susceptibility or progression. We anticipated that the candidate genetic makers are beneficial for importing GD management. We recruited 262 GD patients from the Outpatient Department of Endocrine and 200 healthy controls from the Health Screening Center of Chang Gung Memorial Hospital in Kaohsiung.The GD patients were divided into three groups: recurred within 9 months (n=91), between 10-36 months (n=65), and more than 36 months (n=106). Clinical and laboratory attributes included: the genotypes of CTLA-4, CD28, ICOS, PD-1 and CD40; serum levels of T4, T3 and TSH; goiter size and TSH-receptor antibodies at the beginning and end of treatment. Genomic DNA was extracted from peripheral blood leucocytes by kit. The single nuclotide polymorphisms of the candidate genes were genotyped by polymerase chain reaction- restriction fragment length polymorphism and TaqMan® SNP Genotyping Assays with specific primers. Linkage disequilibuium between pairs of polymorphism was estimated by Haploview software. Haplotype analyses were performed using the Hap-Clustering program. Variance and correlation of data was statistically analyzed by Chi-square, general liner model, multiple logistic regression analysis and Kaplan-Meier plot. A p value <0.01 was considered significant. The results showed:(1) Genetic polymorphism within the costimulatory molecules affected the susceptibility and progression of GD; (2) GD patients carried more risk alleles than the controls; (3) Within the GD group, patients harboring more risk alleles wound relapse earlier after drug withdrawal; (4) Number of risk alleles, goiter size and TBII levels at end of treatment were independent predictors of disease relapse; (5) A risk score calculation based on odds ratio of risk alleles correlated with patients¡¦ relapse time after drug withdrawal. We concluded that patients¡¦ genetic makers of costimulatory molecules may be helpful in choosing appropriate treatment for GD.

<p>There is a continuous development of different crop varieties in the crop trade. The cultivated crops tend to be more and more alike which require an effective method for crop identification. Crop type and crop type purity has become a quality measure in crop trade both nationally and internationally. A number of well known quality attributes of interest in the crop trade can be correlated to the specific crop type and therefore it is of great importance to reliably be able to identify different crop varieties. It is well known from the literature that there exist genomic variations at the nucleotide level between different crop varieties and these variations might potentially be useful for automated variety identification.</p><p>This project deals with the crop variety identification area where the possibilities of distinguishing between different wheat varieties are investigated. Experience from performing wheat variety identification at protein level has shown unsatisfactory results and therefore DNA-based techniques are proposed instead. DNA-based techniques are dependent upon the availability of sequence data from the wheat genome and some work has concerned examining the availability of sequence data from wheat. But the focus of the work has been on defining a method for computational detection of single nucleotide variations in ESTs from wheat and to experimentally test that method. Results from these experiments show that the method defined in this project detects polymorphic variations that can be correlated to variety variations</p>

GWAS have identified several chromosomal loci associated with ovarian cancer risk. However, the mechanism underlying these associations remains elusive. We identify candidate functional Single Nucleotide Polymorphisms (SNPs) at the 9p22.2 ovarian cancer susceptibility locus, several of which map to transcriptional regulatory elements active in ovarian cells identified by FAIRE-seq (Formaldehyde assisted isolation of regulatory elements followed by sequencing) and ChIP-seq (Chromatin Immunoprecipitation followed by sequencing) in relevant cell types. Reporter and electrophoretic mobility shift assays (EMSA) determined the extent to which candidate SNPs had allele specific effects. Chromosome conformation capture (3C) reveals a physical association between Basonuclin 2 (BNC2) and SNPs with functional properties. This establishes BNC2 as a major target of four candidate functional SNPs in at least two distinct elements. BNC2 codes for a putative transcription regulator containing three pairs of zinc finger (ZF) domains. Furthermore, bnc2 mutation in zebrafish leads to developmental defects including dysmorphic ovaries and sterility, clearly implicating this protein in cellular processes associated with ovarian development. We show that BNC2 is a transcriptional regulator with a specific DNA recognition sequence of targets enriched in genes involved in cell communication through DNA binding assays, ChIP-seq, and expression analysis. This study reveals a comprehensive regulatory landscape at the 9p22.2 locus and indicates that a likely mechanism of susceptibility to ovarian cancer may include multiple allele-specific changes in DNA regulatory elements some of which alter BNC2 expression. This study begins to identify the underlying mechanisms of the 9p22.2 locus association with ovarian cancer and aims to provide data to support advances in care based on one’s genetic composition.

Prostate-specific antigen (PSA) testing has caused a steep increase in the incidence of prostate cancer, especially the incidence of localised low risk disease. In order to decrease the overdiagnosis accompanied by PSA testing, analysis of inherited genetic variants have been suggested as potential tools for clinical assessment of disease risk. With the aim of minimizing overtreatment and postpone side-effects of curative treatment for low risk prostate cancer, active surveillance, a treatment strategy with initial surveillance and deferred radical prostatectomy at the time of progression has evolved.  The aim of this thesis was to study the validity of PSA (paper I) and inherited genetic variants (paper II) for early diagnosis of prostate cancer, to assess the extent of PSA testing in Sweden (paper III), and to study the safety of deferred radical prostatectomy in localised low to intermediate risk prostate cancer (paper IV). The study designs were i) case-control studies nested within the Västerbotten intervention project (paper I and II), ii) observational study in the Cancer Register of Sweden (paper III), and iii) observational study in the NPCR Follow-up study (paper IV). PSA had a high validity in predicting a prostate cancer diagnosis with an area under the receiver operating characteristics (ROC) curve of 0.86 (95% CI, 0.84 to 0.88). A combined test, including PSA, the ratio of free to total PSA, and 33 single nucleotide polymorphisms (SNPs) in a genetic risk score, increased the area under curve to 0.87 (95% CI, 0.85 to 0.89). The estimated uptake of PSA testing among men aged 55 to 69 years increased from zero to 56% between 1997 and 2007 and there were large variations in the uptake of PSA testing between counties in Sweden. After a median follow-up time of eight years there was no significant difference in presence of any one or more adverse pathology features or prostate cancer specific mortality after primary compared to deferred radical prostatectomy in localised low to intermediate risk prostate cancer. Results from these studies indicate that PSA and the hitherto identified SNPs are not suitable biomarkers in single-test prostate cancer screening. It is possible to estimate the uptake of PSA testing on a population level. Initial surveillance and deferred radical prostatectomy represent a feasible treatment strategy in localised low to intermediate risk prostate cancer.