Ph.D. Theses
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Browsing Ph.D. Theses by Author "Çağlayan, S. Hande."
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Item Absence epilepsy in Turkish patients: a novel gene at susceptibility locus 2q36 and the role of GABRG2(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2009., 2009.) Çapan, Özlem Yalçın.; Çağlayan, S. Hande.Idiopathic absence epilepsies (IAE) are complex disorders mainly caused by genetic factors. Two major whole-genome linkage studies performed on many IAE samples pointed to chromosome 2q36 as a susceptibility locus for absence epilepsies. Whole genome linkage study on absence epilepsy model Wag/Rij rats, also showed the syntenic 2q33-37 region to be linked to the quantative trait of absence seizures. Candidate ion channel genes at 2q36 were screened but causative mutation could not be identified. On the other hand, mutations have been found in the subunits of GABA receptors and Ca channels in a few patients. At present, therefore, the complete picture of pathogenesis of the absence seizures is not known. In this study, to assess the possible role of 2q36 region in absence epilepsy, 205 Turkish absence patients and 219 healthy controls were used in an association analysis. Based on the haplotype block structure of the Turkish population in this region 10 tagSNPs were selected to cover the 160kb region at 2q36. The patients were subgrouped according to the syndrome and seizure types. The results revealed a significant association of two neighboring SNPs (rs7588807 and rs2840128) with JAE syndrome and even higher significant association with GTCS with the same SNP, rs7588807 that resided in the INHA gene. The point mutation and qPCR analysis of the INHA gene revealed mutations/variations in several patients and a large deletion that covered 30-50 kb in at least seven JAE patients supporting the association of INHA with the epilepsy phenotype and its establishment as a novel gene involved in the pathogenesis of JAE. The presence of other candidate genes in the deleted region paves the way for further molecular genetic analysis to reveal the role of each candidate gene in the pathogenesis of epilepsies, if any. The study further supports the role of GABRG2 in the pathogenesis of absence seizures by the identification of novel variations/mutations especially affecting the splice sites in CAE patients.Item Identification of novel genes involved in the etiology of benign neonatal / infantile epilepsy syndromes and genetic epilepsy with febrile seizures plus (GEFS+)(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2015., 2015.) Usluer, Sunay.; Çağlayan, S. Hande.Epilepsy is among the most prevalent episodic neurological disorders. Genetic factors play a major role in the etiology of epilepsy. This thesis included analysis of families with distinct epilepsy phenotypes in order to delineate their complex genetic background using advanced and highthroughput current technologies. The first part of the thesis comprised a large family with BFIS phenotype which was analyzed and found to have a synonymous change in the SCN1B gene affecting splicing efficiency as shown in neuronal cell culture and by in silico tools. It was the first time SCN1B gene was shown to be associated with the BFIS phenotype. Several patients in the family also had KCNQ2 gene copy number gain and a frameshift mutation in the PRRT2 gene. The lower penetrance of these two BFIS associated gene mutations indicated the oligogenic nature of the disease. Additional families with BFIS phenotype were also analyzed for point mutations in the SCN1B and PRRT2 genes. A frameshifting 2 bp deletion in the PRRT2 gene was found in one family and rare SNPs in SCN1B genes were identified in other families. Five BFNS patients with neonatal disease onset, on the other hand, had inherited KCNQ2 gene copy number gain mutations suggesting that KCNQ2 duplications mutations may also be implicated in the etiology of BFIS/BFNS phenotypes. In the second part of the study a large multiplex, multigenerational kindred with epilepsy similar to GEFS+ phenotype and with patients having idiopathic generalized or partial epilepsy subtypes was analyzed by current genomic technologies and found to have a VNTR expansion on the mir137 gene in significantly higher numbers in individuals with epilepsy phenotypes. The VNTR expansion disrupts the expression of mir137 that targets all the genes involved in schizophrenia, synapses formation and important ion channel genes involved in epilepsy.Item Molecular analyses of germ line methylation patterns and of the common intron 22 inversion mutation in the factor VIII gene(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1998., 1998.) El-Maarri, Osman A.; Çağlayan, S. Hande.The factor VIII gene includes two major mutation hotspots: the intron 22 inversion and transitions at CpG dinucleotides, both of which have been examined in the context of this thesis. A non-radioactive southern blot approach was implemented for the detection of the inversion, that allowed an accurate diagnosis for about 1/4 of the Turkish hemophilia A families. About 45 % of all point mutations in the factor VIII gene occur at CpG sites. Previous studies had pointed to a bias in paternal origin for transition mutation at CpG dinucleotides. This was believed to be a direct reflection of the hypomethylation in the female germ cells. However, to date there was no direct proof for a differential level of methylation in the germ cells, at human disease causing codons. In this study, an original investigation was undertaken to determine the methylation status of mature germ cells at selected sites in the human factor VIII and the FGFR3 genes. An equally high level of methylation, at non-cluster CpG sites, was observed in mature eggs, spermatocytes and polar bodies. This result shows that the higher mutation rate in the male germ line is apparently not a simple reflection of sex specific methylation differences.Item Molecular analysis of the factor IX gene in the Turkish population(Thesis (Ph.D.) - Bogazici University. Institute for Graduate Studies in Science and Engineering, 1999., 1999.) Onay, Ü. Venüs.; Çağlayan, S. Hande.Hemophilia B, the third common hereditary coagulopathy, is very heterogeneous at both phenotypic and genotypic levels. This X-linked recessive disease is caused by the production of either reduced amounts or functionally defective forms of the coagulation factor IX. In order to undertake a comprehensive molecular analysis of the FIX gene in the Turkish population 41 hemophilia B patients were screened for mutations by ddF and direct DNA sequencing to contribute to the knowledge of genotype-phenotype correlations in hemophilia B and to construct a Turkish mutation profile. A hypervariable polymorphic site within the FIX gene have also been analyzed. Thirty-two mutations were identified in Turkish hemophilia B patients, including 4 novel single base changes and 2 novel gross rearrangements. The mutation profile of the Turkish population was found to be similar to the general profile observed worldwide. Haplotype analysis revealed the independent origin of 4 recurrent mutations. All patient data was compiled in a national database, which efficiently shows the mutation/phenotype/haplotype relations. The analysis of the hypervariable region in intron 1 in 85 Turkish individuals revealed the presence of a novel allele and showed that the Turkish population carries the Caucasian specific allele as the most frequent one.Item Mutation profile of hemophilia a patients with inhibitors and association of interleukin and cytokine gene polymorphisms with inhibitor development(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2010., 2010.) Fidancı, İnanç Değer.; Çağlayan, S. Hande.Hemophilia A (HA) is an X linked recessive bleeding disorder characterized by qualitative and quantitative deficiency in the factor VIII (FVIII) protein, mainly caused by Factor 8 (F8) gene mutations. A severe complication in the replacement therapy of HA patients is the development of allo-antibodies (inhibitors) against FVIII which neutralize the substituted FVIII. Genetic risk factors along with F8 gene mutations influence the development of inhibitors. Interleukins and cytokines such as IL4, IL5, IL10, TGFB1 and IFNG that are involved in the regulation of B lymphocyte development are possible targets as other genetic risk factors. The aim of this dissertation was to reveal the F8 gene mutation profile of severe HA patients who developed inhibitors using various methods to assess the possible associations between 9 selected interleukin and cytokine gene polymorphisms with inhibitor development in HA patients with a null mutation in the F8 gene. The most prevalent mutation in inhibitor patients was intron 22 inversion followed by nonsense mutations and large deletions with major effects on FVIII function. Therefore, severe HA patients were screened for intron 22 inversion to constitute inhibitor (+) and inhibitor (–) patient subgroups to carry out a case-control association study. A significant association with the T-allele of rs2069812 located in IL5 gene promoter and patients with inhibitors was found with a p-value of 0.0251. The TT genotype was also significantly associated with the inhibitor (+) patient group with a p-value of 0.0082 and OR of about 7, suggesting that the T-allele as the recessive susceptibility allele and C-allele was the dominant protective allele. The present findings are highly informative about the role played by the polymorphisms in genes involved in B lymphocyte development as genetic risk factors in antibody development in severe HA patients with null mutations and paves the way for furthe studies in the field.Item The molecular landscape of ALS in Turkey: A multifaceted approach to the complex genetics of ALS(Thesis (Ph.D.)-Bogazici University. Institute for Graduate Studies in Science and Engineering, 2018., 2018.) İskender, Ceren.; Çağlayan, S. Hande.; Başak, A. Nazlı.Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease (NDD), characterized by degeneration of both upper and lower motor neurons leading to muscle wasting. With an incidence of two and a prevalence of four in 100.000/year, it is the third most common NDD after Alzheimer’s and Parkinson’s diseases. The last decade has proven that the ‘condition’ called ALS is both clinically and genetically heterogenous, and that the genetic component in 90% of the cases that are considered as sporadic, might be stronger than expected. In this thesis, we investigated the complex genetics of ALS in the ethnically heterogeneous yet inbred Turkish population. Familial ALS account for 22% of our cases (159/722) and 563 cases were classified as sporadic (78%). Consanguinity is calculated as 25% among familial and 17% in sporadic cases. Conventional screening of the most common ALS genes (C9orf72, SOD1, TARDBP and FUS) in patients with a family history of disease, explained the disease cause in only 33%, pointing towards marked locus heterogeneity within the population. C9orf72 hexanucleotide repeat expansion was further detected in 3% of ‘apparently sporadic’ patients. Application of whole exome sequencing (WES) in dominant and recessive Turkish pedigrees presenting with ALS or non-ALS motor neuron diseases (MNDs), revealed distinct rare or novel mutations in 20 out of 39 families and enabled differential diagnosis in cases with atypical ALS features. Common current themes in ALS, like oligogenic inheritance and possible genetic modifiers are addressed in families with incomplete penetrance and in C9orf72 expansion carriers. Oligogenic inheritance of known ALS genes was not prominent in the Turkish C9orf72-positive cases. Hypermethylation in the promoter region of C9orf72 was confirmed in Turkish patients, however it did not seem to modify age of onset. Finally, analyses of whole genome sequencing data of 625 Turkish ALS patients and 152 healthy controls in the framework of Project MinE showed population-specific aspects and once more substantiated the concept of low penetrance of rare ALS genes among sporadic patients.