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Öğe Main Genome Editing Tools: An Overview of the Literature, Future Applications and Ethical Questions(Trakya Üniversitesi, 2021) Şenödeyici, Eylül; Şahintürk, Dengiz Koray; Akbolat, Bilge Rana; Dindar, Arzu; Sefer, Selin; Anğay, Gül Feride; Demir, SelmaThe popularity of genome editing technologies in the scientific community has been on the rise for several years. These technologies are slowly becoming a ray of hope for many patients with genetic diseases, thanks to their immense potential for clinical application. New genome editing tools are being rap- idly developed and introduced, while pre-existing ones are being perfected. In the process beginning with the completion of the Human Genome Project to the first clinical trials focusing on cancer immunotherapy and treating blindness, studies on genome editing have increased exponentially. The clustered regularly interspaced short palindromic repeats system is a Nobel Prize-winning genome editing tool celebrated by many researchers and is often praised due to its ease of use, low cost, and efficiency compared to other acknowledged genome editing tools. This review aims to discuss the historical development, working mechanisms, present and future clinical applications of zinc-finger nucleases, transcription activator-like effector nucleases, clustered regularly inter- spaced short palindromic repeats, and prime editors, while presenting the ethical aspects of using these genome editing tools. Keywords: Zinc-finger nucleases, transcription activator-like effector nucleases, clustered regularly interspaced short palindromic repeats, gene editingÖğe Effective Use of Next Generation Sequencing For Genetic Diagnosis of a Patient With a Mosaic Tsc2 Variant(Trakya Üniversitesi, 2018) Çifcibaşı, Hilal Sena; Gülbal, Elçin; Erdoğan, Ayşenur; Demirci, Ayşenur; Demir, SelmaAims: Tuberous sclerosis complex is a genetic disorder characterized by mutations in Tuberous Sclerosis Complex 1 (* 605284) or Tuberous Sclerosis Complex 2 (* 191092) genes. PALB2 (* 610355) gene has long been known to be associated with increased breast and pancreatic cancer risk. Its association with risk of stomach and lung cancers has also been established recently. In this case report, it is aimed to present a case of a 24-year-old female patient, who has been diagnosed with both novel mosaic Tuberous Sclerosis Complex 2 pathogenic variation and pathogenic PALB2 variation at the same time. Case Report: A 24-year-old female patient was admitted to Trakya University Genetic Diseases Center with suspected tuberous sclerosis complex. Her primary complaints were a continuous headache and fatigue. She had no history of convulsion and seizure. There were bilateral facial angiofibromas around her nose. When genomic DNA was isolated, both novel mosaic Tuberous Sclerosis Complex 2 pathogenic variation and pathogenic PALB2 variation were observed. Conclusion: This case report shows that in cancer predisposing syndromes, Next-generation sequencing is a powerful technique to portrait a detailed genetic profile of patient, investigating for any mosaicism or other risk allelesÖğe Retrospective Analysis of Chronic Myeloid Leukemia Patients in Trakya University School of Medicine(Trakya Üniversitesi, 2019) Akay, Fatih Erkan; Koçyiğit, Beliz; Tan, Berfin; Atlı, Emine İkbal; Baş, Volkan; Kırkızlar, Hakkı OnurAims: This study aims to establish the data; including demographic features, molecular response status, disease characteristics, and survival rate of chronic myeloid leukemia patients treated with tyrosine kinase inhibitors in Trakya University School of Medicine. Methods: In this study, the data of 102 patients over 18 years old who were diagnosed with chronic myeloid leukemia in Trakya University School of Medicine between January 2003-October 2019 were analyzed retrospectively. Data was analyzed using SPSS 23.0.0.0. Results: The total number of patients in the study was 102. There were 95 (93.1%) patients on chronic phase and 6 (5.9%) patients on accelerated phase. Eighty-three (81.4%) of the patients had at least a major molecular response and 17 (16.7%) patients could not achieve at least a major molecular response. Conclusion: As our study showed, first line treatment with imatinib may not be enough for some of the patients to recover and therefore different TKIs such as dasatinib, nilotinib, bo-sutinib, and ponatinib are being used in the treatment of CML. Inadequate response, drug side effects and incompliances are the causes of switching the drug choice. Further studies are needed to thoroughly reveal the epidemiology and treatment regimens.Keywords: Chronic myeloid leukemia, tyrosine kinase, neoplasmsÖğe Two Cases of Cystic Fibrosis with Compound Heterozygous Variants Reported for the First Time(2020) Yalçıntepe, Sinem; Gürkan, Hakan; Atlı, Engin; Sayın, Niyazi Cenk; Başaran, Ümit Nusret[Abtract Not Available]Öğe Genetic Diagnosis of Hereditary Hemorrhagic Telangiectasia: Four Novel Pathogenic Variations in Turkish Patients(2020) Baysal, Mehmet; Demir, Selma; Ümit, Elif G.; Gürkan, Hakan; Baş, Volkan; Gülarslan, Sedanur Karaman; Demir, Ahmet MuzafferAims: Hereditary hemorrhagic telangiectasia is an autosomal dominant disorder characterized by telangiectasia, epistaxis, and vascular malformations. Pathogenic mutations were found in ENG, AVCRL1, SMAD4, and GDF genes. In this study, we present our database of patients with hereditary hemorrhagic telangiectasia regarding the phenotype-genotype relations and discuss two novel ENG gene pathogenic variations in two unrelated families. Methods: Next Generation Sequencing analysis was performed on the peripheral blood of nine patients with hereditary hemorrhagic telangiectasia in four unrelated families. All patients were diagnosed with hereditary hemorrhagic telangiectasia according to the Curaçao criteria. Data on treatment and screenings of visceral involvement were recorded from files. Results: We have found a pathogenic variation in either the ENG or ACVRL1 gene in each family. Two novel pathogenic variations in the ENG gene, including NM_000118.3 (ENG): c.416delC (p.P139fs*24) and NM_000118.3(ENG): c.1139dupT (p.Leu380PhefsTer16), were found in the same family. The NM_000020.2(ACVRL1): c.1298C>T (p.Pro433Leu) pathogenic variation in the ACVRL1 gene in our first family and a novel heterozygous likely pathogenic NM_000020.2(ACVRL1): c.95T>C (p.Val32Ala) variation was found in our second family. Seven of the nine patients were treated with thalidomide for controlling bleeding episodes. All patients responded to thalidomide. In one patient, the response to thalidomide was lost and switched to bevacizumab. Conclusion: In hereditary hemorrhagic telangiectasia, certain types of mutations correlate with disease phenotypes and with next generation sequencing methods. New pathogenic variations can be revealed, which might help manage patients with hereditary hemorrhagic telangiectasiaÖğe Nonoccupational Exposure of Agricultural Area Residents to Pesticides: Pesticide Accumulation and Evaluation of Genotoxicity(Springer, 2018) Doganlar, Zeynep Banu; Doganlar, Oguzhan; Tozkir, Hilmi; Gokalp, Fulya Dilek; Dogan, Ayten; Yamac, Ferah; Askin, Orhan Onur; Aktas, Ummuhan ErsinAlthough many studies related the toxic effects of pesticides on agricultural workers, little research has been done about agricultural area residents. The purpose of this work was to monitor the presence of pesticides, as well as their genotoxic and cytotoxic potential, in humans with blood samples collected from control and intensive agricultural areas in the Thrace region. Pesticide accumulations were determined by LC-MS/MS. Cytotoxicity and genotoxicity were analyzed by comet assay, and the effect of pesticide accumulation on oxidative stress, DNA repair, and molecular chaperone response were analyzed by qRT-PCR assays in the human blood samples. The agricultural area residents had a significantly higher concentration of pesticides than those in the control area at all three sampling times, and the total pesticide amounts were 4.3 and 10 times significantly higher in blood sampled in the pesticide use period (August 2015 and 2016, respectively) than in the nonuse period (November 2015). The results showed that the pesticide level in blood during the use period led to oxidative stress, DNA damage (mean comet length and % tail DNA), and unfolded/misfolded protein response. Particularly, in pesticide use season, difference between these parameters was found statistically significant with comparison to control. Our results indicate that individuals residing around a monoculture rice farming area comprise an at-risk group as a result of increased genotoxicity evidenced in human blood. We suggest that biological monitoring efforts should be used to control nonoccupational exposures to pesticides and thus safeguard the health of agricultural area residents.Öğe Eprenatal diagnosis of a new case: de novo balanced non-obertsonian translocation involving(Macedonian Acad Sciences Arts, 2018) Atli, E., I. (Trakya author); Gurkan, H.; Tozkir, H.; Varol, G. F.; Inan, C.The balanced non-Robertsonian translocation (ROB) associated with acrocentric chromosomes is an unusual phenomenon. We report the case of rare non-ROB involving chromosomes 15 and 22 with cytogenetic and molecular cytogenetic findings of 46, XY, t(15;22)(p11.2;q11.2). To the best of our knowledge, t(15;22) is the first report of this breakpoint that is not the usual non-ROB. The karyotype of the chorionic villus cell was 46, XY, t(15;22)(p11.2;q11.2) from two different initial cultures. This is different from the usual non-ROB of acrocentric chromosomes. Comparative genomic hybridization has been performed to determine the chromosomal origin. Non-Robertsonian translocation associated with acrocentric chromosomes is an unusual event and only a few cases have been reported. In this study, we observed acrocentric chromosomes 15 and 22 as a rarely balanced non-ROB, where satellites of chromosome 15 translocated to chromosome 22 and part of chromosome 22 were translocated to chromosome 15. To the best of our knowledge, our patient is the first case reported in the literature for this translocation in prenatal and postnatal periods.
